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1.  Electron spin resonance studies of trityl OX063 at optimal concentration for DNP 
We have performed temperature-dependent electron spin resonance (ESR) measurements of the stable free radical trityl OX063, an efficient polarizing agent for dissolution dynamic nuclear polarization (DNP), at the optimum DNP concentration (15 mM). We have found that (i) when compared to the W-band electron spin-lattice relaxation rate T1e−1 of other free radicals used in DNP at the same concentration, trityl OX063 has slower T1e−1 than BDPA and 4-oxo-TEMPO. At T> 20 K, the T1e−1 vs T data of trityl OX063 appears to follow a power law dependence close to the Raman process prediction whereas at T<10 K, electronic relaxation slows and approaches the direct process behaviour. (ii) Gd3+ doping, a factor known to enhance DNP, of trityl OX063 samples measured at W-band resulted in monotonic increases of T1e−1 especially at temperatures below 20–40 K while the ESR lineshapes remained essentially unchanged. (iii) The high frequency ESR spectrum can be fitted with an axial g-tensor with a slight g-anisotropy: gx=gy=2.00319(3) and gz=2.00258(3). Although the ESR linewidth D monotonically increases with field, the temperature-dependent T1e −1 is almost unchanged as the ESR frequency is increased from 9.5 GHz to 95 GHz, but becomes faster at 240 GHz and 336 GHz. The ESR properties of trityl OX063 reported here may provide insights into the efficiency of DNP of low-γ nuclei performed at various magnetic fields, from 0.35 T to 12 T.
PMCID: PMC3698225  PMID: 23676994
2.  Superstructure based on β-CD self-assembly induced by a small guest molecule† 
The size, shape and surface chemistry of nanoparticles play an important role in cellular interaction. Thus, the main objective of the present study was the determination of the β-cyclodextrin (β-CD) self-assembly thermodynamic parameters and its structure, aiming to use these assemblies as a possible controlled drug release system. Light scattering measurements led us to obtain the β-CD’s critical aggregation concentration (cac) values, and consequently the thermodynamic parameters of the β-CD spontaneous self-assembly in aqueous solution: ΔaggGo = − 16.31 kJ mol−1, ΔaggHo = − 26.48 kJ mol−1 and TΔaggSo = − 10.53 kJ mol−1 at 298.15 K. Size distribution of the self-assembled nanoparticles below and above cac was 1.5 nm and 60–120 nm, respectively. The number of β-CD molecules per cluster and the second virial coefficient were identified through Debye’s plot and molecular dynamic simulations proposed the three-fold assembly for this system below cac. Ampicillin (AMP) was used as a drug model in order to investigate the key role of the guest molecule in the self-assembly process and the β-CD:AMP supramolecular system was studied in solution, aiming to determine the structure of the supramolecular aggregate. Results obtained in solution indicated that the β-CD’s cac was not affected by adding AMP. Moreover, different complex stoichiometries were identified by nuclear magnetic resonance and isothermal titration calorimetry experiments.
PMCID: PMC4059046  PMID: 22234498
3.  Copper(II)–human amylin complex protects pancreatic cells from amylin toxicity†‡ 
Human amylin-derived oligomers and aggregates are believed to play an important role in the pathogenesis of type II diabetes mellitus (T2DM). In addition to amylin-evoked cell attrition, T2DM is often accompanied by elevated serum copper levels. Although previous studies have shown that human amylin, in the course of its aggregation, produces hydrogen peroxide (H2O2) in solution, and that this process is exacerbated in the presence of copper(II) ions (Cu2+), very little is known about the mechanism of interaction between Cu2+ and amylin in pancreatic β-cells, including its pathological significance. Hence, in this study we investigated the mechanism by which Cu2+ and human amylin catalyze formation of reactive oxygen species (ROS) in cells and in vitro, and examined the modulatory effect of Cu2+ on amylin aggregation and toxicity in pancreatic rat insulinoma (RIN-m5F) β-cells. Our results indicate that Cu2+ interacts with human and rat amylin to form metalo-peptide complexes with low aggregative and oxidative properties. Human and non-amyloidogenic rat amylin produced minute (nM) amounts of H2O2, the accumulation of which was slightly enhanced in the presence of Cu2+. In a marked contrast to human and rat amylin, and in the presence of the reducing agents glutathione and ascorbate, Cu2+ produced μM concentrations of H2O2 surpassing the amylin effect by several fold. The current study shows that human and rat amylin not only produce but also quench H2O2, and that human but not rat amylin significantly decreases the amount of H2O2 in solution produced by Cu2+ and glutathione. Similarly, human amylin was found to also decrease hydroxyl radical formation elicited by Cu2+ and glutathione. Furthermore, Cu2+ mitigated the toxic effect of human amylin by inhibiting activation of pro-apoptotic caspase-3 and stress-kinase signaling pathways in rat pancreatic insulinoma cells in part by stabilizing human amylin in its native conformational state. This sacrificial quenching of metal-catalyzed ROS by human amylin and copper’s anti-aggregative and anti-apoptotic properties suggest a novel and protective role for the copper–amylin complex.
PMCID: PMC4041291  PMID: 23793354
4.  Influence of deuteration in the glassing matrix on 13C dynamic nuclear polarization† 
Replacement of protons by deuterons in the glassing solvents led to 2–3-fold improvement of the 13C dynamic nuclear polarization (DNP) solid-state NMR signal for samples doped with large electron spin resonance (ESR) linewidth free radicals galvinoxyl, DPPH, and 4-oxo-TEMPO. Meanwhile, the reverse effect is observed for 13C DNP using small ESR linewidth free radicals BDPA and trityl OX063.
PMCID: PMC3681295  PMID: 23552448
5.  Connecting the (quantum) dots: Towards hybrid photovoltaic devices based on chalcogenide gels 
CdSe(ZnS) core(shell) aerogels were prepared from the assembly of quantum dots into mesoporous colloidal networks. The sol-gel method produces inorganic particle interfaces with low resistance to electrical transport while maintaining quantum-confinement. The photoelectrochemical properties of aerogels and their composites with poly(3-hexylthiophene) are reported for the first time.
PMCID: PMC4028160  PMID: 23034484
6.  Molecular Sentinel-on-Chip for SERS-Based Biosensing† 
The development of DNA detection techniques on large-area plasmonics-active platforms is critical for many medical applications such as high-throughput screening, medical diagnosis and systems biology research. Here, we report for the first time a unique “molecular sentinel-on-chip” (MSC) technology for surface-enhanced Raman scattering (SERS)-based DNA detection. This unique approach allows label-free detection of DNA molecules on chips developed on a wafer scale using large area nanofabrication methodologies. To develop plasmonics-active biosensing platforms in a repeatable and reproducible manner, we employed a combination of deep UV lithography, atomic layer deposition, and metal deposition to fabricate triangular-shaped nanowire (TSNW) arrays having controlled sub-10 nm gaps nanostructures over an entire 6-inch wafer. The detection of a DNA sequence of the Ki-67 gene, a critical breast cancer biomarker, on the TSNW substrate illustrates the usefulness and potential of the MSC technology as a novel SERS-based DNA detection method.
PMCID: PMC4022304  PMID: 23493773
7.  Recovering degraded quasi-solid-state dye-sensitized solar cells by applying electrical pulses 
Physical chemistry chemical physics : PCCP  2013;15(18):10.1039/c3cp51071a.
We discovered a method of applying forward pulsed bias to recover the degradation of quasi-solid-state dye-sensitized solar cells (DSSCs). Up to 30.7% of the power conversion efficiency (η) of a degraded poly (vinylidene fluoride) (PVDF) based DSSC was recovered by a double-pulse. The recovered η remained higher than that before the double-pulse treatment for at least 28 days. It is deduced that the blocking of ion-transport channels in the quasi-solid-state electrolyte causes degradation of the DSSCs. This study will shed light on the efficiency enhancement and long-term stability of quasi-solid-state DSSCs.
PMCID: PMC3650726  PMID: 23545782
8.  Improving Correlated SERS Measurements with Scanning Electron Microscopy: An Assessment of the Problem Arising from the Deposition of Amorphous Carbon 
For surface-enhanced Raman scattering (SERS) substrates with nonspherical symmetry, it is critical to correlate spectroscopy measurements with imaging by scanning electron microscopy (SEM). However, the deposition of carbon resulting from e-beam exposure during SEM imaging contaminates the surface of nanoparticles, potentially preventing their further functionalization with Raman probe molecules. In addition, the deposited carbon leads to unwanted background SERS signals. In this study, we systematically investigated the deposition of carbon during SEM imaging and examined how it affects the functionalization of nanoparticles with probe molecules and impacts the detection of SERS signals. Significantly, we found that the carbon could be removed or replaced from the surface of Ag nanoparticles through a chemical or physical means, rendering the nanoparticles the capability for correlated SEM/SERS studies.
PMCID: PMC3615672  PMID: 23416796
Surface-enhanced Raman scattering; silver nanoparticle; carbon deposition; self-assembled monolayer; plasma etching
9.  Microsecond kinetics in model single- and double-stranded amylose polymers† †Electronic supplementary information (ESI) available: Detailed structural definitions, methodological descriptions, analyses of the simulations and computed and experimental molecular properties are provided. See DOI: 10.1039/c4cp00570h Click here for additional data file.  
Physical Chemistry Chemical Physics  2014;16(17):8119-8126.
Amylose, a component of starch with increasing biotechnological significance, is a linear glucose polysaccharide that self-organizes into single- and double-helical assemblies.
Amylose, a component of starch with increasing biotechnological significance, is a linear glucose polysaccharide that self-organizes into single- and double-helical assemblies. Starch granule packing, gelation and inclusion-complex formation result from finely balanced macromolecular kinetics that have eluded precise experimental quantification. Here, graphics processing unit (GPU) accelerated multi-microsecond aqueous simulations are employed to explore conformational kinetics in model single- and double-stranded amylose. The all-atom dynamics concur with prior X-ray and NMR data while surprising and previously overlooked microsecond helix–coil, glycosidic linkage and pyranose ring exchange are hypothesized. In a dodecasaccharide, single-helical collapse was correlated with linkages and rings transitioning from their expected syn and 4 C 1 chair conformers. The associated microsecond exchange rates were dependent on proximity to the termini and chain length (comparing hexa- and trisaccharides), while kinetic features of dodecasaccharide linkage and ring flexing are proposed to be a good model for polymers. Similar length double-helices were stable on microsecond timescales but the parallel configuration was sturdier than the antiparallel equivalent. In both, tertiary organization restricted local chain dynamics, implying that simulations of single amylose strands cannot be extrapolated to dimers. Unbiased multi-microsecond simulations of amylose are proposed as a valuable route to probing macromolecular kinetics in water, assessing the impact of chemical modifications on helical stability and accelerating the development of new biotechnologies.
PMCID: PMC4006424  PMID: 24652085
10.  Microsecond folding experiments and simulations: a match is made 
For the past two decades, protein folding experiments have been speeding up from the second or millisecond time scale to the microsecond time scale, and full-atom simulations have been extended from the nanosecond to the microsecond and even millisecond time scale. Where the two meet, it is now possible to compare results directly, allowing force fields to be validated and refined, and allowing experimental data to be interpreted in atomistic detail. In this perspective we compare recent experiments and simulations on the microsecond time scale, pointing out the progress that has been made in determining native structures from physics-based simulations, refining experiments and simulations to provide more quantitative underlying mechanisms, and tackling the problems of multiple reaction coordinates, downhill folding, and complex underlying structure of unfolded or misfolded states.
PMCID: PMC3632410  PMID: 23361200
11.  Molecules in the mirror: how SERS backgrounds arise from the quantum method of images† †Electronic supplementary information (ESI) available: Additional derivation of eqn (5). See DOI: 10.1039/c4cp00093e Click here for additional data file.  
Physical Chemistry Chemical Physics  2014;16(14):6544-6549.
The SERS background can be derived from the interaction of a molecule near a plasmonic surface with its image molecule.
The Raman coupling of light to molecular vibrations is strongly modified when they are placed near a plasmonic metal surface, with the appearance of a strong broad continuum background in addition to the normal surface-enhanced Raman scattering (SERS) peaks. Using a quantum method of images approach, we produce a simple but quantitative explanation of the inevitable presence of the background, due to the resistive damping of the image molecule. This model thus suggests new strategies for enhancing the SERS peak to background ratio.
PMCID: PMC4047623  PMID: 24584480
12.  A Kirkwood-Buff Force Field for the Aromatic Amino Acids 
In a continuation of our efforts to develop a united atom non-polarizable protein force field based upon the solution theory of Kirkwood and Buff i.e., the Kirkwood-Buff Force Field (KBFF) approach, we present KBFF models for the side chains of phenylalanine, tyrosine, tryptophan, and histidine, including both tautomers of neutral histidine and doubly-protonated histidine. The force fields were specifically designed to reproduce the thermodynamic properties of mixtures over the full composition range in an attempt to provide an improved description of intermolecular interactions. The models were developed by careful parameterization of the solution phase partial charges to reproduce the experimental Kirkwood-Buff integrals for mixtures of solutes representative of the amino acid sidechains in solution. The KBFF parameters and simulated thermodynamic and structural properties are presented for the following eleven binary mixtures: benzene + methanol, benzene + toluene, toluene + methanol, toluene + phenol, toluene + p-cresol, pyrrole + methanol, indole + methanol, pyridine + methanol, pyridine + water, histidine + water, and histidine hydrochloride + water. It is argued that the present approach and models provide a reasonable description of intermolecular interactions which ensures that the required balance between solute-solute, solute-solvent, and solvent-solvent distributions is obtained.
PMCID: PMC3910502  PMID: 21931889
13.  CoCrMo Metal-on-Metal Hip Replacements 
Physical chemistry chemical physics : PCCP  2013;15(3):10.1039/c2cp42968c.
After the rapid growth in the use of CoCrMo metal-on-metal hip replacements since the second generation was introduced circa 1990, metal-on-metal hip replacements have experienced a sharp decline in the last two years due to biocompatibility issues related to wear and corrosion products. Despite some excellent clinical results, the release of wear and corrosion debris and the adverse response of local tissues have been of great concern. There are many unknowns regarding how CoCrMo metal bearings interact with the human body. This perspective article is intended to outline some recent progresses in understanding wear and corrosion of metal-on-metal hip replacement both in-vivo and in-vitro. The materials, mechanical deformation, corrosion, wear-assisted corrosion, and wear products will be discussed. Possible adverse health effects caused by wear products will be briefly addressed, as well as some of the many open questions such as the detailed chemistry of corrosion, tribochemical reactions and the formation of graphitic layers. Nowadays we design almost routinely for high performance materials and lubricants for automobiles; humans are at least as important. It is worth remembering that a hip implant is often the difference between walking and leading a relatively normal life, and a wheelchair.
PMCID: PMC3530782  PMID: 23196425
14.  Peptide modified mesoporous silica nanocontainers† 
Here we report a new peptide modified mesoporous silica nanocontainer (PMSN) as a novel controlled release system. The peptides are part of a stimuli responsive nanovalve and ensure an efficient cellular uptake.
PMCID: PMC3893924  PMID: 21739680
15.  The effect of protein composition on hydration dynamics 
Physical chemistry chemical physics : PCCP  2013;15(10):10.1039/C3CP44582H.
Water dynamics at the surface of two homologous proteins with different thermal resistances is found to be unaffected by the different underlying amino-acid compositions, and when proteins are folded it responds similarly to temperature variations. Upon unfolding the water dynamics slowdown with respect to bulk decreases of a factor of two. Our findings are explained by the dominant topological perturbation induced by the protein on the water hydrogen bond dynamics.
PMCID: PMC3827537  PMID: 23381660
16.  Exploring a charge-central strategy in the solution of Poisson’s equation for biomolecular applications 
Continuum solvent treatments based on the Poisson–Boltzmann equation have been widely accepted for energetic analysis of biomolecular systems. In these approaches, the molecular solute is treated as a low dielectric region and the solvent is treated as a high dielectric continuum. The existence of a sharp dielectric jump at the solute–solvent interface poses a challenge to model the solvation energetics accurately with such a simple mathematical model. In this study, we explored and evaluated a strategy based on the “induced surface charge” to eliminate the dielectric jump within the finite-difference discretization scheme. In addition to the use of the induced surface charges in solving the equation, the second-order accurate immersed interface method is also incorporated to discretize the equation. The resultant linear system is solved with the GMRES algorithm to explicitly impose the flux conservation condition across the solvent–solute interface. The new strategy was evaluated on both analytical and realistic biomolecular systems. The numerical tests demonstrate the feasibility of utilizing induced surface charge in the finite-difference solution of the Poisson–Boltzmann equation. The analysis data further show that the strategy is consistent with theory and the classical finite-difference method on the tested systems. Limitations of the current implementations and further improvements are also analyzed and discussed to fully bring out its potential of achieving higher numerical accuracy.
PMCID: PMC3518737  PMID: 23147243
17.  Liquid Water Simulations with Density Fragment Interaction Approach 
Physical chemistry chemical physics : PCCP  2012;14(21):10.1039/c2cp23714h.
We reformulate the density fragment interaction (DFI) approach [J. Chem. Phys. 129, 054102 (2008)] to achieve linear-scaling quantum mechanical calculations for large molecular systems. Two key approximations are developed to improve the DFI efficiency and thus enable the calculations for large molecules: the electrostatic interactions between fragments are computed efficiently by means of polarizable electrostatic-potential-fitted atomic charges; and frozen fragment pseudopotentials, similar to the effective fragment potentials that can be fitted from interactions between small molecules, are employed to take into account the Pauli repulsion effect among fragments. Our reformulated and parallelized DFI method demonstrates excellent parallel performance based on the benchmarks for the system of 256 water molecules. Molecular dynamics simulations for the structural properties of liquid water also show a good agreement with experimental measurements including the heat capacity, binding energy per water molecule, and the radial distribution functions of for atomic pairs of O-O, O-H and H-H. With this approach, large-scale quantum mechanical simulations for water and other liquids become feasible.
PMCID: PMC3856182  PMID: 22466097
Electrostatic potential; Pauli repulsion; linear-scaling; effective potential
18.  Experimental and Modeling Study of the Oxidation of n-Butane in a Jet Stirred Reactor using cw-CRDS Measurements 
Physical chemistry chemical physics : PCCP  2013;15(45):10.1039/c3cp53335b.
The gas-phase oxidation of n-butane has been studied in an atmospheric jet-stirred reactor (JSR) at temperatures up to 950 K. For the first time, continuous wave cavity ring-down spectroscopy (cw-CRDS) in the near-infrared has been used, together with gas chromatography (GC), to analyze the products formed during the oxidation. In addition to the quantification of formaldehyde and water, which is always difficult by GC, cw-CRDS allowed as well the quantification of hydrogen peroxide (H2O2). A comparison of the obtained mole fraction temperature profiles with simulations using a detailed gas-phase mechanism shows a good agreement at temperatures below 750 K, but an overestimation of the overall reactivity above this temperature. Also, a strong overestimation was found for the H2O2 mole fraction at the higher temperatures. In order to improve the agreement between model and experimental results, two modifications have been implemented to the model: (a) the rate constant for the decomposition of H2O2 (+M) ↔ 2 OH (+M) has been updated to the value recently proposed by Troe (Combust. Flame, 2011, 158, 594-601) and (b) a temperature dependant heterogeneous destruction of H2O2 on the hot reactor walls with assumed rate parameters has been added. The improvement (a) slows down the overall reactivity at higher temperatures, but has a negligible impact on the maximal H2O2 mole fraction. Improvement (b) has also a small impact on the overall reactivity at higher temperatures, but a large effect on maximal H2O2 mole fraction. Both modifications lead to an improved agreement between model and experiment for the oxidation of n-butane in a JSR at temperatures above 750 K.
PMCID: PMC3833050  PMID: 24135810
19.  Volumetric Stability of Lipid Bilayers 
In agreement with recent reports, a commercial densimeter has yielded a gradual decrease in lipid molecular volume of DPPC multilamellar vesicle dispersions in the gel phase upon repeated thermal cycling between 10ºC and 50ºC. The considerable size of this decrease would have significant implications for the physical chemistry of biomembranes. In contrast, neutral buoyancy measurements performed with similar thermal cycling indicate no gradual change in lipid volume in the gel phase at 20ºC. Remixing the lipid in the densimeter shows that the apparent volume decrease is an artifact. We conclude that gel phase DPPC bilayers exist in a volumetrically stable phase.
PMCID: PMC3498488  PMID: 23069984
20.  Panchromatic porous specular back reflectors for efficient transparent dye solar cells† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c3cp53939c Click here for additional data file.  
A panchromatic specular reflector that mimics the reflection properties of a standard diffuse scattering layer in a broad spectral range within the visible is coupled to a dye sensitized nanocrystalline titania electrode to attain a solar cell of largely enhanced efficiency that, at the same time, preserves its transparency.
A panchromatic specular reflector based dye solar cell is presented herein. Photovoltaic performance of this novel design is compared to that of cells in which standard diffuse scattering layers are integrated. The capability of the proposed multilayer structures to both emulate the broad band reflection of diffuse scattering layers of standard thickness (around 5 microns) and give rise to similarly high light harvesting and power conversion efficiencies, yet preserving the transparency of the device, is demonstrated. Such white light reflectors are comprised of stacks of different porous optical multilayers, each one displaying a strong reflection in a complementary spectral range, and are designed to leave transmittance unaltered in a narrow red-frequency range in which the sensitized electrode shows negligible absorption, thus allowing us to see through the cell. The reflectance bandwidth achieved is three times as broad as the largest bandwidth previously achieved using any photonic structure integrated into a dye solar cell.
PMCID: PMC3894859  PMID: 24263620
21.  Damage to amino acid–nucleotide pairs induced by 1 eV electrons 
Physical chemistry chemical physics : PCCP  2010;12(32):10.1039/b926267a.
We have investigated the role of two selected amino acids, glycine and arginine, on damage induced to a short chain of single stranded DNA, the tetramer GCAT, during 1 eV electron exposure. At this energy, DNA has a high cross section for DNA damage via exclusively dissociative electron attachment. Surprisingly, at low ratios of glycine : GCAT, an increase in the total fragmentation yield is observed, whilst at higher ratios, glycine and arginine appear to protect DNA from the direct action of electrons. In addition, binding energies were calculated by molecular modelling of the interactions between these amino acids and either nucleobases or nucleotides. These binding energies appear to be related to the ability of amino acids to protect DNA against low energy electron damage.
PMCID: PMC3828173  PMID: 20563347 CAMSID: cams1992
22.  Solution, surface, and single molecule platforms for the study of DNA-mediated charge transport 
The structural core of DNA, a continuous stack of aromatic heterocycles, the base pairs, which extends down the helical axis, gives rise to the fascinating electronic properties of this molecule that is so critical for life. Our laboratory and others have developed diverse experimental platforms to investigate the capacity of DNA to conduct charge, termed DNA-mediated charge transport (DNA CT). Here, we present an overview of DNA CT experiments in solution, on surfaces, and with single molecules that collectively provide a broad and consistent perspective on the essential characteristics of this chemistry. DNA CT can proceed over long molecular distances but is remarkably sensitive to perturbations in base pair stacking. We discuss how this foundation, built with data from diverse platforms, can be used both to inform a mechanistic description of DNA CT and to inspire the next platforms for its study: living organisms and molecular electronics.
PMCID: PMC3478128  PMID: 22850865
23.  Vibrationally Assisted Electron Transfer Mechanism of Olfaction: Myth or Reality? 
Smell is a vital sense for animals. The mainstream explanation of smell is based on recognition of the odorant molecules through characteristics of their surface, e.g., shape, but certain experiments suggest that such recognition is complemented by recognition of vibrational modes. According to this suggestion an olfactory receptor is activated by electron transfer assisted through odorant vibrational excitation. The hundreds to thousands of different olfactory receptors in an animal recognize odorants over a discriminant landscape with surface properties and vibrational frequencies as the two major dimensions. In the present paper we introduce the vibrationally assisted mechanism of olfaction and demonstrate for several odorants that, indeed, a strong enhancement of an electron tunneling rate due to odorant vibrations can arise. We discuss in this regard the influence of odorant deuteration and explain, thereby, recent experiments performed on Drosophila melanogaster. Our demonstration is based on known physical properties of biological electron transfer and on ab initio calculations on odorants carried out for the purpose of the present study. We identify a range of physical characteristics which olfactory receptors and odorants must obey for the vibrationally assisted electron transfer mechanism to function. We argue that the stated characteristics are feasible for realistic olfactory receptors, noting, though, that the receptor structure presently is still unknown, but can be studied through homology modeling.
PMCID: PMC3478898  PMID: 22899100
24.  Interfacial Hydration, Dynamics and Electron Transfer: Multi-Scale ET Modeling of the Transient [Myoglobin, Cytochrome b5] Complex 
Formation of a transient [myoglobin (Mb), cytochrome b5 (cyt b5)] complex is required for the reductive repair of inactive ferri-Mb to its functional ferro-Mb state. The [Mb, cyt b5] complex exhibits dynamic docking (DD), with its cyt b5 partner in rapid exchange at multiple sites on the Mb surface. A triple mutant (Mb(3M)) was designed as part of efforts to shift the electron-transfer process to the simple docking (SD) regime, in which reactive binding occurs at a restricted, reactive region on the Mb surface that dominates the docked ensemble.1 An electrostatically-guided Brownian dynamics (BD) docking protocol was used to generate an initial ensemble of reactive configurations of the complex between unrelaxed partners. This ensemble samples a broad and diverse array of heme-heme distances and orientations. These configurations seeded all-atom constrained molecular dynamics simulations (MD) to generate relaxed complexes for the calculation of electron tunneling matrix elements (TDA) through tunneling-pathway analysis. This procedure for generating an ensemble of relaxed complexes combines the ability of BD calculations to sample the large variety of available conformations and interprotein distances, with the ability of MD to generate the atomic level information, especially regarding the structure of water molecules at the protein-protein interface, that defines electron-tunneling pathways. We used the calculated TDA values to compute ET rates for the [Mb(wt), cyt b5] complex and for the complex with a mutant that has a binding free energy strengthened by three D/E → K charge-reversal mutations, [Mb(3M), cyt b5]. The calculated rate constants are in agreement with the measured values, and the mutant complex ensemble has many more geometries with higher TDA values than does the wild-type Mb complex. Interestingly, water plays a double role in this electron-transfer system, lowering the tunneling barrier as well as inducing protein interface remodeling that screens the repulsion between the negatively-charged proprionates of the two hemes.
PMCID: PMC3490627  PMID: 22955681
25.  On Rate Limitations of Electron Transfer in the Photosynthetic Cytochrome b6f Complex 
Considering information in the crystal structures of the cytochrome b6f complex relevant to the rate-limiting step in oxygenic photosynthesis (1–5), it is enigmatic that electron transport in the complex is not limited by the large distance, approximately 26 Å, between the iron-sulfur cluster (ISP) and its electron acceptor, cytochrome f. This enigma has been explained for the respiratory bc1 complex by a crystal structure with a greatly shortened cluster-heme c1 distance (6), leading to a concept of ISP dynamics in which the ISP soluble domain undergoes a translation-rotation conformation change and oscillates between positions relatively close to the cyt c1 heme and a membrane-proximal position close to the ubiquinol electron-proton donor. Comparison of cytochrome b6f structures shows a variation in cytochrome f heme position that suggests the possibility of flexibility and motion of the extended cytochrome f structure that could entail a transient decrease in cluster-heme f distance. The dependence of cyt f turnover on lumen viscosity (7) is consistent with a role of ISP - cyt f dynamics in determination of the rate-limiting step under conditions of low light intensity.
Under conditions of low light intensity and proton electrochemical gradient present, for example, under a leaf canopy, it is proposed that a rate limitation of electron transport in the b6f complex may also arise from steric constraints in the entry/exit portal for passage of the plastoquinol and -quinone to/from its oxidation site proximal to the iron-sulfur cluster.
PMCID: PMC3505453  PMID: 22890107
not in title: cytochrome bc1 complex; oxygenic photosynthesis; plastoquinone

Results 1-25 (98)