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PLoS Comput Biol. 2010 December; 6(12): e1001031.
Published online 2010 December 16. doi:  10.1371/journal.pcbi.1001031
PMCID: PMC3002991

Kinetics of Rhodopsin Deactivation and Its Role in Regulating Recovery and Reproducibility of Rod Photoresponse

Rama Ranganathan, Editor

Abstract

The single photon response (SPR) in vertebrate phototransduction is regulated by the dynamics of R* during its lifetime, including the random number of phosphorylations, the catalytic activity and the random sojourn time at each phosphorylation level. Because of this randomness the electrical responses are expected to be inherently variable. However the SPR is highly reproducible. The mechanisms that confer to the SPR such a low variability are not completely understood. The kinetics of rhodopsin deactivation is investigated by a Continuous Time Markov Chain (CTMC) based on the biochemistry of rhodopsin activation and deactivation, interfaced with a spatio-temporal model of phototransduction. The model parameters are extracted from the photoresponse data of both wild type and mutant mice, having variable numbers of phosphorylation sites and, with the same set of parameters, the model reproduces both WT and mutant responses. The sources of variability are dissected into its components, by asking whether a random number of turnoff steps, a random sojourn time between steps, or both, give rise to the known variability. The model shows that only the randomness of the sojourn times in each of the phosphorylated states contributes to the Coefficient of Variation (CV) of the response, whereas the randomness of the number of R* turnoff steps has a negligible effect. These results counter the view that the larger the number of decay steps of R*, the more stable the photoresponse is. Our results indicate that R* shutoff is responsible for the variability of the photoresponse, while the diffusion of the second messengers acts as a variability suppressor.

Author Summary

Reception and transmission of biological stimuli such as vision, olfaction, taste, and hormone and neurotransmitter signal transduction, contain inherently variable components. Yet, biological functions are stable and reliable. For each signaling process, it is of interest to investigate the causes of variability and the mechanisms by which variability is mitigated to yield responses that reliably reflect the strength of the stimulus. We have investigated the variability of the single photon response in rod photoreceptors. A photon of light is captured by a receptor rhodopsin, and it goes through a series of biochemical states ending with a random shutoff. We have created a mathematical model of such a process, based on the recent biochemical findings on activation/deactivation, capable of reproducing the peculiar experimental features of visual trasduction both in wild type and genetically modified mice. We have found that the randomness of the time that rhodopsin sojourns in each of these biochemical states is the dominant cause of variability, whereas diffusion of molecules carrying the signal within the cell acts as variability mitigators.

Introduction

In retinal rod photoreceptors, rhodopsin activated by photons of light, denoted by An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e001.jpg, initiates a signal transduction cascade to produce a suppression of electrical current flowing into rod outer segment (ROS). Following isomerization, a molecule An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e002.jpg undergoes a random number of phosphorylations by rhodopsin kinase (RK) and finally is inactivated by arrestin (Arr) binding. Activated rhodopsin An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e003.jpg, moving along its random path, during its random lifetime from isomerization to Arr binding, keeps activating its cognate G-protein (G) transducin, while its catalytic activity declines with increasing level of phosphorylation. The active G-protein (An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e004.jpg) associates with the effector protein phosphodiesterase (E) forming an active An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e005.jpg-An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e006.jpg complex, which by hydrolyzing cGMP reduces its concentration, thereby generating a current response on the outer shell of the ROS. The dynamics of An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e007.jpg during its lifetime, including the random number of phosphorylations, the catalytic activity and the random sojourn time at each phosphorylation level, regulates the production of An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e008.jpg and therefore the current response. Because of the randomness in the components of the activation/deactivation cascade, the electrical responses are expected to be inherently variable. However, the single photon response (SPR) exhibits a low variability in the sense that the amplitude and shape of the electrical responses, corresponding to a set of activation-deactivation events, are similar. It is reported that the Coefficient of Variation (CV = standard deviation/mean) of the SPR area for mouse is about An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e009.jpg [1]. However, the mechanisms that confer high reproducibility of the SPR are not completely understood.

Several studies [1][7] attribute the high reproducibility of the SPR mainly to the mechanisms regulating rhodopsin deactivation. Although the models proposed in these studies account for the low variability of the response, they impose, in one way or another, certain restrictions on the biochemistry of rhodopsin deactivation. For example, if rhodopsin's integrated activity occurs in An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e010.jpg independent steps, it is assumed that each step controls an equal fraction of rhodopsin's integrated catalytic activity [1], [2]. It is then natural to ask what is the statistical mean An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e011.jpg of the number An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e012.jpg, as a way of testing both the models and the supporting biochemical assumptions. Mechanistically, one might ask which of the components of the deactivation cascade contribute more importantly to the variability.

A major difficulty with these issues is to experimentally separate the various components that contribute to the variability. To our knowledge, the activation/deactivation module of the cascade is not, to date, experimentally separable from the transduction module. We have shown in [8] that diffusion of the second messengers in the cytoplasm acts as a variability suppressor. The separation between the activation cascade on the disks and the diffusion of the second messengers cGMP and An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e013.jpg in the cytoplasm is realized by a mathematical model [8][11]. Likewise several fine properties of the biochemical and biophysical mechanisms regulating the recovery and reproducibility of SPR are not, to our knowledge, experimentally separable. Here we attempted to tease apart the various components of the An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e014.jpg shutoff mechanism and analyze to what extent each of them contributes to the variability of the SPR. Unlike the transduction part of the cascade, where the intricacy is of geometrical nature [9][11], the main difficulty here is stochastic. Rhodopsin inactivation can occur by several mechanisms, including Arr binding and thermal decay to opsin. We only model the former, as the latter occurs on a much longer time scale [12], [13]. Shutoff of An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e015.jpg by Arr binding can follow, in principle, an infinite number of paths, depending on the random number of phosphorylated states, and the random sojourn times in those states.

The biochemistry that regulates rhodopsin deactivation is put into a stochastic framework, which reproduces the SPR both in WT and in mutant mice, and is capable of analyzing the randomness of each phosphorylation state of An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e016.jpg. This is interfaced with the spatio-temporal model in [8], [9], [11], capable of tracking the diffusion of the second messengers in the cytoplasm and of detecting the effects of geometrical changes of the ROS on the photoresponse.

We find that the randomness of the sojourn times of An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e017.jpg in each of its phosphorylation states acts as the dominant factor contributing to the CV of the response. At the same time the number of available phosphorylation sites or the random number of An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e018.jpg phosphorylations before shutoff, is shown to contribute little to variability suppression.

We also find that, in addition to changed biochemistry, the geometry of the ROS might be important for the light response in mutant mice.

Results

The technical aspects of the mathematical model are presented in Methods. Here we illustrate the main links between statistics, biochemistry and geometry. Label by the integer An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e019.jpg the state at which activated rhodopsin An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e020.jpg has acquired An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e021.jpg phosphates. Thus for example if An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e022.jpg then An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e023.jpg has acquired An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e024.jpg phosphates. Then either An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e025.jpg can acquire a further phosphate at a rate An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e026.jpg (determined by RK phosphorylation rate), or it can be quenched by Arr at a rate An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e027.jpg (determined by Arr on-rate). While in the An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e028.jpg state, An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e029.jpg activates G protein with catalytic activity An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e030.jpg. Finally An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e031.jpg remains in the An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e032.jpg state a random sojourn time An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e033.jpg, of mean An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e034.jpg. This is a typical sequence of Bernoulli trials whose statistical description by a Continuous Time Markov Chain (CTMC) is well known and standard [2], [14][16].

The main point of the model is in introducing a theoretical scheme that identifies the parameters of each of these steps in terms of their biochemical role. It turns out that WT responses alone are not sufficient to identify the parameters An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e035.jpg. They are identified using recent experimental data obtained in genetically modified mice ([17][20]).

When these parameters are identified, the CTMC translates the deactivation cascade into the probabilities An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e036.jpg for rhodopsin to be in the An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e037.jpg state at time An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e038.jpg. The output of the activation/deactivation cascade, computed by this CTMC scheme, and measured in terms of activated effector An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e039.jpg, is then used as input in the spatio-temporal model introduced in [8][11]. The latter describes the dynamics of the second messengers cGMP and An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e040.jpg in the cytoplasm of the ROS, and the generation of photocurrent An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e041.jpg flowing through the cell membrane of the ROS, as a function of time An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e042.jpg. These two modules, so interfaced, provide a systems approach to phototransduction by mathematically separating, and then blending, the random events of the activation cascade occurring on a disk, the diffusion of second messengers in the cytoplasm, and current suppression on the outer shell.

The variability of the effector An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e043.jpg is described by the following functionals:

equation image
(1)

The last two are scalar quantities and their CV is reported in Table 1. The first two are functions of time. The CV of the second, as a function of time is reported in Figure 1 (left). The natural variable functionals of the photocurrent are

equation image
(2)

While the last one is the value of the first at peak time, we have listed it separately since it is frequently reported in the literature [5], [6], [21]. An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e046.jpg is a scalar quantity and its CV is tabulated in Table 1. The first two are functions of time. The CV of the second is graphed as a function of An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e047.jpg in Figure 1 (right). The quantity An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e048.jpg is the total relative charge produced over the entire time course of the phenomenon following isomerization by a single photon and is referred to as the SPR area [1], [2], [4], [22].

Figure 1
Comparing the CVs of the total activated effectors An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e049.jpg at time An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e050.jpg with the CVs of the total relative charge An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e051.jpg up to time An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e052.jpg.
Table 1
Coefficients of variation, An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e060.jpg ms.

Simulating the SPR in Transgenic Mice

Deactivation of rhodopsin with one or several mutant phosphorylation sites, can be simulated by suitable choices of the sequences An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e077.jpg and An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e078.jpg as indicated in the section of numerical procedures and methods.

Mutant mouse rhodopsins bearing fewer than 6 phosphorylation sites generate SPRs of significantly extended durations (Figure 2A). The rate of recovery increases with increasing numbers of phosphorylation sites (Figure 2A), in qualitative and quantitative agreement with the experimental results of [3] (Figure 2B).

Figure 2
Simulations SPR for mutant phosphorylation sites of An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e079.jpg, or with Arr knockout.

Inactivation of all rhodopsin phosphorylation sites is realized by either mutation of all six serines and threonines to alanines [1], [3], or rhodopsin kinase knockout [23]. The corresponding SPRs are similar, exhibiting larger amplitude and longer duration than WT (Figure 2B,D for (0P)).

A prolonged SPR in mutant mouse rods lacking arrestin is reported in [24] (Figure 2D). This is realized by setting An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e084.jpg for all An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e085.jpg in the model. The activated rhodopsin gets phosphorylated until all six sites are occupied. Its activity is reduced with increased phosphorylations, and kept fixed after the last phosphorylation for the remainder of the process. The remaining activity yields a response with an asymptotic tail at almost half of its peak value. The initial fall of the response is triggered by phosphorylation. The simulations are shown by (–/–) in Figure 2C, and are qualitatively and quantitatively in agreement with the experimental studies of [24] (Figure 2D).

In Table 2 we report the simulated characteristics of SPRs from WT rods and those expressing rhodopsin mutants. By increasing the number of phosphorylation sites, the peaks of the current response An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e086.jpg decrease; the time to peak An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e087.jpg decreases; and the SPR area An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e088.jpg decreases significantly. For mutants that exhibit very slow recovery (0P, 1P, 2P) the corresponding An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e089.jpg is large because the current remains high for an extended period of time. The value of An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e090.jpg has been computed by integrating the photocurrent over the time of simulation (An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e091.jpg).

Table 2
Characteristics of SPRs, An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e092.jpg ms and An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e093.jpg ms.

When only one phosphorylation site was mutated, the SPR was almost like that of WT but recovery was slightly slower. Consistent with this slower recovery, the SPR area An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e109.jpg of the response of rhodopsin with five phosphorylation sites (5P) was about An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e110.jpg larger than those for wild type. Taken together, these results are consistent with the experimental observations of [3] and the notion that normal kinetics of An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e111.jpg deactivation requires the presence of all six phosphorylation sites.

We finally comment on the largest rising curves coded in red in Figure 2B and D. Various experimental studies [3], [23] show that the response amplitude for the case (0P) is roughly twice as large as the response for the case (1P). In [3] the case (0P), is realized by CSM, and in [23] by RK knockout. In both cases all phosphorylation sites are removed or made inoperative, and both cases exhibit the double amplitude response, suggesting a common mechanism. This issue is not discussed in the indicated papers and we are not aware of an explanation or hypothesis for a possible biochemical mechanism. However, Figure 2 of [3] shows that the ROS in CSM mice were about An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e112.jpg shorter than WT. Geometrical changes due to genetic manipulations are also discussed in [23] (page 3720), and [24], (Figure 3d, page 506). We repeated the simulations with a ROS whose height An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e113.jpg was reduced by An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e114.jpg, while all the remaining parameters were kept fixed. In particular, the number of channels was kept fixed, thereby increasing their density. Since the response is localized close to the activation site [10], [11], the augmented channel density yields a larger response. The resulting simulation is reported in Figure 2A for (0P*) as the largest amplitude (red curve). While the agreement with corresponding experimental curve in Figure 2B is striking, at this point we refrain from suggesting that this as the only functional mechanism.

Figure 3
State diagram of CTMC model for rhodopsin deactivation.

Variability

The CTMC model permits one to test independently the effects of the random components of the variability on the response. For example one can separate the effects of the randomness of the sojourn time from the randomness of number of shutoff steps. To achieve this, we performed the following sets of simulations:

  • Case 1. Fix the number of steps to An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e115.jpg shutoff at that integer closest to its mean An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e116.jpg, and let An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e117.jpg have random sojourn time An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e118.jpg at the corresponding state. The random numbers An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e119.jpg are generated according to their exponential distribution with mean An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e120.jpg.
  • Case 2. Fix the sojourn times of An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e121.jpg at their mean An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e122.jpg and let An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e123.jpg be shut off in An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e124.jpg random steps. The random number An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e125.jpg of An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e126.jpg shutoff steps is generated by a series of Bernoulli trails, in which the probability of phosphorylation is An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e127.jpg and the probability of Arr binding is An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e128.jpg. Thus the mean An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e129.jpg of the random number An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e130.jpg is computed from Eq:10–Eq:11.
  • Case 3. Both sojourn time An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e131.jpg and the number of shutoff steps An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e132.jpg are random. This is the biologically realistic case, although the previous cases extract the effect of the randomness of each component on the variability of the response.

Stochastic simulations are effected for WT and each of the knock-out cases of COOH-terminal truncations [24], [25] and RK knockout [1], [3]. After about 5,000 numerical simulations, up to 3 s, mean, standard deviation and CV are computed for effector and normalized current suppression. Further technical details are in Methods.

Variability of An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e133.jpg

The first two lines of Table 1 report the CV of the scalar quantities An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e134.jpg, and An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e135.jpg defined in Eq:1, and for An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e136.jpg bearing An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e137.jpg phosphorylation sites. The first result is that the CV for Case 2 is negligible (computationally up to 2 decimal points). This indicates that the randomness of the number of An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e138.jpg shutoff steps does not significantly contribute to the CV of An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e139.jpg. The second result is that the CVs produced by Case 1, to which only the randomness of sojourn time of An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e140.jpg contributes, are roughly the same as those of Case 3, where all components are allowed to be random. It appears from the table that the randomness of the sojourn times of An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e141.jpg in its phosphorylated states is largely responsible for the CV of An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e142.jpg in this model.

For mutant An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e143.jpg with zero phosphorylation sites (0P), the CV of any of these quantities is zero in all cases. Since An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e144.jpg could neither be phosphorylated nor be bound by Arr (An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e145.jpg), it remains in state 1 indefinitely and the process has no random components, within the time scale of the simulation. On a longer time scale, eventually active metarhodopsin II releases bound all-trans-retinal and decays to opsin, losing most of its ability to activate transducin. It is not surprising that An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e146.jpg with deactivation deficit leads to a highly reproducible SPR in the very first few seconds (3 s in our simulations), as no inactivation occurs.

The observations in [1] (see Figure 3, Panel F of [1]), indicate that the SPRs generated by unphosphorylated An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e147.jpg are highly reproducible within the very first few seconds (about An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e148.jpg). Later shutoff of unphosphorylated An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e149.jpg is believed to be due to thermal decay of An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e150.jpg to opsin [12]. Here we are interested in the deactivation of An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e151.jpg within the time scale of normal SPR (3 s in our simulations) and the effects that could be involved beyond this time period are not considered.

For mutant An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e152.jpg with one phosphorylation site (1P, An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e153.jpg), the CV of any one of the variability functionals in Eq:1–Eq:2 is very small. Such a mutant An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e154.jpg could be phosphorylated to one level, but it could not be shut off by Arr binding since mono-phosphorylated An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e155.jpg has the same low Arr binding levels as unphosphorylated An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e156.jpg (see the discussion in Methods and [20]). The randomness of one extra level of phosphorylation causes a noticeable increase in uncertainty as measured by the CVs. From Eq:7–Eq:11 one computes An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e157.jpg and An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e158.jpg. Therefore An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e159.jpg remains in the unphosphorylated state 1, for a random sojourn time An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e160.jpg of mean An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e161.jpg; then it transitions to state 2 by acquiring a phosphate and it remains indefinitely in that state. The only randomness is due to the sojourn time An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e162.jpg, which affects the CV of An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e163.jpg. Since An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e164.jpg is never turned off (within the 3 s time frame used here), the functional An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e165.jpg, is uniformly large for all trials, and therefore it exhibits negligible variability.

Compared with the CV of 1P, the mutant An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e166.jpg with two phosphorylation sites (2P, An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e167.jpg) exhibits a larger CV for any of the variability functionals, the increase in uncertainty being due to the second phosphorylation site. The only randomness of the process is due to sojourn times An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e168.jpg of means An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e169.jpg, as the number of possible steps (An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e170.jpg) is not random. In the case of 2P the uncertainty of An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e171.jpg is compounded, with respect to the case 1P, by the uncertainty of the random sojourn times An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e172.jpg and An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e173.jpg, although their mean is smaller. Accordingly all functionals exhibit larger variability. Also for the case 2P shutoff does not occur since An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e174.jpg (from Eq:7–Eq:9). Therefore, for the cases 0P, 1P and 2P, the CVs of the functionals An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e175.jpg and An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e176.jpg reported in Table 1 is not due to variations caused by inactivation, as the latter, theoretically, never occurs. In reality, inactivation does occur, although by different mechanisms, for example thermal decay to opsin, on a much larger time scale.

As the number of available phosphorylation sites increases (An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e177.jpg), one might expect that the uncertainty of the sojourn times An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e178.jpg, be compounded by the randomness of the number of steps An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e179.jpg to An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e180.jpg shutoff. However Table 1 shows no significant difference in the CV of all functionals, between Case 1, where the number of steps to An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e181.jpg shutoff is kept fixed to its mean An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e182.jpg, and Case 3, where all components are permitted to be random. This suggests that the behavior of the various CVs reflects the randomness of the sojourn times.

For An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e183.jpg fixed at its mean An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e184.jpg (Case 1), the CV of An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e185.jpg is computed by the explicit formula [8]

equation image
(3)

This formula is valid provided

equation image
(4)

The latter condition stipulates that the system returns to its original dark state after a sufficiently large time. Therefore this formula holds true only for the cases 3P-6P.

For Case 1, with the number of steps to shutoff fixed at the closest integer to the mean An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e188.jpg, we have computed explicitly the sequences An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e189.jpg and An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e190.jpg from Eq:7–Eq:9 and have computed the corresponding CV from formula Eq:3. These theoretical CVs are reported in line 7 of Table 1 and show a reasonably good agreement with the simulated values of CV(An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e191.jpg).

In Figure 1 (left), we report the graphs of the CV for An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e192.jpg as function of time, only for Case 3. Indeed, this is the biologically realistic case, where all the components of the phenomenon are permitted to be random. This variability functional is defined in Eq:1. Similarly as observed in the context of Table 1, the CV for 0P is negligible and the CV of 1P and 2P are relatively small.

The CV of An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e193.jpg, for wild type (6P), stabilizes from An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e194.jpg with a value of An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e195.jpg, and the CV of the same functional for 3P, stabilizes from An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e196.jpg with a value of An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e197.jpg. By increasing the number of phosphorylation sites from 3P to 6P, the stabilized CVs of the functional An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e198.jpg decrease (Table 1), and the time at which the CVs begins to stabilize decreases.

The functional An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e199.jpg compounds the variability of the process at all times, up to recovery, and therefore its CV is expected to be larger than the CV of An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e200.jpg.

Variability of the photocurrent

In the last two rows of Table 1 we have reported the CV of the scalar quantities An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e201.jpg and An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e202.jpg, defined in Eq:2, for each of the Test Cases 1,2,3, and for a An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e203.jpg bearing An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e204.jpg phosphorylation sites. The results exhibit a pattern similar to the CVs of An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e205.jpg and An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e206.jpg although at considerably lower values of CV. A CV of about An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e207.jpg for An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e208.jpg is reduced to a CV of about An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e209.jpg for the corresponding photocurrent An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e210.jpg. Thus the diffusion part of the process acts as variability suppressor, in agreement with the results of [8].

The simulations show that CV of An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e211.jpg is essentially constant with respect to the number of available phosphorylation sites 3–6.

Figure 1 (right) reports the CV of the total relative charge An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e212.jpg produced up to time An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e213.jpg, for the physically realistic Case 3, where all random components are present. The results exhibit a pattern similar to those in the left panel of the CV for An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e214.jpg although, again, at considerably lower values of CV. The CV of 0P is zero and the CV of 1P and 2P is relatively small. For An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e215.jpg with three or more phosphorylation sites, the CV increases with increasing phosphorylation sites, at the early times of the activation. Thereafter, the CVs for different number of phosphorylation sites tends to stabilize with stabilization time inversely proportional to the number of available sites, i.e., the more sites An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e216.jpg has, the faster CV stabilizes.

Discussion

Variability of the photoresponse hinges on a coordinated system behavior of several components. The main two modules are the activation/deactivation part and the transduction part of the cascade. The latter, given its input, is essentially deterministic as it involves the diffusion of the second messengers cGMP and An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e217.jpg in the cytoplasm and a subsequent current drop through the closure of the cGMP -gated channels. The former is essentially stochastic as it involves the biochemistry of rhodopsin shutoff, which occurs in several random steps. An understanding of the process hinges upon teasing apart all these components, analyzing them separately and blending them together into a system behavior. This point of view began in [8], by separating the role of the transduction from that of the activation/deactivation. This separation was made possible by a mathematical model capable of distinguishing the biochemistry of An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e218.jpg shutoff, from the functional role of the transduction [8], [9], [11]. A surprising finding was that, while An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e219.jpg shutoff is responsible for the variability of the photoresponse, the diffusion of the second messengers acts as a variability suppressor.

Here we have further separated the various steps of the deactivation cascade by (a) prescribing a probabilistic mechanism (CTMC) by which the system selects its random states, and (b) by interrogating the known biochemistry to trace patterns and parameters.

It is not sufficient to determine these parameters unambiguously using WT mice. Experimental information from some mutant and knock-out animals is needed. Specifically, the choice of the catalytic activities An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e220.jpg by formula Eq:6, while based on known biochemistry [26], hinges upon the basic parameter An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e221.jpg, which in turn is determined by the biochemistry of the cascade in mutant mouse (section on parameters in Methods). The same holds true for the transition parameters An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e222.jpg, given by formula Eq:7 and depending upon the parameter An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e223.jpg. Thus, a first remark is that our approach, while mathematical and computational, parallels the biology; that is, information is extracted in a complementary way from the data on genetically modified as well as WT animals. Next the model populated by the indicated parameters is validated against WT and mutant responses as in Figure 2. The model has a deterministic component, and a stochastic component. The first regards the transduction part of the cascade, which is geometry dependent, and deterministic, being based on the diffusion of the second messengers cGMP and An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e224.jpg in the cytoplasm.

Importantly, this model permits one to test the response against geometrical variations of the ROS. The response in mice expressing CSM or RK knock out is rather unusual, exhibiting a double amplitude with respect to WT [3], [23]. An examination of the immunofluorescence micrographs in Figure 2 of [3], suggests that the length of ROS in CSM mice is reduced by about An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e225.jpg relative to WT. Geometrical modifications presumably due to genetic manipulations are also discussed in [23]. Keeping the same stochastic biochemical scheme and changing the length of the ROS, the model reproduced the double-amplitude phenomenon described in [3], [23] (Figure 2 A,B), suggesting that the modified geometry of mutant ROS, might contribute, along with the changed biochemistry, to this phenomenon. This results, along with a recent study of rod signaling in mice expressing supra-physiological levels of rhodopsin ([27]), emphasize the importance of investigating the ROS geometry in genetically modified mouse lines. Our analysis shows that the changes in ROS length, which were analyzed in very few mouse lines, can have dramatic effects on photoresponse.

The stochastic component permits one to single out those parts of the activation/deactivation cascade that dominantly contribute to the variability of the response. The main result is that variability is largely generated by the randomness of the sojourn times of An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e226.jpg in its phosphorylation states. The prevailing point of view is that the activation cascade is responsible for the variability, although in a non quantified way, and that deactivation of An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e227.jpg is responsible for variability suppression, and further, the larger the number of decay steps of An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e228.jpg, the more stable the photoresponse [1], [3][7]. This view was expressed in [1], where mice expressing rhodopsin with 0,1,2,5, and 6 phosphorylation sites were used. The analysis presented in [1] has some inconsistencies. Although the experimental points seem to be best fitted by a straight line (Figure 1 of [1]) the authors describe them by An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e229.jpg, with An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e230.jpg being the number of available phosphorylation sites. The lines with 3 and 4 phosphorylation sites, which would have allowed to discriminate between these functions, were not analyzed in [1]. In addition, by comparing the CV of mice with 0,1, and 2 sites, which do not demonstrate rapid recovery ([4]), with those having 5 or 6 (WT) sites that recover with essentially the same fast rate, the authors inappropriately lump together two disparate phenomena. In the latter case, normal two-step rhodopsin inactivation by RK phosphorylation and arrestin binding is fully operative, whereas in the former rhodopsin is inactivated by stochastic thermal decay taking place on a much longer time course. The idea that multiple inactivation steps are necessary to suppress variability was recently expressed in [2], where the authors conclusions were largely based on two assumptions. The first is that An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e231.jpg activity is nearly equally distributed among the deactivation steps. The second is that in Ames' solution, that yields much greater and longer-lasting SPR than Locke's ([2], [28]), rhodopsin inactivation is rate-limiting and dominates the recovery kinetics. The biochemical scheme we propose argues against the first assumption, on experimental grounds (see a discussion below and On the Parameters An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e232.jpg and An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e233.jpg). The second assumption has been recently questioned in [28], where the authors showed that RGS9 overexpression similarly accelerates the recovery measures in Locke's and Ames' solutions, indicating that transducin inactivation is rate limiting in both cases. Additional issues with data analysis of [1] were discussed in [28]. Thus, no compelling experimental evidence that the number of inactivation steps reduces variability can be found in the literature.

Our results offer a different perspective; demonstrating that variability is generated by the randomness of the sojourn times of An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e234.jpg in its phosphorylated states, and that increasing the number of these states does not lead to variability suppression.

The number of steps to deactivation does not coincide with the number of available phosphorylation sites. The experimental studies of [20] suggest that one phosphorylation is not sufficient for Arr binding, and the probability of quenching becomes large after 3 phosphorylations. Specifically An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e235.jpg corresponds to An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e236.jpg by which Eq:7–Eq:8 give An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e237.jpg and hence An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e238.jpg by Eq:9. Thus, the system remains indefinitely activated (in reality it is stochastically inactivated by the thermal decay of rhodopsin, which is too slow to be captured by 3 s simulations used here). The case An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e239.jpg for An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e240.jpg corresponds to An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e241.jpg respectively and one computes An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e242.jpg from Eq:9 and hence An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e243.jpg from Eq:12; the system goes through An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e244.jpg steps and then remains “indefinitely” active (see above about thermal decay). Thus the CV of An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e245.jpg and An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e246.jpg in Table 1 and Table S1 in the supplementary material, are not due to variations caused by An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e247.jpg shutoff by Arr binding. The first case when An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e248.jpg and deactivation is possible, is the case An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e249.jpg corresponding to An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e250.jpg reported in Eq:13. Going from 3P to 6P, the An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e251.jpg and the An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e252.jpg remain essentially the same.

To illustrate the rationale of our main results, consider mutant rhodopsin with only 3 available phosphorylation sites. Since 3 phosphates are needed for Arr binding [20], no randomness is present in the deactivation process, if randomness is only measured in terms of steps to shutoff. This suggest that the source of variability is in other components of the process. Table 1 indeed shows that if the sojourn times of An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e253.jpg in each of its phosphorylation states are taken to be deterministic (Case 2), then the variability of the photoresponse is negligible. If on the other hand such sojourn times are permitted to be random, then the variability rises to experimentally observed levels (Figure 1), both for WT and genetically modified An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e254.jpg with 3-5P. This should not be interpreted, however, as though the reproducibility decreases as the number An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e255.jpg of available phosphorylation sites increases. We stress that increasing An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e256.jpg does not necessarily mean that the mean number An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e257.jpg to An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e258.jpg shutoff increases. The latter depends on the biochemistry of the process via Eq:10–Eq:11. Likewise the expected average An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e259.jpg of the random lifetime of An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e260.jpg is generated by the biochemistry in Eq:7–Eq:12 and An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e261.jpg; in particular it is different for different genetically modified mice (0P,1P,etc.). The lifetime of An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e262.jpg is randomly chosen by the biochemistry in each of its random trials.

For WT mouse, and only in this case, the expected lifetime An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e263.jpg of An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e264.jpg, as defined by formula Eq:9–Eq:12, coincides with the experimentally measured, effective average lifetime An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e265.jpg. In [29] it is reported An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e266.jpg as an upper limit, whereas several recent studies [28], [30], [31] suggest that An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e267.jpg might be as low as 40 ms (see An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e268.jpg Parameters).

Therefore, we performed all simulations for both values, which yielded very similar CVs, both functionally and numerically (Figure 1 and Tables 23, and Figure S1 and Tables S1,S3, in the supplementary material). These similarities suggest that reproducibility is independent of the actual value of An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e269.jpg and depends only on the functional, sequence of the deactivation cascade, as predicted by our biochemical scheme (Eq:9– Eq:12). Further remarks on these two parameters and corresponding CVs are in An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e270.jpg On the Parameters An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e271.jpg and An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e272.jpg.

Table 3
The sequences An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e273.jpg for the dynamics of An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e274.jpgms and An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e275.jpg.

We stress that the model includes only the deactivation mechanism due to Arr binding and does not include An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e320.jpg inactivation due to other causes such as thermal decay to opsin occurring over a time course of An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e321.jpg ([13]).

In [1] the An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e322.jpg is computed over a time course of over 15 s, which is beyond the time course An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e323.jpg of An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e324.jpg inactivation. According to our scheme, based on direct biochemical measurements of arrestin binding to separated rhodopsin species with different numbers of attached phosphates ([20]), cases An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e325.jpg, An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e326.jpg and An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e327.jpg do not permit shutoff by Arr binding and An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e328.jpg remains active much longer than the 3 s of our simulations. Thus the CV due to An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e329.jpg deactivation reflects its thermal decay to opsin ([12]). In this case, shutoff is an abrupt 1-step process, implying, by Poisson statistic, CV = 1. This is essentially what is reported in [1]. For the cases An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e330.jpg and An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e331.jpg, although the experiments of [1] are carried over a time course of 15 s the An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e332.jpg is essentially due to shutoff by arrestin binding, which occurs within a time course of 0.1 s, whereas decay to opsin is much slower. Considering the slow rate of thermal inactivation of rhodopsin, the probability of thermal decay within the first 0.1 s is negligible relative to the probability of decay due to Arr binding. Accordingly, the An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e333.jpg reported in [1] for An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e334.jpg and An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e335.jpg is similar, as we find. The crucial cases An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e336.jpg and An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e337.jpg were not measured in [1].

The CTMC scheme we propose here differs from the Poisson statistics used in [1], [2], where the CV of An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e338.jpg is claimed to be proportional to An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e339.jpg. It should be noted that the number of available sites does not coincide with the average number of steps to shutoff and that each step weighs differently in the deactivation process, due to its biochemical history.

We return briefly to the explicit, theoretical formula Eq:3, valid under the assumptions of Eq:4, and hence for the cases 3-6P. We have already remarked that its theoretical values (for Case 1) are in agreement with our simulations (lines 2 and 3 of Table 1). If one would artificially concoct a biochemistry by which all the products An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e340.jpg are the same for all An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e341.jpg, then formula Eq:3 would give An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e342.jpg. This occurrence might suggest that the CV of the photoresponse decreases as the reciprocal of the square root of the number An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e343.jpg of steps to shutoff. A calculation from Eq:7–Eq:11, in agreement with known biochemistry ([20]), shows that the products An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e344.jpg are not constant (Table 3). In addition, even if this were the case, the variability of the photocurrent is very different from that of An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e345.jpg, as the relation between these functionals is highly non-linear [8], [11].

A further examination of Table 3 for 3-6P, shows that in all cases (WT or mutant), only the first few steps contribute significantly to the total activity An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e346.jpg; the remaining ones being negligible. In view of the theoretical formula Eq:3, this is further evidence that increasing the number of steps does not significantly decrease the CV(An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e347.jpg).

In all cases (WT or mutant) we found that the diffusion of the second messengers cGMP and An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e348.jpg in the cytoplasm acts as the dominant variability suppressor, thereby confirming the results of [8] and extending the analysis to a variety of transgenic models.

These results are made possible by separating the activation/deactivation module from the transduction module. In addition, in the activation/deactivation module, one further separates the biochemical effects of each phosphorylation contributing to the responses, thereby allowing an examination of the role of the underlying biochemistry during An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e349.jpg deactivation. Incorporating the sequence of biochemical steps, described in Methods, allowed us to recapitulate experimental results qualitatively and quantitatively (Figure 2). It is worth noting that with realistic biochemistry, where Arr acquires a high binding affinity after 3 phosphorylation steps [20], the number of inactivation steps actually involved in shutting down individual SPRs varies very little. Therefore the fact that this number contributes virtually nothing to SPR variability, is one of the mechanisms maintaining the reproducibility of SPR.

Methods

The Mathematical CTMC Model

The state diagram of the CTMC describing An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e350.jpg deactivation by Rhodopsin Kinase (RK) phosphorylating the C-terminal serines and threonines in rhodopsin, is shown in Figure 3 with circles and arrows denoting states and transitions respectively.

The states are labeled by the indices An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e353.jpg, and the transitions between connected states are labeled by transition rates An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e354.jpg and An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e355.jpg. The An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e356.jpg catalytic activity in its An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e357.jpg state is An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e358.jpg. The number An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e359.jpg of phosphorylation levels is determined by the number An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e360.jpg of phosphorylation sites of rhodopsin, which varies in different species. In mouse, rhodopsin has six phosphorylation sites [3]. State 1 is the non-phosphorylated level, representing newly activated rhodopsin with catalytic activity An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e361.jpg; the state An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e362.jpg represents fully deactivated rhodopsin with catalytic activity An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e363.jpg; states 2 to An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e364.jpg represent different phosphorylation levels, in which rhodopsin holds An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e365.jpg sites available for phosphorylation, with An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e366.jpg sites already phosphorylated, and has catalytic activity An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e367.jpg. The states 1 to An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e368.jpg are active states and the state An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e369.jpg is the inactive state. Specifically for WT mouse, there are seven (An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e370.jpg) active states, including state 1 where An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e371.jpg is active and not phosphorylated. Transitions between active states are governed by the phosphorylation rates An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e372.jpg. For notation consistency, we let An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e373.jpg. Transitions between active states and the inactive state are governed by the arrestin binding rates An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e374.jpg. Arrestin binds with high affinity only to phosphorylated rhodopsin [20], [26], [32], [33], therefore, An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e375.jpg.

A newly isomerized rhodopsin is in state 1. It undergoes a random number of phosphorylations before it transitions to the fully deactivated state An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e376.jpg. A rhodopsin with An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e377.jpg available phosphorylation sites could be phosphorylated at most An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e378.jpg times to state An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e379.jpg. Generally, in state An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e380.jpg, rhodopsin either interacts with rhodopsin kinase adding one more phosphate and transitions to the next phosphorylation level with a rate of An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e381.jpg, or it binds arrestin which quenches its catalytic activity, and transitions to the inactive state with a rate of An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e382.jpg. This process is a Bernoulli trial with the probability of a further phosphorylation given by An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e383.jpg and the probability of arrestin binding given by An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e384.jpg. This statistical scheme permits one to model rhodopsin deactivation also in transgenic animals with different number of rhodopsin phosphorylation sites. For example, if An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e385.jpg of the An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e386.jpg phosphorylation sites are mutated, we could set

equation image

to reflect the effect of the mutation. It should be pointed out that, given An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e388.jpg mutated sites, the model removes any An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e389.jpg of the available sites with no discriminating criterion such as their ordering on the C-terminus. Although the phosphorylation of different sites in WT rhodopsin apparently proceeds in some order [34], the overall number of rhodopsin-attached phosphates, rather than their positions on the C-terminus, determines arrestin binding [3], [20], [35]. Accordingly, the model treats them as equal by attributing them the same biochemical function of holding a phosphate.

Let An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e390.jpg denote the probability that a single An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e391.jpg is in the state An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e392.jpg. Then the mathematical description of the CTMC model shown in Figure 3 is [14], [15]

equation image
(5)

Note that the integer An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e394.jpg used to label the state of An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e395.jpg is one plus the corresponding level of phosphorylation, which is An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e396.jpg. For example, the phosphorylation level 0 corresponds to state 1, and An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e397.jpg sites are phosphorylated in state An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e398.jpg. The sojourn time An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e399.jpg of An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e400.jpg in state An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e401.jpg, is taken as an exponentially distributed random variable with mean An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e402.jpg. The sequences of the phosphorylation rates by RK An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e403.jpg, the activities of Arr An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e404.jpg, and the catalytic activities An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e405.jpg, depend on the underlying biochemistry, and vary with phosphorylation levels [26], [36].

The Sequence An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e406.jpg of Catalytic Activities of An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e407.jpg

The catalytic activity An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e408.jpg of An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e409.jpg in the An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e410.jpg state is the production rate of activated G protein An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e411.jpg by An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e412.jpg. While An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e413.jpg is active in each state An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e414.jpg, including the first unphosphorylated state (An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e415.jpg), its activity decreases with increasing phosphorylation levels. The catalytic activity of rhodopsin with different numbers of attached phosphates was experimentally measured by Wilden [26]. In this study differentially phosphorylated rhodopsin species were actually separated, so the conclusions were based on direct measurements and did not involve untested assumptions. Although similar conclusions were later reached by Gibson et al. [32], these authors did not separate differentially phosphorylated rhodopsin species, using preparation with different average phosphorylation levels instead. Their calculations are based on the assumption of Poisson distribution of rhodopsin species with different number of phosphates ([32]). This does not appear realistic, considering the distribution determined by rhodopsin fractionation ([26], [33]). Therefore, our model assumes that the binding affinity of phosphorylated An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e416.jpg for An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e417.jpg decreases exponentially with each added phosphate. Thus, based on data published by Wilden [26], we assume

equation image
(6)

where An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e419.jpg is the catalytic activity of An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e420.jpg in its initial, unphosphorylated state, and An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e421.jpg is positive. The value of An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e422.jpg in Eq:6 has been extracted from the published data after an extensive consistency and sensitivity analysis ([37]). The parameters An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e423.jpg and An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e424.jpg are linked and subject to mutual limitations. It has been shown that in arrestin knockout mice, the initial kinetics of single photon response deactivation closely resembles that of WT, whereas the later phase of deactivation is abrogated (Xu et al., 1997). Initial deactivation is attributable to rhodopsin phosphorylation, which is preserved in these animals. Then deactivation stops at about An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e425.jpg of the peak current suppression, and remains essentially steady thereafter. This level of current drop reflects the ability of fully phosphorylated mouse rhodopsin to activate transducin, corresponding to the catalytic activity An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e426.jpg when all 6 sites are phosphorylated. Thus from Eq:6 one has An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e427.jpg. Mutual calibration of An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e428.jpg and An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e429.jpg is discussed in the section on parameters. Here we stress that they are determined from experimental data for both WT and mutant mice, and not chosen by fitting.

Phosphorylation Rates {An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e430.jpg} and Affinity of R-RK

While the explicit dependence of An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e431.jpg-RK binding affinity and the An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e432.jpg phosphorylation rates on the various biochemical states is not known, there is qualitative biochemical support for the notion that An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e433.jpg-RK affinity decreases systematically with the phosphorylation level of An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e434.jpg [38]. It is shown in Buczylko et al. [39], that phosphorylated RK has significantly lower ability to phosphorylate already phosphorylated An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e435.jpg than unphosphorylated An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e436.jpg. Moreover, Mendez et al. [3] showed that the rate of An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e437.jpg deactivation depends not on the identity of the available sites, but on their total number. We used the biochemically realistic assumption that the rate of phosphorylation is proportional to the number of serines and threonines still available for RK on the rhodopsin molecule. Mechanistically this means that the probability that upon binding to light-activated rhodopsin RK dissociates without adding another phosphate increases with the number of phosphates present, reaching 1 when all six sites are already phosphorylated. This assumption is consistent with in vivo observations by Mendez et al [3] that the removal of even one or two rhodopsin phosphorylation sites slows down photoresponse inactivation. Note that An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e438.jpg is the rate at which RK phosphorylates An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e439.jpg in its An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e440.jpg state. It depends on the on-rate of RK binding to An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e441.jpg in this state, and the rate of phosphate transfer, which were never separated experimentally and were not separated in our model.

We set the sequence An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e442.jpg as linearly decreasing by increasing phosphorylation levels, that is the phosphorylation rate is proportional to the total number of the available sites and is independent of their biochemical identity. Thus

equation image
(7)

where An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e444.jpg is a rate constant, discussed and calibrated in the section on parameters. Formula Eq:7 can be arrived at by postulating that RK has a fixed affinity for binding to An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e445.jpg and that each of the phosphorylation sites could be occupied with an equal rate An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e446.jpg. Therefore An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e447.jpg phosphorylation rate depends on the number of phosphorylation sites available for RK. Since An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e448.jpg in state An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e449.jpg has An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e450.jpg available phosphorylation sites it has a phosphorylation rate An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e451.jpg. Note that this model, similar to previously proposed ones, is based on the assumption that a single site is phosphorylated as a result of each rhodopsin encounter with RK. This assumption has not been experimentally tested.

Arr Binding Rate An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e452.jpg and Affinity of R-Arr

Arrestin binding ensures the timely termination of An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e453.jpg signaling, and it depends on the An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e454.jpg-Arr affinity. Several studies [26], [32], [36], suggest that arrestin affinity increases with increasing phosphorylation levels. Note that only the “irreversible” binding that terminates rhodopsin activity is taken into account here; that is the binding which occurs with high enough affinity to make the complex half-life much greater than the time course of the SPR. In a recent study, Vishnivetskiy et al. [20] found that unphosphorylated and mono-phosphorylated An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e455.jpg show the same low Arr binding levels. In particular, a single receptor-attached phosphate does not facilitate Arr binding; two are necessary to induce higher affinity interaction, and An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e456.jpg with three phosphates is fully capable of binding Arr with the affinity that makes the interaction essentially irreversible on the time scale of the SPR. Moreover, higher phosphorylation levels do not increase the stability of Arr complex with light-activated rhodopsin [20]. Based on the data in [20], we set the sequence An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e457.jpg for Arr binding rate by the phosphorylation level as

equation image
(8)

where An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e459.jpg is the Arr binding rate when Arr affinity reaches its maximum after several phosphorylations. Note that An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e460.jpg in the model describes arrestin binding that terminates transducin activation. Thus, it reflects the rate of formation of arrestin-rhodopsin complexes that are stable enough to survive significantly longer than the time course of a single photon response analyzed here. Since the stability of arrestin complex with unphosphorylated and mono-phosphorylated rhodopsin is much lower [20], [40][42], allowing for arrestin dissociation and consequent rhodopsin reactivation within this time, we set An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e461.jpg. Since An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e462.jpg, An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e463.jpg in states An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e464.jpg surely transitions to the states An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e465.jpg respectively. The data in vivo [3] and in vitro [20] also suggest that two rhodopsin-attached phosphates are not sufficient to induce Arr binding with high enough affinity for rapid deactivation. Therefore, we set An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e466.jpg.

The effect of the level of rhodopsin phosphorylation on arrestin binding was explored in two studies. Gibson et al [32] concluded that arrestin affinity linearly increases with the level of phosphorylation in the range of 1–4 phosphates per rhodopsin. The authors used preparations of phosphorylated rhodopsin in native disc membranes that are well known to be highly heterogeneous, containing rhodopsin species carrying from zero to seven phosphates (bovine rhodopsin has seven RK phosphorylation sites) [26], [43]. The authors attempted to solve this problem by using several assumptions (that were not experimentally tested) to compute the fraction of rhodopsin molecules with different phosphorylation levels as a function of average phosphorylation, which was the only parameter actually measured [32]. The authors calculations were based on an additional assumption that unphosphorylated rhodopsin does not bind arrestin, even though specific low affinity binding of wild type arrestin to light-activated unphosphorylated rhodopsin in vitro [40], [41], and its role in inactivation of unphosphorylated rhodopsin in vivo [12], [23], [42] was shown. Arrestin binding in this study was measured using “extra Meta II” assay developed by Schleicher et al in 1989 [44]. This assay is based on the stabilization of active Metarhodopsin II state by bound arrestin. The most significant drawback of this assay is that it does not work above An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e467.jpg. At physiological temperatures extra Meta II is not detectable, even though it is obvious that arrestin effectively quenches rhodopsin signaling in mammals at An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e468.jpgAn external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e469.jpg. In another study Vishnivetskiy et al [20] separated rhodopsin species with different levels of phosphorylation by chromatofocusing. Importantly, the authors quantitatively determined the presence of particular phospho-rhodopsin species in each fraction by mass-spectrometry of proteolytically removed rhodopsin C-terminus [34], obviating the need for calculations based on untested assumptions. Moreover, the binding assay in this study was performed at physiological temperature, An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e470.jpg. Based on their data, Vishnivetskiy et al concluded that arrestin demonstrates the same low affinity for rhodopsin carrying zero and one phosphate. The presence of two phosphates somewhat increases arrestin affinity, whereas arrestin binds rhodopsin with three, four, five, and six phosphates with the same high affinity, forming physiologically relevant long-lived complexes with stability sufficient for reliable quenching without possibility of reactivation on the time scale of the photoresponse [20]. These conclusions are in remarkable agreement with the work of Mendez et al in genetically modified mice expressing rhodopsin with different number of phosphorylation sites [3]. The authors of this study found that in vivo light activation of rhodopsin carrying zero, one, or two phosphorylation sites yields responses that last for many seconds, whereas rhodopsin carrying three or more phosphorylation sites is inactivated by wild type arrestin with sub-second kinetics [3]. Therefore, we based the modeling on the conclusions of these two studies [3], [20]. The parameters An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e471.jpg and An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e472.jpg appearing in Eq:7–Eq:8 are calibrated by WT and mutant experimental data, and not by fitting (see section on parameters).

Random Sojourn Times An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e473.jpg and Random Steps to An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e474.jpg Shutoff

In the state An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e475.jpg, An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e476.jpg maintains its catalytic activity An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e477.jpg for a random time An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e478.jpg, until further phosphorylation or Arr binding. The sojourn times An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e479.jpg, for An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e480.jpg are exponentially distributed random variables with mean An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e481.jpg. The average lifetime An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e482.jpg of An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e483.jpg being deactivated after An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e484.jpg random biochemical states visited by An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e485.jpg before quenching, and is the sum of the An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e486.jpg up to An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e487.jpg. Thus

equation image
(9)

Hence An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e489.jpg and An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e490.jpg are determined by the biochemistry of the process through the sequences An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e491.jpg and An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e492.jpg.

The number An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e493.jpg of steps after which An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e494.jpg binds to Arr is itself a random variable An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e495.jpg. The probability of An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e496.jpg shutoff in An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e497.jpg steps, or equivalently the probability of An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e498.jpg undergoing An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e499.jpg steps of phosphorylation and a final step for Arr binding, is

equation image
(10)

The mean steps of An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e501.jpg shutoff, or equivalently the expected value of the first moment of An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e502.jpg, is denoted by An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e503.jpg and is given by

equation image
(11)

Thus An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e505.jpg is the mean of the discrete valued random variable An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e506.jpg.

The lifetime An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e507.jpg of An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e508.jpg is itself a random variable with expected value

equation image
(12)

These remarks permit one to detect the pattern of the means An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e510.jpg of the random sojourn times An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e511.jpg. First, the expected lifetime An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e512.jpg of An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e513.jpg, as a function of the number An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e514.jpg of available phosphorylation sites, decreases with increasing An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e515.jpg; second, the sojourn times An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e516.jpg, while increasing in number, each have a smaller mean An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e517.jpg. For example for 3P (An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e518.jpg), from Eq:7–Eq:9, and Eq:10–Eq:11, one computes

equation image
(13)

We stress that the number An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e520.jpg of available phosphorylation sites does not coincide with the mean number An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e521.jpg of steps to An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e522.jpg quenching. The number An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e523.jpg is fixed by the structure of rhodopsin, whereas An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e524.jpg depends on the biochemistry, through the probabilities An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e525.jpg.

Numerical Procedures and Methods

The dynamics of An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e526.jpg during deactivation is analyzed by the CTMC model in Eq:5, which is numerically integrated in the Matlab platform. Its output is integrated into the spatio-temporal model and its Matlab code introduced in [8], [11]. This produces pointwise values of the effector An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e527.jpg, An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e528.jpg and An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e529.jpg on the ROS and permit one to compute the current response An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e530.jpg as a function of time and thus the functionals of effector and current in Eq:1–Eq:2.

Simulations were performed for each of the 3 Test Cases. Random numbers are generated according to the exponential distribution of the random sojourn times An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e531.jpg, for each of wild type, transgenic and Arr knock-out cases indicated above. The corresponding An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e532.jpg dynamics is computed and the functionals in Eq:1–Eq:2 are evaluated. For each case, after about 5,000 numerical simulations, we compute the mean, the standard deviation and the coefficient of variation (CV) of these functionals.

For WT mice the sequences An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e533.jpg and An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e534.jpg are chosen as in Eq:6–Eq:7. For mice lacking phosphorylation whether by COOH-terminal truncations ([24], [25]) or RK knockout ([1], [3]), in the CTMC one sets An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e535.jpg in Eq:5 and An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e536.jpg, so that An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e537.jpg would remain in state 1 with catalytic activity An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e538.jpg for the whole process. If An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e539.jpg of the six phosphorylation sites are mutated out, we would have a CTMC model with An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e540.jpg. For mice lacking Arr ([24]), we let An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e541.jpg, for An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e542.jpg in the CTMC model in Eq:5.

Parameters

In [37], we have generated a complete, self-consistent set of parameters for the mouse rod phototransduction, calibrated by least square fitting of the model in [8], [9], [11]. to a set of experimental data kindly provided Dr. C. Makino, leading to Table S2 (Text S1). Note that these parameters describe SPR recorded in Locke's solution used in [3], [7], [24], [25], [28], [29], [42], [45][49], rather than in Ames' solution used in [1], [2]. For reasons that remain to be elucidated, the latter has greater amplitude and duration, although the recovery in both conditions is rate-limited by transducin inactivation ([28]).

Figure 4 compares the simulated SPR by our model with the parameters of Table S2, and the experimental SPR kindly provided by C. Makino. The new parameters involved in the present investigation are the biochemical sequences An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e543.jpg, An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e544.jpg and An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e545.jpg. Below we indicate in detail how they have been determined. Their estimated values are reported in Table 4. Given the catalytic rate An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e546.jpg the sequence An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e547.jpg is determined from Eq:6 whence the rate An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e548.jpg is known.

Figure 4
Mouse SPRs by simulation (black) and experiment (red).
Table 4
CTMC model parameters.

Estimate of An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e572.jpg

In the experiments of [26] a large pool of G proteins, PDE and cGMP was mixed with a large quantity of rhodopsin An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e573.jpg with a known number An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e574.jpg of phosphates. Then the An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e575.jpg were activated by a brief flash of light to produce a number of isomerizations An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e576.jpg per An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e577.jpg, and the rate of depletion cGMP was recorded. Since only three purified proteins are present in this assay, rhodopsin, transducin, and PDE, rapid inactivation mechanisms present in vivo do not operate. Therefore, the number of activated transducin molecules is proportional to the number of light-activated rhodopsins and their activity, and the number of active PDE molecules is proportional to the number of active transducins and does not change in time.

The number of molecules involved, all in the same environment, is so large as to justify a lumped description of the phenomenon by means of standard balance equations

equation image
(14)

where An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e579.jpg is the number of molecules of fully activated PDE per An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e580.jpg, and An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e581.jpg, in An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e582.jpg is the rate of hydrolysis of cGMP by An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e583.jpg. If An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e584.jpg is sufficiently large, the system saturates in the sense that all available molecules of PDE are fully activated. Denoting by An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e585.jpg the limiting saturation, one computes

equation image

where An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e587.jpg is the activity of An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e588.jpg in its An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e589.jpg state, and An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e590.jpg is the decay rate of An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e591.jpg. It is assumed that for large An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e592.jpg the time to saturation is very small so that, in Eq:14, one approximates An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e593.jpg. from the second of Eq:14. These remarks in Eq:14 imply

equation image
(15)

where the indexed An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e595.jpg signifies that in principle the solution of such equation depends on the activity of the An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e596.jpg phosphorylation state of An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e597.jpg. At saturating light levels the rates An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e598.jpg reach a limiting value independent of An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e599.jpg. Moreover at such limiting rates the An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e600.jpg are essentially the same for all An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e601.jpg, since they are hydrolyzed by An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e602.jpg. It is reported in [26] that the same rate of depletion An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e603.jpg for an experiment with rhodopsin An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e604.jpg (no phosphates) with activity An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e605.jpg, and number of isomerizations An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e606.jpg, can be obtained from an experiment with rhodopsin An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e607.jpg (6 phosphates), and catalytic activity An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e608.jpg, provided the number of isomerizations An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e609.jpg is 10 times larger than An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e610.jpg. Equation Eq:15 with these data and indicated assumptions yields

equation image

From this and Eq:6 one computes An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e612.jpg or An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e613.jpg.

Determining the sequences An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e614.jpg and {An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e615.jpg}

The modeling assumptions contained in Eq:7–Eq:8 reduce these sequences to the determination of An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e616.jpg and An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e617.jpg. These are constrained by Eq:12. Therefore, if the expected lifetime An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e618.jpg of activated rhodopsin, given by Eq:12, is experimentally estimated, then only one of these parameters, An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e619.jpg or An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e620.jpg, is independent. When An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e621.jpg is fixed at a particular value, the remaining free parameter is estimated against the experimental results of [24] for SPR in transgenic mice lacking arrestin, as follows. In the absence of arrestin, the activated rhodopsin gets phosphorylated from one level to another until all its six sites are occupied. Its activity is reduced with phosphorylation, and kept fixed after the last phosphorylation, for the remainder of the process. Such activity causes the response tail to maintain almost a half of its peak value (Figure 2C,D). Thus An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e622.jpg and An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e623.jpg are constrained by Eq:8 and by the requirement that putting An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e624.jpg in the CTMC Eq:5 and An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e625.jpg for all An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e626.jpg the time asymptotic current suppression is about An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e627.jpg of the peak current suppression.

It is worth stressing that the parameter calibration has been effected by enforcing at the same time, the WT response, the response of transgenic mice lacking arrestin, and by linking the rates An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e628.jpg and An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e629.jpg to the experimental value of An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e630.jpg by Eq:12. It is also worth noting that here we simulated the first 3 s of the photoresponse. Light-activated rhodopsin can also be inactivated in an RK- and Arr-independent manner via thermal decay to opsin with very low activity towards transducin. Since this process is very slow, with half-life of An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e631.jpg s in mouse photoreceptors [13], we did not take it into account in our modeling.

On the parameters An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e632.jpg and An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e633.jpg

In Table S2, An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e634.jpg is the reciprocal of the experimental value of the average lifetime of An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e635.jpg for WT mouse, denoted by An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e636.jpg, and determined as the time constant of an exponential decay function used to approximate An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e637.jpg lifetime ([28], [30], [31]). As such An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e638.jpg is an “effective lifetime”. In [29] An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e639.jpg is an upper limit of An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e640.jpg lifetime.

The expected value An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e641.jpg of An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e642.jpg lifetime given by Eq:12 is the average of the times it takes An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e643.jpg to be quenched after An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e644.jpg steps, weighted by the probabilities of quenching after An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e645.jpg steps. This number depends only on the biochemistry defined by the sequences An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e646.jpg and An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e647.jpg.

If one knew these sequences a-priori, no knowledge of An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e648.jpg would be needed. The numerical value of the latter is used to generate an extra link between the parameters An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e649.jpg and An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e650.jpg, for WT mouse (An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e651.jpg) to reduce the number of free parameters. Thus the underlying assumption is that for WT mouse, the expected value An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e652.jpg of the random variable An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e653.jpg is numerically comparable with the experimentally measured numerical value of An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e654.jpg, and thus one sets numerically An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e655.jpg. For this reason, when referring to WT mouse, and only in this case, we use An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e656.jpg and An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e657.jpg interchangeably. However for genetically modified mice (An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e658.jpg) the expected values of An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e659.jpg given by formula Eq:13 differ from An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e660.jpg.

It should be pointed out however that An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e661.jpg is a derived parameter through formula Eq:12. It is the biochemistry that determines An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e662.jpg through the RK on-rates An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e663.jpg and the Arr on-rates An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e664.jpg. Thus An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e665.jpg changes in genetically modified mice according to the number of mutated sites, and the resulting biochemistry.

Several recent studies give a lower estimate An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e666.jpg for WT [30]. Because of the importance of this parameter we have reproduced our simulations also for An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e667.jpg, and found no appreciable difference in the numerical values or the general pattern of the resulting variability functionals (see Figure S1 and Tables S1,S3 of the supplementary material). Thus, the functional conclusions of this study do not depend on the numerical value of An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e668.jpg.

By taking a shorter An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e669.jpg, the SPR for WT mouse can be reproduced by imposing a larger catalytic rate An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e670.jpg (i.e., activation of transducin by rhodopsin every 2 ms). A few other parameters have been slightly modified the most noticeable of which are the RK on-rate An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e671.jpg and the Arr on-rate An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e672.jpg. Using the pair An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e673.jpg and An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e674.jpg and computing An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e675.jpg and An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e676.jpg as indicated in the previous section, one estimates An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e677.jpg and An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e678.jpg. Using the pair An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e679.jpg and An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e680.jpg, one estimates An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e681.jpg and An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e682.jpg. All the indicated simulations have been run for both sets of parameters with no appreciable difference in the results (Figure 1 and Tables 23, and Figure S1 and Table S1,S3 in the supplementary material).

The value of An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e683.jpg reported in Table S2 corresponds to the value An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e684.jpg as calculated from Eq:6 for An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e685.jpg. The (random) production of An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e686.jpg by An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e687.jpg in its An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e688.jpg state is An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e689.jpg. If shutoff occurs in An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e690.jpg steps, the average activity over these steps is

equation image
(16)

This is a random variable whose expectation is the expected (average) activity An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e692.jpg of the process

equation image
(17)

A calculation for 6P and An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e694.jpg gives An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e695.jpg. This value is within the published range of average An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e696.jpg activity as discussed in [37]. A similar calculation for 6P and the faster dynamics An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e697.jpg gives An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e698.jpg.

Remaining in the context of WT mouse, the shortening of An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e699.jpg from An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e700.jpg to An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e701.jpg forces a faster dynamics so that the total activity remains unchanged. One verifies that the activity An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e702.jpg remains the same for both values of An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e703.jpg. The two dynamics generate two different biochemical sequences, say for example

equation image

An examination of Table 3 and Table S3 in the supplementary material reveals that, for each fixed An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e705.jpg the products An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e706.jpg and An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e707.jpg, are essentially the same for the two dynamics. Thus the total An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e708.jpg activity is redistributed in “equal bits”, although in different time intervals An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e709.jpg and An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e710.jpg, and different catalytic activities An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e711.jpg and An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e712.jpg. The theoretical formula Eq:3 then gives

equation image

This explains why the CVs of An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e714.jpg, and hence those of An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e715.jpg are so similar, for each of these dynamics. A further examination of Table 3 and Table S3 of the supplementary material shows that to the total activity An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e716.jpg contribute essentially only the first few steps, the remaining ones being negligible. In view of the theoretical formula Eq:3, this is further evidence that increasing the number of steps, does not significantly decrease the CV(An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e717.jpg).

The main difference between the CVs in Table 1 and Table S1 in the supplementary material occurs for the pointwise functionals An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e718.jpg and An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e719.jpg, which depend on a point evaluation at An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e720.jpg and An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e721.jpg respectively, and do not depend on the total, integral activity up to time An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e722.jpg.

The average number of steps to shutoff

This number is computed from Eq:10–Eq:11, and therefore it is not expected to be an integer.

For An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e723.jpg and An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e724.jpg and the corresponding An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e725.jpg and An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e726.jpg, one estimates An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e727.jpg. For the faster dynamics An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e728.jpg, and An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e729.jpg, one estimates An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e730.jpg.

The parameters of Table S2 and Table 4 have been slightly calibrated to satisfy simultaneously all the indicated constraints. Figure 4 compares the simulated and experimental single photon response in WT mouse. The simulations for transgenic mouse in Figure 2 are compared with the experimental data of [1], [3], [23][25]. The dynamics of the WT mouse SPR reported in [1], is, in absolute time, slower than that reported in [3], [23][25]. The difference might be the result of using different solutions for single cell recording [2], [28]. The underlying mechanism of this phenomenon remains unknown. To achieve a functional comparison with all these contributions we have reported our simulations in units of An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e731.jpg and likewise we have rescaled the graphs reported in [3], [23] in units of their own An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e732.jpg. The output (given in pA in the original papers) has been rescaled in relative current suppression An external file that holds a picture, illustration, etc.
Object name is pcbi.1001031.e733.jpg.

Supporting Information

Figure S1

Comparing the CVs of the total activated effectors at time t with the CVs of the total relative charge up to time t.

(0.05 MB PDF)

Figure S2

Simulations SPR for mutant phosphorylation sites of R* or with Arr knockout.

(0.08 MB PDF)

Table S1

CVs of effector and current for WT and mutant mouse SPR.

(0.04 MB PDF)

Table S2

Parameter table for WT SPR.

(0.06 MB PDF)

Table S3

Table of distribution of activities for WT and mutant mouse SPR.

(0.03 MB PDF)

Text S1

References.

(0.04 MB PDF)

Acknowledgments

This work has been conducted in part using the resources of the Advanced Computing Center for Research and Education at Vanderbilt University, Nashville, TN. We thank Dr. Clint Makino, for mouse electrophysiological data.

Footnotes

The authors have declared that no competing interests exist.

This work was supported by NIH grants EY011500(VVG), 1RO1GM068953(ED), EY006062(HEH) and NSF-DMS 0652385. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

References

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