Models for excluded volume interaction between an unfolded protein and rigid macromolecular cosolutes: macromolecular crowding and protein stability revisited

Are current atomistic force fields accurate enough to study proteins in crowded environments?

The high concentration of macromolecules in the crowded cellular interior influences different thermodynamic and kinetic properties of proteins, including their structural stabilities, intermolecular binding affinities and enzymatic rates. Moreover, various structural biology methods, such as NMR or different spectroscopies, typically involve samples with relatively high protein concentration. Due to large sampling requirements, however, the accuracy of classical molecular dynamics (MD) simulations in capturing protein behavior at high concentration still remains largely untested. Here, we use explicit-solvent MD simulations and a total of 6.4 µs of simulated time to study wild-type (folded) and oxidatively damaged (unfolded) forms of villin headpiece at 6 mM and 9.2 mM protein concentration. We first perform an exhaustive set of simulations with multiple protein molecules in the simulation box using GROMOS 45a3 and 54a7 force fields together with different types of electrostatics treatment and solution ionic strengths. Surprisingly, the two villin headpiece variants exhibit similar aggregation behavior, despite the fact that their estimated aggregation propensities markedly differ. Importantly, regardless of the simulation protocol applied, wild-type villin headpiece consistently aggregates even under conditions at which it is experimentally known to be soluble. We demonstrate that aggregation is accompanied by a large decrease in the total potential energy, with not only hydrophobic, but also polar residues and backbone contributing substantially. The same effect is directly observed for two other major atomistic force fields (AMBER99SB-ILDN and CHARMM22-CMAP) as well as indirectly shown for additional two (AMBER94, OPLS-AAL), and is possibly due to a general overestimation of the potential energy of protein-protein interactions at the expense of water-water and water-protein interactions. Overall, our results suggest that current MD force fields may distort the picture of protein behavior in biologically relevant crowded environments.

Protein behavior is strongly affected by highly crowded and interaction-rich environments, i.e., typical conditions in both biologically relevant systems, such as the cellular interior, and solution-based structural experiments, including NMR and different spectroscopies. On the other hand, primarily because of limited computational power, molecular dynamics (MD) simulations, a premier high-resolution method for analyzing structure, dynamics and interactions of proteins, have been predominantly used to study individual proteins at infinite dilution. To fill this gap, we use MD simulations to study the behavior of wild-type (aggregation-resistant) and oxidatively damaged (aggregation-prone) forms of villin headpiece at high concentration, and reveal unexpected limitations and inaccuracies of modern-day MD force fields when it comes to modeling proteins at physiologically or experimentally relevant concentrations.

Quantification of excluded volume effects on the folding landscape of Pseudomonas aeruginosa apoazurin in vitro

Proteins fold and function inside cells that are crowded with macromolecules. Here, we address the role of the resulting excluded volume effects by in vitro spectroscopic studies of Pseudomonas aeruginosa apoazurin stability (thermal and chemical perturbations) and folding kinetics (chemical perturbation) as a function of increasing levels of crowding agents dextran (sizes 20, 40, and 70 kDa) and Ficoll 70. We find that excluded volume theory derived by Minton quantitatively captures the experimental effects when crowding agents are modeled as arrays of rods. This finding demonstrates that synthetic crowding agents are useful for studies of excluded volume effects. Moreover, thermal and chemical perturbations result in free energy effects by the presence of crowding agents that are identical, which shows that the unfolded state is energetically the same regardless of method of unfolding. This also underscores the two-state approximation for apoazurin's unfolding reaction and suggests that thermal and chemical unfolding experiments can be used in an interchangeable way. Finally, we observe increased folding speed and invariant unfolding speed for apoazurin in the presence of macromolecular crowding agents, a result that points to unfolded-state perturbations. Although the absolute magnitude of excluded volume effects on apoazurin is only on the order of 1-3 kJ/mol, differences of this scale may be biologically significant.

Single-molecule spectroscopy reveals polymer effects of disordered proteins in crowded environments

Intrinsically disordered proteins (IDPs) are involved in a wide range of regulatory processes in the cell. Owing to their flexibility, their conformations are expected to be particularly sensitive to the crowded cellular environment. Here we use single-molecule Förster resonance energy transfer to quantify the effect of crowding as mimicked by commonly used biocompatible polymers. We observe a compaction of IDPs not only with increasing concentration, but also with increasing size of the crowding agents, at variance with the predictions from scaled-particle theory, the prevalent paradigm in the field. However, the observed behavior can be explained quantitatively if the polymeric nature of both the IDPs and the crowding molecules is taken into account explicitly. Our results suggest that excluded volume interactions between overlapping biopolymers and the resulting criticality of the system can be essential contributions to the physics governing the crowded cellular milieu.

Denatured state structural property determines protein stabilization by macromolecular crowding: a thermodynamic and structural approach

Understanding of protein structure and stability gained to date has been acquired through investigations made under dilute conditions where total macromolecular concentration never surpasses 10 g l⁻¹. However, biological macromolecules are known to evolve and function under crowded intracellular environments that comprises of proteins, nucleic acids, ribosomes and carbohydrates etc. Crowded environment is known to result in altered biological properties including thermodynamic, structural and functional aspect of macromolecules as compared to the macromolecules present in our commonly used experimental dilute buffers (for example, Tris HCl or phosphate buffer). In this study, we have investigated the thermodynamic and structural consequences of synthetic crowding agent (Ficoll 70) on three different proteins (Ribonuclease-A, lysozyme and holo α-lactalbumin) at different pH values. We report here that the effect of crowding is protein dependent in terms of protein thermal stability and structure. We also observed that the structural characteristics of the denatured state determines if crowding will have an effect or not on the protein stability.

Force-induced unzipping transitions in an athermal crowded environment

Using theoretical arguments and extensive Monte Carlo (MC) simulations of a coarse-grained three-dimensional off-lattice model of a β-hairpin, we demonstrate that the equilibrium critical force, Fc, needed to unfold the biopolymer increases nonlinearly with increasing volume fraction occupied by the spherical macromolecular crowding agent. Both scaling arguments and MC simulations show that the critical force increases as Fc ≈ φc(α). The exponent α is linked to the Flory exponent relating the size of the unfolded state of the biopolymer and the number of amino acids. The predicted power law dependence is confirmed in simulations of the dependence of the isothermal extensibility and the fraction of native contacts on φc. We also show using MC simulations that Fc is linearly dependent on the average osmotic pressure (P) exerted by the crowding agents on the β-hairpin. The highly significant linear correlation coefficient of 0.99657 between Fc and P makes it straightforward to predict the dependence of the critical force on the density of crowders. Our predictions are amenable to experimental verification using laser optical tweezers.

Singular value decomposition of the radial distribution function for hard sphere and square well potentials

We compute the singular value decomposition of the radial distribution function g(r) for hard sphere, and square well solutions. We find that g(r) decomposes into a small set of basis vectors allowing for an extremely accurate representation at all interpolated densities and potential strengths. In addition, we find that the coefficient vectors describing the magnitude of each basis vector are well described by a low-order polynomial. We provide a program to calculate g(r) in this compact representation for the investigated parameter range.

Effects of Macromolecular Crowding on the Conformational Ensembles of Disordered Proteins

Due to their conformational malleability, intrinsically disordered proteins (IDPs) are particularly susceptible to influences of crowded cellular environments. Here we report a computational study of the effects of macromolecular crowding on the conformational ensemble of a coarse-grained IDP model, by using two approaches. In one, the IDP is simulated along with the crowders; in the other, crowder-free simulations are postprocessed to predict the conformational ensembles under crowding. We found significant decreases in the radius of gyration of the IDP under crowding, and suggest repulsive interactions with crowders as a common cause for chain compaction in a number of experimental studies. The postprocessing approach accurately reproduced the conformational ensembles of the IDP in the direct simulations here, and holds enormous potential for realistic modeling of IDPs under crowding, by permitting thorough conformation sampling for the proteins even when they and the crowders are both represented at the all-atom level.

The extracellular protein VlsE is destabilized inside cells

We use U2OS cells as in vivo "test tubes" to study how the same cytoplasmic environment has opposite effects on the stability of two different proteins. Protein folding stability and kinetics were compared by fast relaxation imaging, which combines a temperature jump with fluorescence microscopy of FRET (Förster resonance energy transfer)-labeled proteins. While the stability of the cytoplasmic enzyme PGK (phosphoglycerate kinase) increases in cells, the stability of the cell surface antigen VlsE, which presumably did not evolve for stability inside cells, decreases. VlsE folding also slows down more than PGK folding in cells, relative to their respective aqueous buffer kinetics. Our FRET measurements provide evidence that VlsE is more compact inside cells than in aqueous buffer. Two kinetically distinct protein populations exist inside cells, making a connection with previous in vitro crowding studies. In addition, we confirm previous studies showing that VlsE is stabilized by 150mg/mL of the carbohydrate crowder Ficoll, even though it is destabilized in the cytoplasm relative to aqueous buffer. We propose two mechanisms for the observed destabilization of VlsE in U2OS cells: long-range interactions competing with crowding or shape-dependent crowding favoring more compact states inside the cell over the elongated aqueous buffer native state.

Quinary protein structure and the consequences of crowding in living cells: leaving the test-tube behind

Although the importance of weak protein-protein interactions has been understood since the 1980s, scant attention has been paid to this "quinary structure". The transient nature of quinary structure facilitates dynamic sub-cellular organization through loose grouping of proteins with multiple binding partners. Despite our growing appreciation of the quinary structure paradigm in cell biology, we do not yet understand how the many forces inside the cell--the excluded volume effect, the "stickiness" of the cytoplasm, and hydrodynamic interactions--perturb the weakest functional protein interactions. We discuss the unresolved problem of how the forces in the cell modulate quinary structure, and to what extent the cell has evolved to exert control over the weakest biomolecular interactions. We conclude by highlighting the new experimental and computational tools coming on-line for in vivo studies, which are a critical next step if we are to understand quinary structure in its native environment.

Direct observation of protein unfolded state compaction in the presence of macromolecular crowding

Proteins fold and function in cellular environments that are crowded with other macromolecules. As a consequence of excluded volume effects, compact folded states of proteins should be indirectly stabilized due to destabilization of extended unfolded conformations. Here, we assess the role of excluded volume in terms of protein stability, structural dimensions and folding dynamics using a sugar-based crowding agent, dextran 20, and the small ribosomal protein S16 as a model system. To specifically address dimensions, we labeled the protein with BODIPY at two positions and measured Trp-BODIPY distances under different conditions. As expected, we found that dextran 20 (200 mg/ml) stabilized the variants against urea-induced unfolding. At conditions where the protein is unfolded, Förster resonance energy transfer measurements reveal that in the presence of dextran, the unfolded ensemble is more compact and there is residual structure left as probed by far-ultraviolet circular dichroism. In the presence of a crowding agent, folding rates are faster in the two-state regime, and at low denaturant concentrations, a kinetic intermediate is favored. Our study provides direct evidence for protein unfolded-state compaction in the presence of macromolecular crowding along with its energetic and kinetic consequences.

Folding free energy surfaces of three small proteins under crowding: validation of the postprocessing method by direct simulation

We have developed a 'postprocessing' method for modeling biochemical processes such as protein folding under crowded conditions (Qin and Zhou 2009 Biophys. J. 97 12-19). In contrast to the direct simulation approach, in which the protein undergoing folding is simulated along with crowders, the postprocessing method requires only the folding simulation without crowders. The influence of the crowders is then obtained by taking conformations from the crowder-free simulation and calculating the free energies of transferring to the crowders. This postprocessing yields the folding free energy surface of the protein under crowding. Here the postprocessing results for the folding of three small proteins under 'repulsive' crowding are validated by those obtained previously by the direct simulation approach (Mittal and Best 2010 Biophys. J. 98 315-20). This validation confirms the accuracy of the postprocessing approach and highlights its distinct advantages in modeling biochemical processes under cell-like crowded conditions, such as enabling an atomistic representation of the test proteins.

Entropic stabilization of the folded states of RNA due to macromolecular crowding

We review the effects of macromolecular crowding on the folding of RNA by considering the simplest scenario when excluded volume interactions between crowding particles and RNA dominate. Using human telomerase enzyme as an example, we discuss how crowding can alter the equilibrium between pseudoknot and hairpin states of the same RNA molecule-a key aspect of crowder-RNA interactions. We summarize data showing that the crowding effect is significant only if the size of the spherical crowding particle is smaller than the radius of gyration of the RNA in the absence of crowding particles. The implication for function of the wild type and mutants of human telomerase is outlined by using a relationship between enzyme activity and its conformational equilibrium. In addition, we discuss the interplay between macromolecular crowding and ionic strength of the RNA buffer. Finally, we briefly review recent experiments which illustrate the connection between excluded volume due to macromolecular crowding and the thermodynamics of RNA folding.

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 highlighted 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.

Preparation of an adipogenic hydrogel from subcutaneous adipose tissue

The ability to generate controlled amounts of adipose tissue would greatly ease the burden on hospitals for reconstructive surgery. We have previously shown that a tissue engineering chamber containing a vascular pedicle was capable of forming new fat; however, further refinements are required to enhance fat formation. The development and maintenance of engineered adipose tissue requires a suitable source of growth factors and a suitable scaffold. A hydrogel derived from adipose tissue may fulfil this need. Subcutaneous fat was processed into a thermosensitive hydrogel we refer to as adipose-derived matrix (ADM). Protein analysis revealed high levels of basement membrane proteins, collagens and detectable levels of growth factors. Adipose-derived stem cells exposed to this hydrogel differentiated into adipocytes with >90% efficiency and in vivo testing in rats showed significant signs of adipogenesis after 8 weeks. ADM's adipogenic properties combined with its simple gelation, relatively long shelf life and its tolerance to multiple freeze-thaw cycles, makes it a promising candidate for adipose engineering applications.

Effects of macromolecular crowding agents on protein folding in vitro and in silico

Proteins fold and function inside cells which are environments very different from that of dilute buffer solutions most often used in traditional experiments. The crowded milieu results in excluded-volume effects, increased bulk viscosity and amplified chances for inter-molecular interactions. These environmental factors have not been accounted for in most mechanistic studies of protein folding executed during the last decades. The question thus arises as to how these effects-present when polypeptides normally fold in vivo-modulate protein biophysics. To address excluded volume effects, we use synthetic macromolecular crowding agents, which take up significant volume but do not interact with proteins, in combination with strategically selected proteins and a range of equilibrium and time-resolved biophysical (spectroscopic and computational) methods. In this review, we describe key observations on macromolecular crowding effects on protein stability, folding and structure drawn from combined in vitro and in silico studies. As expected based on Minton's early predictions, many proteins (apoflavodoxin, VlsE, cytochrome c, and S16) became more thermodynamically stable (magnitude depends inversely on protein stability in buffer) and, unexpectedly, for apoflavodoxin and VlsE, the folded states changed both secondary structure content and, for VlsE, overall shape in the presence of macromolecular crowding. For apoflavodoxin and cytochrome c, which have complex kinetic folding mechanisms, excluded volume effects made the folding energy landscapes smoother (i.e., less misfolding and/or kinetic heterogeneity) than in buffer.

Simulation and Modeling of Crowding Effects on the Thermodynamic and Kinetic Properties of Proteins with Atomic Details

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.

Polymer crowders and protein crowders act similarly on protein folding stability

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.

Effect of molecular crowding on the temperature-pressure stability diagram of ribonuclease A

FT-IR spectroscopic and thermodynamic measurements were designed to explore the effect of a macromolecular crowder, dextran, on the temperature and pressure-dependent phase diagram of the protein Ribonuclease A (RNase A), and we compare the experimental data with approximate theoretical predictions based on configuration entropy. Exploring the crowding effect on the pressure-induced unfolding of proteins provides insight in protein stability and folding under cell-like dense conditions, since pressure is a fundamental thermodynamic variable linked to molecular volume. Moreover, these studies are of relevance for understanding protein stability in deep-sea organisms, which have to cope with pressures in the kbar range. We found that not only temperature-induced equilibrium unfolding of RNase A, but also unfolding induced by pressure is markedly prohibited in the crowded dextran solutions, suggesting that crowded environments such as those found intracellularly, will also oppress high-pressure protein unfolding. The FT-IR spectroscopic measurements revealed a marked increase in unfolding pressure of 2 kbar in the presence of 30 wt % dextran. Whereas the structural changes upon thermal unfolding of the protein are not significantly influenced in the presence of the crowding agent, through stabilization by dextran the pressure-unfolded state of the protein retains more ordered secondary structure elements, which seems to be a manifestation of the entropic destabilization of the unfolded state by crowding.

Effects of macromolecular crowding on burst phase kinetics of cytochrome c folding

Excluded volume and viscosity effects of crowding agents that mimic crowded conditions in vivo on "classical" burst phase folding kinetics of cytochrome c are assessed in vitro. Upon electron transfer-triggered folding of reduced cytochrome c, far-UV time-resolved circular dichroism (TRCD) is used to monitor folding under different conditions. Earlier work has shown that folding of reduced cytochrome c from the guanidinium hydrochloride-induced unfolded ensemble in dilute phosphate buffer involves kinetic partitioning: one fraction of molecules folds rapidly, on a time scale identical to that of reduction, while the remaining population folds more slowly. In the presence of 220 mg/mL dextran 70, a synthetic macromolecular crowding agent that occupies space but does not interact with proteins, the population of the fast folding step for cytochrome c is greatly reduced. Increasing the viscosity with sucrose to the same microviscosity exhibited by the dextran solution showed no significant decrease in the amplitude of the fast-folding phase of cytochrome c. Experiments show that the unfolded-state heme ligation remains bis-His in the presence of dextran 70, but coarse-grained simulations suggest that the unfolded-state ensemble becomes more compact in the presence of crowders. We conclude that excluded volume effects alter unfolded cytochrome c such that access to fast-folding conformations is reduced.

Principles and applications of steric exclusion chromatography

We introduce a chromatography method for purification of large proteins and viruses that works by capturing them at a non-reactive hydrophilic surface by their mutual steric exclusion of polyethylene glycol (PEG). No direct chemical interaction between the surface and the target species is required. We refer to the technique as steric exclusion chromatography. Hydroxyl-substituted polymethacrylate monoliths provide a hydrophilic surface and support convective mass transport that is unaffected by the viscosity of the PEG. Elution is achieved by reducing PEG concentration. Selectivity correlates with molecular size, with larger species retained more strongly than smaller species. Retention increases with PEG size and concentration. Salts weaken retention in proportion to their concentration and Hofmeister ranking. Retention is enhanced near the isoelectric point of the target species. Virus binding capacity was measured at 9.9×10(12) plaque forming units per mL of monolith. 99.8% of host cell proteins and 93% of DNA were eliminated. Mass recovery exceeded 90%. IgM capacity was greater than 60 mg/mL. 95% of host cell proteins were eliminated from IgM produced in protein-free media, and mass recovery was up to 90%. Bioactivity was fully conserved by both viruses and antibodies. Process time ranged from less than 30 min to 2 h depending on the product concentration in the feed stream.

Myoglobin unfolding in crowding and confinement

Crowding and confinement have often been used synonymously with regard to their effect on the structure and dynamics of proteins. In this work, we have investigated the unfolding of the protein myoglobin (Mb) entrapped in the confinement of the water pool of AOT reverse micelles and in the presence of some commonly used macromolecular crowding agents (Ficoll 70, Dextran 70, and Dextran 40). Our results reveal that confinement effects can be quite destabilizing in nature for Mb with the extent of distortion depending on a host of factors apart from the size of the confining cage. Effects of the crowding agents on myoglobin also show a deviation from the general notion that synthetic macromolecular crowding agents are always stabilizing in nature. Ficoll 70 was observed to be particularly destabilizing in its influence on Mb unfolding. Moreover, tryptophan lifetime studies point to the fact that the Trp-heme distance in Mb might not always be a reliable probe of the secondary structural dissolution of the protein.

Influence of the shape of crowding particles on the structural transitions in a polymer

We investigate the structural transitions in a polymer induced by spherical and nonspherical crowding particles over a wide range of conditions. The polymer conformations are specified by the radius of gyration and the quality of the solvent in the absence of crowding particles. In the presence of crowding particles, the structures are altered by the volume fraction, size, shape, and polydispersity of the crowders. We show that crowding induces an array of structural changes, ranging from helix, helical hairpin (HH), and multiple helix bundles (HBs), depending on the interplay of multiple length and energy scales including the solvent quality, length of the polymer, temperature, and the characteristics of the crowding agents. In nearly good solvents, the polymer undergoes coil-helix transition in accord with the predictions based on the entropic stabilization mechanism. Higher-order (HH and HB) structures are obtained in poor or moderately poor solvents. In a binary mixture of spherical crowders, the effect of the two components is largely additive with the polymer undergoing greater compaction at higher volume fraction. In contrast to spherical crowders, spherocylinder-like crowders have a dramatically different effect on the diagram of states of the polymer. In the presence of spherocylinders, the polymer prefers to form a nearly ideal helix, especially at low temperatures and high aspect ratios of the crowders, at volume fractions that are not large enough for nematic order. Surprisingly, there is a complete absence of HH and HB in the range of conditions explored here. The dominant formation of spherocylinder-induced helix formation is due to the tendency of the spherocylinders and the polymer to align along the director formed by an increase in nematic order only in the vicinity of the polymer. Our study, which has produced several testable predictions, shows that only by probing the effects of crowding on a polymer (or a protein and RNA) over a wide range of conditions can the diagram of states be quantitatively described.

A physics-based approach of coarse-graining the cytoplasm of Escherichia coli (CGCYTO)

We have investigated protein stability in an environment of Escherichia coli cytoplasm using coarse-grained computer simulations. To coarse-grain a small slide of E. coli's cytoplasm consisting of over 16 million atoms, we have developed a self-assembled clustering algorithm (CGCYTO). CGCYTO uses the shape parameter and asphericity as well as a parameter λ (ranging from 0 to 1) that measures the covolume of a test protein and a macromolecule against the covolume of a test protein and a sphere of equal volume as that of a macromolecule for the criteria of coarse-graining a cytoplasmic model. A cutoff λ(c) = 0.8 was chosen based on the size of a test protein and computational resources and it determined the resolution of a coarse-grained cytoplasm. We compared the results from a polydisperse cytoplasmic model (PD model) produced by CGCYTO with two other coarse-grained hard-sphere cytoplasmic models: 1), F70 model, macromolecules in the cytoplasm were modeled by homogeneous hard spheres with a radius of 55 Å, the size of Ficoll70 and 2), HS model, each macromolecule in the cytoplasm was modeled by a hard sphere of equal volume. It was found that the folding temperature T(f) of a test protein (apoazurin) in a PD model is ~5° greater than that in a F70 model. In addition, the deviation of T(f) in a PD model is twice as much as that in a HS model when an apoazurin is randomly placed at different voids formed by particle fluctuations in PD models.

Conformational sampling of peptides in the presence of protein crowders from AA/CG-multiscale simulations

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 an 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.

Folding dynamics of Trp-cage in the presence of chemical interference and macromolecular crowding. I

Proteins fold and function in the crowded environment of the cell's interior. In the recent years it has been well established that the so-called "macromolecular crowding" effect enhances the folding stability of proteins by destabilizing their unfolded states for selected proteins. On the other hand, chemical and thermal denaturation is often used in experiments as a tool to destabilize a protein by populating the unfolded states when probing its folding landscape and thermodynamic properties. However, little is known about the complicated effects of these synergistic perturbations acting on the kinetic properties of proteins, particularly when large structural fluctuations, such as protein folding, have been involved. In this study, we have first investigated the folding mechanism of Trp-cage dependent on urea concentration by coarse-grained molecular simulations where the impact of urea is implemented into an energy function of the side chain and/or backbone interactions derived from the all-atomistic molecular dynamics simulations with urea through a Boltzmann inversion method. In urea solution, the folding rates of a model miniprotein Trp-cage decrease and the folded state slightly swells due to a lack of contact formation between side chains at the terminal regions. In addition, the equilibrium m-values of Trp-cage from the computer simulations are in agreement with experimental measurements. We have further investigated the combined effects of urea denaturation and macromolecular crowding on Trp-cage's folding mechanism where crowding agents are modeled as hard-spheres. The enhancement of folding rates of Trp-cage is most pronounced by macromolecular crowding effect when the extended conformations of Trp-cast dominate at high urea concentration. Our study makes quantitatively testable predictions on protein folding dynamics in a complex environment involving both chemical denaturation and macromolecular crowding effects.

Crowding effects on the small, fast-folding protein lambda6-85

The microsecond folder lambda6-85 is a small (9.2 kDa = 9200 amu) five helix bundle protein. We investigated the stability of lambda6-85 in two different low-fluorescence crowding matrices: the large 70 kDa carbohydrate Ficoll 70, and the small 14 kDa thermophilic protein SubL. The same thermal stability of secondary structure was measured by circular dichroism in aqueous buffer, and at a crowding fraction phi = 15 +/- 1% of Ficoll 70. Tryptophan fluorescence detection (probing a tertiary contact) yielded the same thermal stability in Ficoll, but 4 degrees C lower in aqueous buffer. Temperature-jump kinetics revealed that the relaxation rate, corrected for bulk viscosity, was very similar in Ficoll and in aqueous buffer. Thus viscosity, hydrodynamics and crowding seem to compensate one another. However, a new fast phase was observed in Ficoll, attributed to crowding-induced downhill folding. We also measured the stability of lambda6-85 in phi = 14 +/- 1% SubL, which acts as a smaller more rigid crowder. Significantly greater stabilization (7 to 13 degrees C depending on probe) was observed than in the Ficoll matrix. The results highlight the importance of crowding agent choice for studies of small, fast-folding proteins amenable to comparison with molecular dynamics simulations.

Conformational flexibility influences degree of hydration of nucleic acid hybrids

Four nucleic acid duplexes-DNA/RNA hybrid, RNA/DNA hybrid, RNA duplex, and DNA duplex-were studied under molecular crowding conditions of osmolytes. Destabilization of duplexes (ΔΔG°(25)) indicated that the ΔΔG°(25) values of hybrids were intermediate between those of DNA and RNA duplexes. In the presence of polyethylene glycol 200, the ΔΔG°(25) values were estimated to be +3.0, +3.5, +3.5, and +4.1 kcal mol(-1) for the DNA duplex, DNA/RNA hybrid, RNA/DNA hybrid, and RNA duplex, respectively. Differences in the number of water molecules taken up (-Δn(w)) upon duplex formations between 0 and 37 °C (Δ(-Δn(w))) were estimated to be 44.8 and 59.7 per duplex structure for the DNA/RNA and RNA/DNA hybrids, respectively. While the Δ(-Δn(w)) value for the DNA/RNA hybrid was intermediate between those of the DNA (26.1) and RNA (59.2) duplexes, the value for RNA/DNA hybrid was close to that of RNA duplex. These differences in the thermodynamic parameters and hydration are probably a consequence of the enhanced global flexibility of the RNA/DNA hybrid structure relative to the DNA/RNA hybrid structure observed in molecular dynamics simulations. This molecular crowding study provides information not only on hydration but also on the flexibility of the conformation of nucleic acid duplexes.

Entropic stabilization of proteins by TMAO

The osmolyte trimethylamine N-oxide (TMAO) accumulates in the cell in response to osmotic stress and increases the thermodynamic stability of folded proteins. To understand the mechanism of TMAO induced stabilization of folded protein states, we systematically investigated the action of TMAO on several model dipeptides (leucine, L(2), serine, S(2), glutamine, Q(2), lysine, K(2), and glycine, G(2)) in order to elucidate the effect of residue-specific TMAO interactions on small fragments of solvent-exposed conformations of the denatured states of proteins. We find that TMAO preferentially hydrogen bonds with the exposed dipeptide backbone but generally not with nonpolar or polar side chains. However, interactions with the positively charged Lys are substantially greater than with the backbone. The dipeptide G(2) is a useful model of the pure amide backbone; interacts with TMAO by forming a hydrogen bond between the amide nitrogen and the oxygen in TMAO. In contrast, TMAO is depleted from the protein backbone in the hexapeptide G(6), which shows that the length of the polypeptide chain is relevant in aqueous TMAO solutions. These simulations lead to the hypothesis that TMAO-induced stabilization of proteins and peptides is a consequence of depletion of the solute from the protein surface provided intramolecular interactions are more favorable than those between TMAO and the backbone. To test our hypothesis, we performed additional simulations of the action of TMAO on an intrinsically disordered Aβ(16-22) (KLVFFAE) monomer. In the absence of TMAO, Aβ(16-22) is a disordered random coil. However, in aqueous TMAO solution, Aβ(16-22) monomer samples compact conformations. A transition from random coil to α-helical secondary structure is observed at high TMAO concentrations. The coil to α-helix transition is highly cooperative especially considering the small number of residues in Aβ(16-22). Our work highlights the potential similarities between the action of TMAO on long polypeptide chains and entropic stabilization of proteins in a crowded environment due to excluded volume interactions. In this sense, the chemical chaperone TMAO is a nanocrowding particle.

Interactions of formulation excipients with proteins in solution and in the dried state

A variety of excipients are used to stabilize proteins, suppress protein aggregation, reduce surface adsorption, or to simply provide physiological osmolality. The stabilizers encompass a wide variety of molecules including sugars, salts, polymers, surfactants, and amino acids, in particular arginine. The effects of these excipients on protein stability in solution are mainly caused by their interaction with the protein and the container surface, and most importantly with water. Some excipients stabilize proteins in solution by direct binding, while others use a number of fundamentally different mechanisms that involve indirect interactions. In the dry state, any effects that the excipients confer to proteins through their interactions with water are irrelevant, as water is no longer present. Rather, the excipients stabilize proteins through direct binding and their effects on the physical properties of the dried powder. This review will describe a number of mechanisms by which the excipients interact with proteins in solution and with various interfaces, and their effects on the physical properties of the dried protein structure, and explain how the various interaction forces are related to their observed effects on protein stability.

Unified regression model of binding equilibria in crowded environments

Molecular crowding is a critical feature distinguishing intracellular environments from idealized solution-based environments and is essential to understanding numerous biochemical reactions, from protein folding to signal transduction. Many biochemical reactions are dramatically altered by crowding, yet it is extremely difficult to predict how crowding will quantitatively affect any particular reaction systems. We previously developed a novel stochastic off-lattice model to efficiently simulate binding reactions across wide parameter ranges in various crowded conditions. We now show that a polynomial regression model can incorporate several interrelated parameters influencing chemistry under crowded conditions. The unified model of binding equilibria accurately reproduces the results of particle simulations over a broad range of variation of six physical parameters that collectively yield a complicated, non-linear crowding effect. The work represents an important step toward the long-term goal of computationally tractable predictive models of reaction chemistry in the cellular environment.

The stability of intramolecular DNA G-quadruplexes compared with other macromolecules

DNA quadruplexes are often conceived as very stable structures. However, most of the free energy of stabilization derives from specific ion binding via inner sphere coordination of the GO6 of the guanine residues comprising the basic quartet. When compared with other nucleic acid structures such as DNA or RNA duplexes and hairpins, or proteins of the same number of atoms, metal-coordinated intramolecular quadruplexes are found to be of comparable or lower thermodynamic stability under similar solution conditions. Furthermore, intramolecular quadruplexes are actually less stable kinetically, than DNA duplexes or hairpins of the same size. Although the literature is incomplete, it is clear that polyelectrolyte ion effects, the influence of solvation and steric crowding on stability are qualitatively different between intramolecular quadruplexes and DNA duplexes. For example, decreasing water activity destabilizes DNA duplexes, whereas quadruplexes are stabilized. The variety of folded conformations accessible to a single sequence further implies strong sensitivity of the conformational ensemble to the solution conditions, compared with DNA duplexes or small single domain proteins. These considerations may have relevance to the conditions prevailing inside cell nuclei and therefore the structures that potentially might form in vivo.

The effect of macromolecular crowding, ionic strength and calcium binding on calmodulin dynamics

The flexibility in the structure of calmodulin (CaM) allows its binding to over 300 target proteins in the cell. To investigate the structure-function relationship of CaM, we combined methods of computer simulation and experiments based on circular dichroism (CD) to investigate the structural characteristics of CaM that influence its target recognition in crowded cell-like conditions. We developed a unique multiscale solution of charges computed from quantum chemistry, together with protein reconstruction, coarse-grained molecular simulations, and statistical physics, to represent the charge distribution in the transition from apoCaM to holoCaM upon calcium binding. Computationally, we found that increased levels of macromolecular crowding, in addition to calcium binding and ionic strength typical of that found inside cells, can impact the conformation, helicity and the EF hand orientation of CaM. Because EF hand orientation impacts the affinity of calcium binding and the specificity of CaM's target selection, our results may provide unique insight into understanding the promiscuous behavior of calmodulin in target selection inside cells.

Proteins are workhorses for driving biological functions inside cells. Calmodulin (CaM) is a protein that can carry cellular signals by triggered conformational changes due to calcium binding that alters target binding. Interestingly, CaM is able to bind over 300 targets. One of the challenges in characterizing CaM's ability to bind multiple targets lies in that CaM is a flexible protein and its structure is easily modulated by the physicochemical changes in its surroundings, particularly inside a complex cellular milieu. In order to determine structure-function relationships of CaM, we employed a combined approach of experiments, computer simulations and statistical physics in the investigation of the effect of calcium-binding, salt concentration, and macromolecular crowding on CaM. The results revealed unique folding energy landscapes of CaM in the absence and presence of calcium ions and the structural implications of CaM are interpreted under cell-like conditions. Further, a large conformational change in CaM in response to environmental impacts, dictates the packing of local helices that may be critical to its function of target binding and recognition among vast target selections.

Protein disorder prevails under crowded conditions

Crowding caused by the high concentrations of macromolecules in the living cell changes chemical equilibria, thus promoting aggregation and folding reactions of proteins. The possible magnitude of this effect is particularly important with respect to the physiological structure of intrinsically disordered proteins (IDPs), which are devoid of well-defined three-dimensional structures in vitro. To probe this effect, we have studied the structural state of three IDPs, α-casein, MAP2c, and p21(Cip1), in the presence of the crowding agents Dextran and Ficoll 70 at concentrations up to 40%, and also the small-molecule osmolyte, trimethylamine N-oxide (TMAO), at concentrations up to 3.6 M. The structures of IDPs under highly diluted and crowded conditions were compared by a variety of techniques, fluorescence spectroscopy, acrylamide quenching, 1-anilino-8-naphthalenesulfonic acid (ANS) binding, fluorescence correlation spectroscopy (FCS), and far-UV and near-UV circular dichroism (CD) spectroscopy, which allow us to visualize various levels of structural organization within these proteins. We observed that crowding causes limited structural changes, which seem to reflect the functional requirements of these IDPs. α-Casein, a protein of nutrient function in milk, changes least under crowded conditions. On the other hand, MAP2c and, to a lesser degree, p21(Cip1), which carry out their functions by partner binding and accompanying partially induced folding, show signs of local structuring and also some global compaction upon crowded conditions, in particular in the presence of TMAO. The observations are compatible with the possible preformation of binding-competent conformations in these proteins. The magnitude of these changes, however, is far from that of the cooperative folding transitions elicited by crowding in denatured globular proteins; i.e., these IDPs do remain in a state of rapidly interconverting structural ensemble. Altogether, our results underline that structural disorder is the physiological state of these proteins.

Glycosaminoglycans promote fibril formation by amyloidogenic immunoglobulin light chains through a transient interaction

Amyloid formation occurs when a precursor protein misfolds and aggregates, forming a fibril nucleus that serves as a template for fibril growth. Glycosaminoglycans are highly charged polymers known to associate with tissue amyloid deposits that have been shown to accelerate amyloidogenesis in vitro. We studied two immunoglobulin light chain variable domains from light chain amyloidosis patients with 90% sequence identity, analyzing their fibril formation kinetics and binding properties with different glycosaminoglycan molecules. We find that the less amyloidogenic of the proteins shows a weak dependence on glycosaminoglycan size and charge, while the more amyloidogenic protein responds only minimally to changes in the glycosaminoglycan. These glycosaminoglycan effects on fibril formation do not depend on a stable interaction between the two species but still show characteristic traits of an interaction-dependent mechanism. We propose that transient, predominantly electrostatic interactions between glycosaminoglycans and the precursor proteins mediate the acceleration of fibril formation in vitro.