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1.  A Didactic Model of Macromolecular Crowding Effects on Protein Folding 
PLoS ONE  2010;5(8):e11936.
A didactic model is presented to illustrate how the effect of macromolecular crowding on protein folding and association is modeled using current analytical theory and discrete molecular dynamics. While analytical treatments of crowding may consider the effect as a potential of average force acting to compress a polypeptide chain into a compact state, the use of simulations enables the presence of crowding reagents to be treated explicitly. Using an analytically solvable toy model for protein folding, an approximate statistical thermodynamic method is directly compared to simulation in order to gauge the effectiveness of current analytical crowding descriptions. Both methodologies are in quantitative agreement under most conditions, indication that both current theory and simulation methods are capable of recapitulating aspects of protein folding even by utilizing a simplistic protein model.
doi:10.1371/journal.pone.0011936
PMCID: PMC2914742  PMID: 20689808
2.  The Effect of Macromolecular Crowding on the Electrostatic Component of Barnase–Barstar Binding: A Computational, Implicit Solvent-Based Study 
PLoS ONE  2014;9(6):e98618.
Macromolecular crowding within the cell can impact both protein folding and binding. Earlier models of cellular crowding focused on the excluded volume, entropic effect of crowding agents, which generally favors compact protein states. Recently, other effects of crowding have been explored, including enthalpically-related crowder–protein interactions and changes in solvation properties. In this work, we explore the effects of macromolecular crowding on the electrostatic desolvation and solvent-screened interaction components of protein–protein binding. Our simple model enables us to focus exclusively on the electrostatic effects of water depletion on protein binding due to crowding, providing us with the ability to systematically analyze and quantify these potentially intuitive effects. We use the barnase–barstar complex as a model system and randomly placed, uncharged spheres within implicit solvent to model crowding in an aqueous environment. On average, we find that the desolvation free energy penalties incurred by partners upon binding are lowered in a crowded environment and solvent-screened interactions are amplified. At a constant crowder density (fraction of total available volume occupied by crowders), this effect generally increases as the radius of model crowders decreases, but the strength and nature of this trend can depend on the water probe radius used to generate the molecular surface in the continuum model. In general, there is huge variation in desolvation penalties as a function of the random crowder positions. Results with explicit model crowders can be qualitatively similar to those using a lowered “effective” solvent dielectric to account for crowding, although the “best” effective dielectric constant will likely depend on multiple system properties. Taken together, this work systematically demonstrates, quantifies, and analyzes qualitative intuition-based insights into the effects of water depletion due to crowding on the electrostatic component of protein binding, and it provides an initial framework for future analyses.
doi:10.1371/journal.pone.0098618
PMCID: PMC4051634  PMID: 24915485
3.  Volume Exclusion and Soft Interaction Effects on Protein Stability under Crowded Conditions† 
Biochemistry  2010;49(33):6984-6991.
Most proteins function in nature under crowded conditions, and crowding can change protein properties. Quantification of crowding effects, however, is difficult because solutions containing hundreds of grams per liter of macromolecules often interfere with observing the protein being studied. Models for macromolecular crowding tend to focus on the steric effects of crowders, neglecting potential chemical interactions between the crowder and the test protein. Here, we report the first systematic, quantitative, residue-level study of crowding effects on the equilibrium stability of a globular protein. We used a system comprising poly(vinylpyrrolidone)s (PVPs) of varying molecular weights as crowding agents and chymotrypsin inhibitor 2 (CI2) as a small globular test protein. Stability was quantified with NMR-detected amide 1H exchange. We analyze the data in terms of hard particle exclusion, confinement, and soft interactions. For all crowded conditions, nearly every observed residue experiences a stabilizing effect. The exceptions are residues where stabilities are unchanged. At a PVP concentration of 100 g/L, the data are consistent with theories of hard particle exclusion. At higher concentrations, the data are more consistent with confinement. The data show that the crowder also stabilizes the test protein by weakly binding its native state. We conclude that the role of native-state binding and other soft interactions need to be seriously considered when applying both theory and experiment to studies of macromolecular crowding.
doi:10.1021/bi100727y
PMCID: PMC2927838  PMID: 20672856
4.  Conformational Sampling of Peptides in the Presence of Protein Crowders from AA/CG-Multiscale Simulations 
The Journal of Physical Chemistry. B  2012;116(29):8610-8620.
Macromolecular crowding is recognized as an important factor influencing folding and conformational dynamics of proteins and nucleic acids. Previous views of crowding have focused on the mostly entropic volume exclusion effect of crowding but recent studies are indicating the importance of enthalpic effects, in particular changes in electrostatic interactions due to crowding. Here, temperature replica exchange molecular dynamics simulations of trp-cage and melittin in the presence of explicit protein crowders are presented to further examine the effect of protein crowders on peptide dynamics. The simulations involve a three-component multiscale modeling scheme where the peptides are represented at atomistic level, the crowder proteins at a coarse-grained level, and the surrounding aqueous solvent as implicit solvent. This scheme optimally balances a physically realistic description for the peptide with computational efficiency. The multiscale simulations were compared with simulations of the same peptides in different dielectric environments with dielectric constants ranging from 5 to 80. It is found that the sampling in the presence of the crowders resembles sampling with reduced dielectric constants between 10 and 40. Furthermore, diverse conformational ensembles are generated in the presence of crowders including partially unfolded states for trp-cage. These findings emphasize the importance of enthalpic interactions over volume exclusion effects in describing the effects of cellular crowding.
doi:10.1021/jp300129u
PMCID: PMC3398202  PMID: 22429139
protein-protein interactions; molecular dynamics; coarse-graining; multiscale simulations; replica exchange; crowding
5.  Simulation and Modeling of Crowding Effects on the Thermodynamic and Kinetic Properties of Proteins with Atomic Details 
Biophysical reviews  2013;5(2):207-215.
Recent experimental studies of protein folding and binding under crowded solutions suggest that crowding agents exert subtle influences on the thermodynamic and kinetic properties of the proteins. While some of the crowding effects can be understood qualitatively from simple models of the proteins, quantitative rationalization of these effects requires an atomistic representation of the protein molecules in modeling their interactions with crowders. A computational approach, known as postprocessing, has opened the door for atomistic modeling of crowding effects. This review summarizes the applications of the postprocessing approach for studying crowding effects on the thermodynamics and kinetics of protein folding, conformational transition, and binding. The integration of atomistic modeling with experiments in crowded solutions promises new insight into biochemical processes in cellular environments.
doi:10.1007/s12551-013-0101-7
PMCID: PMC3659821  PMID: 23710260
macromolecular crowding; protein folding; protein binding; simulation; modeling; postprocessing
6.  Reduced native state stability in crowded cellular environment due to protein-protein interactions 
The effect of cellular crowding environments on protein structure and stability is a key issue in molecular and cellular biology. The classical view of crowding emphasizes the volume exclusion effect that generally favors compact, native states. Here, results from molecular dynamics simulations and NMR experiments show that protein crowders may destabilize native states via protein-protein interactions. In the model system considered here, mixtures of villin head piece and protein G at high concentrations, villin structures become increasingly destabilized upon increasing crowder concentrations. The denatured states observed in the simulation involve partial unfolding as well as more subtle conformational shifts. The unfolded states remain overall compact and only partially overlap with unfolded ensembles at high temperature and in the presence of urea. NMR measurements on the same systems confirm structural changes upon crowding based on changes of chemical shifts relative to dilute conditions. An analysis of protein-protein interactions and energetic aspects suggests the importance of enthalpic and solvation contributions to the crowding free energies that challenge an entropic-centered view of crowding effects.
doi:10.1021/ja3126992
PMCID: PMC3601481  PMID: 23402619
Molecular dynamics simulation; folding; villin; protein-protein interactions
7.  A Generalized Fundamental Measure Theory for Atomistic Modeling of Macromolecular Crowding 
Macromolecular crowding inside cells affects the thermodynamic and kinetic properties of proteins. The scaled particle theory (SPT) has played an important role toward establishing a qualitative picture for the effects of crowding. However, SPT-based modeling lacks molecular details. Molecular dynamics simulations overcome this limitation, but at great computational cost. Here we present a theoretical method for modeling crowding at the atomic level. The method makes it possible to achieve exhaustive conformational sampling in modeling crowding effects and to tackle challenges posed by large protein oligomers and by complex mixtures of crowders.
PMCID: PMC3537823  PMID: 20365782
8.  Folding, Stability and Shape of Proteins in Crowded Environments: Experimental and Computational Approaches 
How the crowded environment inside cells affects folding, stability and structures of proteins is a vital question, since most proteins are made and function inside cells. Here we describe how crowded conditions can be created in vitro and in silico and how we have used this to probe effects on protein properties. We have found that folded forms of proteins become more compact in the presence of macromolecular crowding agents; if the protein is aspherical, the shape also changes (extent dictated by native-state stability and chemical conditions). It was also discovered that the shape of the macromolecular crowding agent modulates the folding mechanism of a protein; in addition, the extent of asphericity of the protein itself is an important factor in defining its folding speed.
doi:10.3390/ijms10020572
PMCID: PMC2660654  PMID: 19333422
Macromolecular crowding; Ficoll® 70; energy landscape theory; off-lattice model; excluded volume effect; protein folding mechanism; spectroscopy
9.  Protein Folding Requires Crowd Control in a Simulated Cell 
Journal of Molecular Biology  2010;397(5):1329-1338.
Macromolecular crowding has a profound effect upon biochemical processes in the cell. We have computationally studied the effect of crowding upon protein folding for 12 small domains in a simulated cell using a coarse-grained protein model, which is based upon Langevin dynamics, designed to unify the often disjoint goals of protein folding simulation and structure prediction. The model can make predictions of native conformation with accuracy comparable with that of the best current template-free models. It is fast enough to enable a more extensive analysis of crowding than previously attempted, studying several proteins at many crowding levels and further random repetitions designed to more closely approximate the ensemble of conformations. We found that when crowding approaches 40% excluded volume, the maximum level found in the cell, proteins fold to fewer native-like states. Notably, when crowding is increased beyond this level, there is a sudden failure of protein folding: proteins fix upon a structure more quickly and become trapped in extended conformations. These results suggest that the ability of small protein domains to fold without the help of chaperones may be an important factor in limiting the degree of macromolecular crowding in the cell. Here, we discuss the possible implications regarding the relationship between protein expression level, protein size, chaperone activity and aggregation.
doi:10.1016/j.jmb.2010.01.074
PMCID: PMC2891488  PMID: 20149797
TM, template modelling; macromolecular crowding; protein structure prediction; protein misfolding; protein aggregation; protein expression
10.  Influence of Nanoparticle Size and Shape on Oligomer Formation of an Amyloidogenic Peptide 
Understanding the influence of macromolecular crowding and nanoparticles on the formation of in-register β-sheets, the primary structural component of amyloid fibrils, is a first step towards describing in vivo protein aggregation and interactions between synthetic materials and proteins. Using all atom molecular simulations in implicit solvent we illustrate the effects of nanoparticle size, shape, and volume fraction on oligomer formation of an amyloidogenic peptide from the transthyretin protein. Surprisingly, we find that inert spherical crowding particles destabilize in-register β-sheets formed by dimers while stabilizing β-sheets comprised of trimers and tetramers. As the radius of the nanoparticle increases crowding effects decrease, implying smaller crowding particles have the largest influence on the earliest amyloid species. We explain these results using a theory based on the depletion effect. Finally, we show that spherocylindrical crowders destabilize the ordered β-sheet dimer to a greater extent than spherical crowders, which underscores the influence of nanoparticle shape on protein aggregation.
doi:10.1021/jz200330k
PMCID: PMC3117580  PMID: 21691423
crowding; in vivo; early events; amyloid
11.  Macromolecular Crowding as a Suppressor of Human IAPP Fibril Formation and Cytotoxicity 
PLoS ONE  2013;8(7):e69652.
The biological cell is known to exhibit a highly crowded milieu, which significantly influences protein aggregation and association processes. As several cell degenerative diseases are related to the self-association and fibrillation of amyloidogenic peptides, understanding of the impact of macromolecular crowding on these processes is of high biomedical importance. It is further of particular relevance as most in vitro studies on amyloid aggregation have been performed in diluted solution which does not reflect the complexity of their cellular surrounding. The study presented here focuses on the self-association of the type-2 diabetes mellitus related human islet amyloid polypeptide (hIAPP) in various crowded environments including network-forming macromolecular crowding reagents and protein crowders. It was possible to identify two competing processes: a crowder concentration and type dependent stabilization of globular off-pathway species and a – consequently - retarded or even inhibited hIAPP fibrillation reaction. The cause of these crowding effects was revealed to be mainly excluded volume in the polymeric crowders, whereas non-specific interactions seem to be most dominant in protein crowded environments. Specific hIAPP cytotoxicity assays on pancreatic β-cells reveal non-toxicity for the stabilized globular species, in contrast to the high cytotoxicity imposed by the normal fibrillation pathway. From these findings it can be concluded that cellular crowding is able to effectively stabilize the monomeric conformation of hIAPP, hence enabling the conduction of its normal physiological function and prevent this highly amyloidogenic peptide from cytotoxic aggregation and fibrillation.
doi:10.1371/journal.pone.0069652
PMCID: PMC3726762  PMID: 23922768
12.  Macromolecular crowding remodels the energy landscape of a protein by favoring a more compact unfolded state 
Journal of the American Chemical Society  2010;132(30):10445-10452.
The interior of cells is highly crowded with macromolecules, which impacts all physiological processes. To explore how macromolecular crowding may influence cellular protein folding, we interrogated the folding landscape of a model β-rich protein, cellular retinoic acid-binding protein I (CRABP I), in the presence of an inert crowding agent (Ficoll 70). Urea titrations revealed a crowding-induced change in the water-accessible polar amide surface of its denatured state, based on an observed ca. 15% decrease in the m-value (the change in unfolding free energy with respect to urea concentration), and the effect of crowding on the equilibrium stability of CRABP I was less than our experimental error (i.e., ≤1.2 kcal/mol). Consequently, we directly probed the effect of crowding on the denatured state of CRABP I by measuring side chain accessibility using iodide quenching of tryptophan fluorescence and chemical modification of cysteines. We observed that the urea-denatured state is more compact under crowded conditions, and the observed extent of reduction of the m value by crowding agent is fully consistent with the extent of reduction of the accessibility of the Trp and Cys probes, suggesting a random and nonspecific compaction of the unfolded state. The thermodynamic consequences of crowding-induced compaction are discussed. In addition, over a wide range of Ficoll concentration, crowding significantly retarded the unfolding kinetics of CRABP I without influencing the urea dependence of the unfolding rate, arguing for no appreciable change in the nature of the transition state. Our results demonstrate how macromolecular crowding may influence protein folding by effects both on the unfolded state ensemble and on unfolding kinetics. (end of abstract)
doi:10.1021/ja103166y
PMCID: PMC2921862  PMID: 20662522
13.  Effect of Mixed Macromolecular Crowding Agents on Protein Folding 
Proteins  2008;72(4):1109-1113.
In cells proteins fold and unfold in the presence of macromolecules with various sizes and shapes. Recent experiments by Liang and co-workers (J Biol Chem 2004;279:55109–55116; J Mol Biol 2006; 364:469–482) show that protein refolding is enhanced by a mixture of two different crowding agents relative to the individual crowding agents, and an optimal mixing ratio exists. Here we present a theory that predicts the existence of an optimal mixing ratio. The theory is based on models for calculating the changes in the chemical potentials of the folded and unfolded states by a mixture of crowders. The existence of an optimal mixing ratio results from the dependences of these chemical-potential changes on crowder sizes and concentrations, which can be argued to be quite general. We further predict that, for any crowding agent, the stabilizing effect can be optimized both by varying the molecular weight and by varying the mixing ratio of two species with different molecular weights.
doi:10.1002/prot.22111
PMCID: PMC2670543  PMID: 18506780
excluded-volume effect; folding stability; folding rate
14.  A Quantitative Model of ERK MAP Kinase Phosphorylation in Crowded Media 
Scientific Reports  2013;3:1541.
Cytoplasm contains a large number of macromolecules at extremely high densities. How this striking nature of intracellular milieu called macromolecular crowding affects intracellular signaling remains uncharacterized. Here, we examined the effect of macromolecular crowding on ERK MAPK phosphorylation by MEK MAPKK. Addition of polyethylene glycol-6000 (PEG-6000) as a crowder to mimic intracellular environments, elicited a biphasic response to the overall ERK phosphorylation rate. Furthermore, probability of processive phosphorylation (processivity) of tyrosine and threonine residues within the activation loop on ERK increased non-linearly for increasing PEG-6000 concentration. Based on the experimental data, we developed for the first time a mathematical model integrating all of the effects of thermodynamic activity, viscosity, and processivity in crowded media, and found that ERK phosphorylation is transition-state-limited reaction. The mathematical model allows accurate estimation of the effects of macromolecular crowding on a wide range of reaction kinetics, from transition-state-limited to diffusion-limited reactions.
doi:10.1038/srep01541
PMCID: PMC3607838  PMID: 23528948
15.  Method to Predict Crowding Effects by Postprocessing Molecular Dynamics Trajectories: Application to the Flap Dynamics of HIV-1 Protease 
The internal dynamics of proteins inside of cells may be affected by the crowded intracellular environments. Here, we test a novel approach to simulations of crowding, in which simulations in the absence of crowders are postprocessed to predict crowding effects, against the direct approach of simulations in the presence of crowders. The effects of crowding on the flap dynamics of HIV-1 protease predicted by the postprocessing approach are found to agree well with those calculated by the direct approach. The postprocessing approach presents distinct advantages over the direct approach in terms of accuracy and speed and is expected to have broad impact on atomistic simulations of macromolecular crowding.
doi:10.1021/jz900023w
PMCID: PMC2837415  PMID: 20228897
16.  Computer Simulations of the Bacterial Cytoplasm 
Biophysical reviews  2013;5(2):109-119.
Ever since the pioneering work of Minton, it has been recognized that the highly crowded interior of biological cells has the potential to cause dramatic changes to both the kinetics and thermodynamics of protein folding and association events relative to behavior that might be observed in dilute solution conditions. One very productive way to explore the effects of crowding on protein behavior has been to use macromolecular crowding agents that exclude volume without otherwise strongly interacting with the protein under study. An alternative, complementary approach to understanding the potential differences between behavior in vivo and in vitro is to develop simulation models that explicitly attempt to model intracellular environments at the molecular scale, and that thereby can be used to directly monitor biophysical behavior in conditions that accurately mimic those encountered in vivo. It is with studies of this type that the present review will be concerned. We review in detail four published studies that have attempted to simulate the structure and dynamics of the bacterial cytoplasm and that have each explored different biophysical aspects of the cellular interior. While each of these studies has yielded important new insights, there are important questions that remain to be resolved in terms of determining the relative contributions made by energetic and hydrodynamic interactions to the diffusive behavior of macromolecules and to the thermodynamics of protein folding and associations in vivo. Some possible new directions for future generation simulation models of the cytoplasm are outlined.
doi:10.1007/s12551-013-0110-6
PMCID: PMC3728174  PMID: 23914257
computer simulation; bacterial cytoplasm; macromolecular crowding; energetic interactions; hydrodynamic interactions
17.  Protein Folding in Confined and Crowded Environments 
Confinement and crowding are two major factors that can potentially impact protein folding in cellular environments. Theories based on considerations of excluded volumes predict disparate effects on protein folding stability for confinement and crowding: confinement can stabilize proteins by over 10kBT but crowding has a very modest effect on stability. On the other hand, confinement and crowding are both predicted to favor conformations of the unfolded state which are compact, and consequently may increase the folding rate. These predictions are largely borne out by experimental studies of protein folding under confined and crowded conditions in the test tube. Protein folding in cellular environments is further complicated by interactions with surrounding surfaces and other factors. Concerted theoretical modeling and test-tube and in vivo experiments promise to elucidate the complexity of protein folding in cellular environments.
doi:10.1016/j.abb.2007.07.013
PMCID: PMC2223181  PMID: 17719556
18.  Polymer Crowders and Protein Crowders Act Similarly on Protein Folding Stability 
FEBS letters  2013;587(5):394-397.
Recently a polymer crowder and two protein crowders were found to have opposite effects on the folding stability of chymotrypsin inhibitor 2 (CI2), suggesting that they interact differently with CI2. Here we propose that all the macromolecular crowders act similarly, with an entropic component favoring the folded state and an enthalpic component favoring the unfolded state. The net effect is destabilizing below a crossover temperature but stabilizing above it. This general trend is indeed observed in recent experiments and hints experimental temperature as a reason for the opposite crowding effects of the polymer and protein crowders.
doi:10.1016/j.febslet.2013.01.030
PMCID: PMC3581760  PMID: 23353683
macromolecular crowding; protein folding; crossover temperature
19.  An upper limit for macromolecular crowding effects 
BMC Biophysics  2011;4:13.
Background
Solutions containing high macromolecule concentrations are predicted to affect a number of protein properties compared to those properties in dilute solution. In cells, these macromolecular crowders have a large range of sizes and can occupy 30% or more of the available volume. We chose to study the stability and ps-ns internal dynamics of a globular protein whose radius is ~2 nm when crowded by a synthetic microgel composed of poly(N-isopropylacrylamide-co-acrylic acid) with particle radii of ~300 nm.
Results
Our studies revealed no change in protein rotational or ps-ns backbone dynamics and only mild (~0.5 kcal/mol at 37°C, pH 5.4) stabilization at a volume occupancy of 70%, which approaches the occupancy of closely packing spheres. The lack of change in rotational dynamics indicates the absence of strong crowder-protein interactions.
Conclusions
Our observations are explained by the large size discrepancy between the protein and crowders and by the internal structure of the microgels, which provide interstitial spaces and internal pores where the protein can exist in a dilute solution-like environment. In summary, microgels that interact weakly with proteins do not strongly influence protein dynamics or stability because these large microgels constitute an upper size limit on crowding effects.
doi:10.1186/2046-1682-4-13
PMCID: PMC3120801  PMID: 21627822
20.  Macromolecular crowding fails to fold a globular protein in cells 
Proteins perform their function in cells where macromolecular solutes reach concentrations of >300 g/L and occupy >30% of the volume. The volume excluded by these macromolecules will stabilize globular proteins because the native state occupies less space than the denatured state. Theory predicts that crowding can increase the ratio of folded to unfolded protein by a factor of 100, amounting to 3 kcal/mol of stabilization at room temperature. We tested the idea that volume exclusion dominates the crowding effect in cells with a variant of protein L, a 7-kDa globular protein with seven lysine residues replaced by glutamic acids. Eighty-four percent of the variant molecules populate the denatured state in dilute buffer at room temperature, compared to 0.1% for the wild-type protein. We then used in-cell nuclear magnetic resonance spectroscopy to show that the cytoplasm of Escherichia coli does not overcome even this modest (~1 kcal/mol) free energy deficit. The data are consistent with the idea that non-specific interactions between cytoplasmic components can overcome the excluded volume effect. Evidence for these interactions is provided by the observation that adding simple salts folds the variant in dilute solution, but increasing the salt concentration inside E. coli does not fold the protein. Our data are consistent with other studies of protein stability in cells, and suggest that stabilizing excluded volume effects, which must be present under crowded conditions, can be ameliorated by non-specific interactions between cytoplasmic components.
doi:10.1021/ja201206t
PMCID: PMC3102155  PMID: 21534566
21.  Effects of Molecular Crowding on the Dynamics of Intrinsically Disordered Proteins 
PLoS ONE  2012;7(11):e49876.
Inside cells, the concentration of macromolecules can reach up to 400 g/L. In such crowded environments, proteins are expected to behave differently than in vitro. It has been shown that the stability and the folding rate of a globular protein can be altered by the excluded volume effect produced by a high density of macromolecules. However, macromolecular crowding effects on intrinsically disordered proteins (IDPs) are less explored. These proteins can be extremely dynamic and potentially sample a wide ensemble of conformations under non-denaturing conditions. The dynamic properties of IDPs are intimately related to the timescale of conformational exchange within the ensemble, which govern target recognition and how these proteins function. In this work, we investigated the macromolecular crowding effects on the dynamics of several IDPs by measuring the NMR spin relaxation parameters of three disordered proteins (ProTα, TC1, and α-synuclein) with different extents of residual structures. To aid the interpretation of experimental results, we also performed an MD simulation of ProTα. Based on the MD analysis, a simple model to correlate the observed changes in relaxation rates to the alteration in protein motions under crowding conditions was proposed. Our results show that 1) IDPs remain at least partially disordered despite the presence of high concentration of other macromolecules, 2) the crowded environment has differential effects on the conformational propensity of distinct regions of an IDP, which may lead to selective stabilization of certain target-binding motifs, and 3) the segmental motions of IDPs on the nanosecond timescale are retained under crowded conditions. These findings strongly suggest that IDPs function as dynamic structural ensembles in cellular environments.
doi:10.1371/journal.pone.0049876
PMCID: PMC3506533  PMID: 23189168
22.  Effects of Macromolecular Crowding on Protein Conformational Changes 
PLoS Computational Biology  2010;6(7):e1000833.
Many protein functions can be directly linked to conformational changes. Inside cells, the equilibria and transition rates between different conformations may be affected by macromolecular crowding. We have recently developed a new approach for modeling crowding effects, which enables an atomistic representation of “test” proteins. Here this approach is applied to study how crowding affects the equilibria and transition rates between open and closed conformations of seven proteins: yeast protein disulfide isomerase (yPDI), adenylate kinase (AdK), orotidine phosphate decarboxylase (ODCase), Trp repressor (TrpR), hemoglobin, DNA β-glucosyltransferase, and Ap4A hydrolase. For each protein, molecular dynamics simulations of the open and closed states are separately run. Representative open and closed conformations are then used to calculate the crowding-induced changes in chemical potential for the two states. The difference in chemical-potential change between the two states finally predicts the effects of crowding on the population ratio of the two states. Crowding is found to reduce the open population to various extents. In the presence of crowders with a 15 Å radius and occupying 35% of volume, the open-to-closed population ratios of yPDI, AdK, ODCase and TrpR are reduced by 79%, 78%, 62% and 55%, respectively. The reductions for the remaining three proteins are 20–44%. As expected, the four proteins experiencing the stronger crowding effects are those with larger conformational changes between open and closed states (e.g., as measured by the change in radius of gyration). Larger proteins also tend to experience stronger crowding effects than smaller ones [e.g., comparing yPDI (480 residues) and TrpR (98 residues)]. The potentials of mean force along the open-closed reaction coordinate of apo and ligand-bound ODCase are altered by crowding, suggesting that transition rates are also affected. These quantitative results and qualitative trends will serve as valuable guides for expected crowding effects on protein conformation changes inside cells.
Author Summary
The biophysical properties of proteins inside cells can be expected to be quite different from those typically measured by in vitro experiments in dilute solutions. In particular, intracellular macromolecular crowding may significantly affect the equilibria and transition rates between different conformations of a protein, and hence its functions. What are the trends and magnitudes of such crowding effects? We address this question here by applying a recently developed approach for modeling crowding. Seven proteins, each with structures for both an open state and a closed state, are studied. Crowding exerts significant effects on the open-closed equilibria of four proteins and more modest effects on the remaining three. Potentials of mean force along the open-closed reaction coordinate, and hence transition rates, are similarly affected. The extent of conformational changes is the main determinant for the magnitudes of crowding effects, but the protein size also plays an important role. The effects of crowding become stronger as the protein size increases. Conformational transitions of the ribosome, an extremely large complex, during translation are predicted to experience particularly strong effects of intracellular crowding. We conclude that deduction of intracellular behaviors from in vitro experiments requires explicit consideration of crowding effects.
doi:10.1371/journal.pcbi.1000833
PMCID: PMC2895631  PMID: 20617196
23.  Crowding Effects on the Mechanical Stability and Unfolding Pathways of Ubiquitin 
The interior of cells is crowded thus making it important to assess the effects of macromolecules on the folding of proteins. Using the Self-Organized Polymer (SOP) model, which is a coarse-grained representation of polypeptide chains, we probe the mechanical stability of Ubiquitin (Ub) monomers and trimers ((Ub)3) in the presence of monodisperse spherical crowding agents. Crowding increases the volume fraction (Φc)-dependent average force (⟨fu(Φc)⟩), relative to the value at Φc = 0, needed to unfold Ub and the polyprotein. For a given Φc, the values of ⟨fu(Φc)⟩ increase as the diameter (σc) of the crowding particles decreases. The average unfolding force ⟨fu(Φc)⟩ depends on the ratio DRg, where D≈σc(π6Φc)13 with Rg being the radius of gyration of Ub (or (Ub)3) in the unfolded state. Examination of the unfolding pathways shows that, relative to Φc = 0, crowding promotes reassociation of ruptured secondary structural elements. Both the nature of the unfolding pathways and ⟨fu(Φc)⟩ for (Ub)3 are altered in the presence of crowding particles with the effect being most dramatic for the subunit that unfolds last. We predict, based on SOP simulations and theoretical arguments, that 〈fu(Φc)〉~Φc13ν, where ν is the Flory exponent that describes the unfolded (random coil) state of the protein.
doi:10.1021/jp807755b
PMCID: PMC2701264  PMID: 19072020
Depletion Effect; Entropic Stabilization; Crowders; AFM; Loading Rate; SOP model
24.  Where soft matter meets living matter -- Protein structure, stability, and folding in the cell 
A protein is a biopolymer that self-assembles through the process of protein folding. A cell is a crowded space where the surrounding macromolecules of a protein can limit the number of ways of folding. These crowding macromolecules can also affect the shape and the size of a physically malleable, or “soft, squishy”, protein with regulatory purposes. In this review, we focus on the in silico approaches of coarse-grained molecular simulations that enable the investigation of protein folding in a cell-like environment. When these simulation results were compared with experimentally measured properties of a protein, such joint effort has yielded new ideas on the specific function of a protein in cells. We also highlight the recent developments of computer modeling and simulations that encompass the importance of the shape of a macromolecule, the interactions between macromolecules, and the hydrodynamic interactions on the kinetics and thermodynamics of a protein in a high concentration of protein solution and in cytoplasmic environments.
doi:10.1016/j.sbi.2013.02.005
PMCID: PMC3708662  PMID: 23474325
25.  Macromolecular Crowding Directs Extracellular Matrix Organization and Mesenchymal Stem Cell Behavior 
PLoS ONE  2012;7(5):e37904.
Microenvironments of biological cells are dominated in vivo by macromolecular crowding and resultant excluded volume effects. This feature is absent in dilute in vitro cell culture. Here, we induced macromolecular crowding in vitro by using synthetic macromolecular globules of nm-scale radius at physiological levels of fractional volume occupancy. We quantified the impact of induced crowding on the extracellular and intracellular protein organization of human mesenchymal stem cells (MSCs) via immunocytochemistry, atomic force microscopy (AFM), and AFM-enabled nanoindentation. Macromolecular crowding in extracellular culture media directly induced supramolecular assembly and alignment of extracellular matrix proteins deposited by cells, which in turn increased alignment of the intracellular actin cytoskeleton. The resulting cell-matrix reciprocity further affected adhesion, proliferation, and migration behavior of MSCs. Macromolecular crowding can thus aid the design of more physiologically relevant in vitro studies and devices for MSCs and other cells, by increasing the fidelity between materials synthesized by cells in vivo and in vitro.
doi:10.1371/journal.pone.0037904
PMCID: PMC3359376  PMID: 22649562

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