Protein folding by the effects of macromolecular crowding

Cell-free protein expression under macromolecular crowding conditions

Background

Cell-free protein expression (CFPE) comprised of in vitro transcription and translation is currently manipulated in relatively dilute solutions, in which the macromolecular crowding effects present in living cells are largely ignored. This may not only affect the efficiency of protein synthesis in vitro, but also limit our understanding of the functions and interactions of biomolecules involved in this fundamental biological process.

Methodology/Principal Findings

Using cell-free synthesis of Renilla luciferase in wheat germ extract as a model system, we investigated the CFPE under macromolecular crowding environments emulated with three different crowding agents: PEG-8000, Ficoll-70 and Ficoll-400, which vary in chemical properties and molecular size. We found that transcription was substantially enhanced in the macromolecular crowding solutions; up to 4-fold increase in the mRNA production was detected in the presence of 20% (w/v) of Ficoll-70. In contrast, translation was generally inhibited by the addition of each of the three crowding agents. This might be due to PEG-induced protein precipitation and non-specific binding of translation factors to Ficoll molecules. We further explored a two-stage CFPE in which transcription and translation was carried out under high then low macromolecular crowding conditions, respectively. It produced 2.2-fold higher protein yield than the coupled CFPE control. The macromolecular crowding effects on CFPE were subsequently confirmed by cell-free synthesis of an approximately two-fold larger protein, Firefly luciferase, under macromolecular crowding environments.

Conclusions/Significance

Three macromolecular crowding agents used in this research had opposite effects on transcription and translation. The results of this study should aid researchers in their choice of macromolecular crowding agents and shows that two-stage CFPE is more efficient than coupled CFPE.

MACROMOLECULAR CROWDING IN BIOLOGICAL SYSTEMS: DYNAMIC LIGHT SCATTERING (DLS) TO QUANTIFY THE EXCLUDED VOLUME EFFECT (EVE)

Macromolecules crowd defined spaces, thereby excluding other like-sized molecules from the volume they occupy. These excluded-volume effect(s) (EVE) are well characterized for intracellular and partially for extracellular compartments such as blood plasma. We showed that EVE in fibroblast culture leads to faster enzymatic procollagen conversion and matrix deposition. Apparently, EVE can be applied to emulate in vivo conditions in an in vitro setting. Thus, we attempted to quantitatively capture the crowding potential of various macromolecules using dynamic light scattering under physiological conditions. We found that charged macromolecules like dextran sulfate (negative, 500 kDa) have a hydrodynamic radii of 46.4 ± 0.3 nm i.e. ~4 fold larger than that of neutral macromolecules like Ficoll (neutral, 400 kDa) and thus show greater EVE potential. At biologically effective concentrations viscosity was not increased. Unexpectedly, we observed a dramatic drop of hydrodynamic radii of all macromolecules tested above a threshold concentration. This suggested a hyper-crowding state in which the crowders compacted themselves mutually. We will use this hyper-crowding threshold to determine retrogradely rules that allow to predict the conditions for optimum crowding effects (such as the half-hyper-crowding concentration) in biological systems. We propose Dynamic Light Scattering (DLS) as a potential tool to estimate EVE in biotechnical applications.

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.

Monitoring the glycosylation status of proteins using Raman spectroscopy

Protein-based biopharmaceuticals are becoming increasingly widely used as therapeutic agents, and the characterization of these biopharmaceuticals poses a significant analytical challenge. In particular, monitoring posttranslational modifications (PTMs), such as glycosylation, is an important aspect of this characterization because these glycans can strongly affect the stability, immunogenicity, and pharmacokinetics of these biotherapeutic drugs. Raman spectroscopy is a powerful tool, with many emerging applications in the bioprocessing arena. Although the technique has a relatively rich history in protein science, only recently has Raman spectroscopy been investigated for assessing posttranslational modifications, including phosphorylation, acetylation, trimethylation, and ubiquitination. In this investigation, we develop for the first time Raman spectroscopy combined with multivariate data analyses, including principal components analysis and partial least-squares regression, for the determination of the glycosylation status of proteins and quantifying the relative concentrations of the native ribonuclease (RNase) A protein and RNase B glycoprotein within mixtures.

Modulation of functionally significant conformational equilibria in adenylate kinase by high concentrations of trimethylamine oxide attributed to volume exclusion

The effect of an inert small molecule osmolyte, trimethyl amine N-oxide (TMAO), upon the conformational equilibria of Escherichia coli adenylate kinase was studied using time-resolved FRET. The relative populations of open and closed clefts between the LID and the CORE domains were measured as functions of the concentrations of the substrate ATP over the concentration range 0-18 mM and TMAO over the concentration range 0-4 M. A model was constructed according to which the enzyme exists in equilibrium among four conformational states, corresponding to combinations of open and closed conformations of the LID-CORE and AMP-CORE clefts. ATP is assumed to bind only to those conformations with the closed LID-CORE cleft, and TMAO is assumed to be differentially excluded as a hard spherical particle from each of the four conformations in accordance with calculations based upon x-ray crystallographic structures. This model was found to describe quantitatively the dependence of the fraction of the closed LID-CORE cleft upon the concentrations of both ATP and TMAO over the entire range of concentrations with just five undetermined parameters.

Applying macromolecular crowding to enhance extracellular matrix deposition and its remodeling in vitro for tissue engineering and cell-based therapies

With the advent of multicellular organisms, the exterior of the cells evolved dramatically from highly aqueous surroundings into an extracellular matrix and space crowded with macromolecules. Cell-based therapies require removal of cells from their crowded physiological context and propagating them in dilute culture medium to attain therapeutically relevant numbers whilst preserving their phenotype. However, bereft of their microenvironment, cells under perform and lose functionality. Major efforts currently aim to modify cell culture surfaces and build three dimensional scaffolds to improve this situation. We discuss here alternative strategies that enable cells to re-create their own microenvironment in vitro, using carbohydrate-based macromolecules as culture media additives that create an excluded volume effect at defined fraction volume occupancies. This biophysical approach dramatically enhances extracellular matrix deposition by differentiated cells and stem cells, and boosts progenitor cell differentiation and proliferation. We begin to understand how well cells really can perform ex vivo if given the chance.

Power-law dependence of the melting temperature of ubiquitin on the volume fraction of macromolecular crowders

The dependence of the melting temperature increase (ΔT(m)) of the protein ubiquitin on the volume fraction (ϕ) of several commonly used macromolecular crowding agents (dextran 6, 40, and 70 and ficoll 70) was quantitatively examined and compared to a recently developed theoretical crowding model, i.e., ΔT(m) ∼ (R(g)∕R(c))(α)φ(α∕3). We found that in the current case this model correctly predicts the power-law dependence of ΔT(m) on φ but significantly overestimates the role of the size (i.e., R(c)) of the crowding agent. In addition, we found that for ubiquitin the exponent α is in the range of 4.1-6.5, suggesting that the relation of α=3∕(3ν-1) is a better choice for estimating α based on the Flory coefficient (ν) of the polypeptide chain. Taken together these findings highlight the importance of improving our knowledge and theoretical treatment of the microcompartmentalization of the commonly used model crowding agents.

Molecular crowding stabilizes folded RNA structure by the excluded volume effect

Crowder molecules in solution alter the equilibrium between folded and unfolded states of biological macromolecules. It is therefore critical to account for the influence of these other molecules when describing the folding of RNA inside the cell. Small angle X-ray scattering experiments are reported on a 64 kDa bacterial group I ribozyme in the presence of polyethylene-glycol 1000 (PEG-1000), a molecular crowder with an average molecular weight of 1000 Da. In agreement with expected excluded volume effects, PEG favors more compact RNA structures. First, the transition from the unfolded to the folded (more compact) state occurs at lower MgCl(2) concentrations in PEG. Second, the radius of gyration of the unfolded RNA decreases from 76 to 64 A as the PEG concentration increases from 0 to 20% wt/vol. Changes to water and ion activities were measured experimentally, and theoretical models were used to evaluate the excluded volume. We conclude that the dominant influence of the PEG crowder on the folding process is the excluded volume effect.

Polymeric crowding agents improve passive biomacromolecule encapsulation in lipid vesicles

Large solutes such as high molecular weight proteins can be difficult to encapsulate in lipid vesicles. Passive trapping of these macromolecular solutes during vesicle formation typically results in concentrations inside the vesicles that are much lower than in the external solution. Here, we investigated the effect of macromolecular crowding on passive encapsulation of biological macromolecules with molecular weights ranging from 52 kDa to 660 kDa within both individual giant lipid vesicles (GVs, > 3 microm diameter) and populations of 200 nm diameter large unilamellar vesicles (LUVs). Fluorescently labeled biomacromolecules were encapsulated during vesicle formation in the presence or absence of three weight percent poly(ethylene glycol) (PEG; 8 kDa) or dextran 500 kDa, which served as crowding agents. Encapsulation efficiency of the labeled biomolecules was higher for the lower molecular weight solutes, with internal concentrations essentially equal to external concentrations for labeled biomacromolecules with hydrodynamic radii (r(h)) less than 10 nm. In contrast, internal concentrations were reduced markedly for larger solutes with r(h) > or = 10 nm. Addition of PEG or dextran during vesicle formation improved encapsulation of these larger proteins up to the same levels as observed for the smaller proteins, such that internal and external concentrations were equal. This observation is consistent with PEG and dextran acting as volume excluders, reducing the hydrodynamic radius of the biomacromolecules and increasing their encapsulation. This work demonstrates a simple and general route to improved encapsulation of otherwise poorly encapsulated macromolecular solutes in both GV and LUVs up to their concentration in the solution present during vesicle formation.

A didactic model of macromolecular crowding effects on protein folding

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.

Compression of random coils due to macromolecular crowding: scaling effects

The addition of a macromolecular crowding agent to a dilute solution of polymer exerts a compressive force that tends to reduce the size of the chain. We study here the effect of changing the size ratio between the random coil and the crowding agent. The compression occurs at lower crowding agent concentration, Φ when polymer molecular weight increases. The Flory exponent ν(Φ) decreases from ν(0)≃0.48 in water down to 0.3 with macromolecular crowding. The effective polymer-polymer interactions change from repulsive to strongly attractive inducing aggregation of the chains. This effect changes drastically for larger polymer sizes, being much more pronounced at high molecular weights.

Microcompartmentation in artificial cells: pH-induced conformational changes alter protein localization

We report artificial cells in which protein localization in a primitive synthetic model for the cytoplasm is controlled by pH. Our model cells are giant lipid vesicles (GVs, ca. 5-30 microm diameter) with two coexisting aqueous compartments generated by phase separation of an encapsulated poly(ethylene glycol) (PEG) and dextran solution. Proteins are localized to a microcompartment by partitioning between the phases. We quantified the local concentration of fluorescently labeled human serum albumin (HSA) via confocal fluorescence microscopy. At pH 6.5, the labeled HSA was more concentrated in the dextran-rich phase, but at partially/fully denaturing pH (4.1 or 12) it was localized in the PEG-rich phase. This partitioning behavior is consistent with a more expanded, hydrophobic conformation at low and high pH. Labeled HSA could be relocalized from the PEG-rich into the dextran-rich phase domain by increasing the pH from 4.1 to 6.5 to renature the protein. This approach to controlling protein localization does not require extensive reorganization of the vesicle interior; coexisting PEG-rich and dextran-rich compartments are maintained throughout the experiments. It is also quite general; we demonstrated that several other proteins varying in size and isoelectric point also relocalized within compartmentalized artificial cells in response to external pH change. This work presents stimulus-responsive protein relocalization between compartments in an artificial cell; such experimental models can provide a framework for investigating the consequences of protein localization in cell biology.

Macromolecular crowding converts the human recombinant PrPC to the soluble neurotoxic beta-oligomers

Prion diseases are fatal neurodegenerative disorders and are linked with the conversion of the cellular isoform of the prion protein (PrP(C)) into the abnormal beta-sheet-rich isoform. It is widely accepted that the soluble oligomers of beta-PrP are neurotoxic and that they are more pathologically significant. To unravel the molecular mechanism under the conversion process, it is critical to identify the factors that can promote the conversion from PrP(C) to the beta-oligomers. By recording circular dichroism spectra and performing a size-exclusion HPLC assay, we found that the conformation of the recombinant human prion protein (rPrP(C)) was converted from an alpha-helical conformation into beta-sheet oligomers under a macromolecular crowding condition. The soluble beta-oligomers of rPrP were resistant to proteinase K digestion and could bind to the dyes thioflavin T and 8-anilino-1-naphthalene sulfonate. Furthermore, by the 3-(4, 5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium assay, we showed that the soluble beta-oligomers were neurotoxic. These results suggest that macromolecular crowding, which has not been considered before, is a key intracellular factor in the formation of soluble neurotoxic beta-oligomers in prion diseases.

Parameter effects on binding chemistry in crowded media using a two-dimensional stochastic off-lattice model

The intracellular environment imposes a variety of constraints on biochemical reaction systems that can substantially change reaction rates and equilibria relative to an ideal solution-based environment. One of the most notable features of the intracellular environment is its dense macromolecular crowding, which, among many other effects, tends to strongly enhance binding and assembly reactions. Despite extensive study of biochemistry in crowded media, it remains extremely difficult to predict how crowding will quantitatively affect any given reaction system due to the dependence of the crowding effect on numerous assumptions about the reactants and crowding agents involved. We previously developed a two dimensional stochastic off-lattice model of binding reactions based on the Green's function reaction dynamics method in order to create a versatile simulation environment in which one can explore interactions among many parameters of a crowded assembly system. In the present work, we examine interactions among several critical parameters for a model dimerization system: the total concentration of reactants and inert particles, the binding probability upon a collision between two reactant monomers, the mean time of dissociation reactions, and the diffusion coefficient of the system. Applying regression models to equilibrium constants across parameter ranges shows that the effect of the total concentration is approximately captured by a low-order nonlinear polynomial model, while the other three parameter effects are each accurately captured by a linear model. Furthermore, validation on tests with multi-parameter variations reveals that the effects of these parameters are separable from one another over a broad range of variation in all four parameters. The simulation work suggests that predictive models of crowding effects can accommodate a wider variety of parameter variations than prior theoretical models have so far achieved.

Effect of macromolecular crowding on protein folding dynamics at the secondary structure level

Macromolecular crowding is one of the key characteristics of the cellular environment and is therefore intimately coupled to the process of protein folding in vivo. While previous studies have provided invaluable insight into the effect of crowding on the stability and folding rate of protein tertiary structures, very little is known about how crowding affects protein folding dynamics at the secondary structure level. In this study, we examined the thermal stability and folding-unfolding kinetics of three small folding motifs (i.e., a 34-residue alpha-helix, a 34-residue cross-linked helix-turn-helix, and a 16-residue beta-hairpin) in the presence of two commonly used crowding agents, Dextran 70 (200 g/L) and Ficoll 70 (200 g/L). We found that these polymers do not induce any appreciable changes in the folding kinetics of the two helical peptides, which is somewhat surprising as the helix-coil transition kinetics have been shown to depend on viscosity. Also to our surprise and in contrast to what has been observed for larger proteins, we found that crowding leads to an appreciable decrease in the folding rate of the shortest beta-hairpin peptide, indicating that besides the excluded volume effect, other factors also need to be considered when evaluating the net effect of crowding on protein folding kinetics. A model considering both the static and the dynamic effects arising from the presence of the crowding agent is proposed to rationalize these results.

Modulation of calmodulin plasticity by the effect of macromolecular crowding

In vitro biochemical reactions are most often studied in dilute solution, a poor mimic of the intracellular space of eukaryotic cells, which are crowded with mobile and immobile macromolecules. Such crowded conditions exert volume exclusion and other entropic forces that have the potential to impact chemical equilibria and reaction rates. In this article, we used the well-characterized and ubiquitous molecule calmodulin (CaM) and a combination of theoretical and experimental approaches to address how crowding impacts CaM's conformational plasticity. CaM is a dumbbell-shaped molecule that contains four EF hands (two in the N-lobe and two in the C-lobe) that each could bind Ca(2+), leading to stabilization of certain substates that favor interactions with other target proteins. Using coarse-grained molecular simulations, we explored the distribution of CaM conformations in the presence of crowding agents. These predictions, in which crowding effects enhance the population of compact structures, were then confirmed in experimental measurements using fluorescence resonance energy transfer techniques of donor- and acceptor-labeled CaM under normal and crowded conditions. Using protein reconstruction methods, we further explored the folding-energy landscape and examined the structural characteristics of CaM at free-energy basins. We discovered that crowding stabilizes several different compact conformations, which reflects the inherent plasticity in CaM's structure. From these results, we suggest that the EF hands in the C-lobe are flexible and can be thought of as a switch, while those in the N-lobe are stiff, analogous to a rheostat. New combinatorial signaling properties may arise from the product of the differential plasticity of the two distinct lobes of CaM in the presence of crowding. We discuss the implications of these results for modulating CaM's ability to bind Ca(2+) and target proteins.

Compression of random coils due to macromolecular crowding

The conformation of a linear polymer chain is studied as a function of the concentration of a macromolecular crowding agent by neutron scattering. Excluded volume to random coil due to macromolecular crowding in cells is predicted to exert a compressive force that will tend to reduce its size. It is shown that when reducing free volume due to macromolecular crowding, we observe a compression of the polymer chain with a reduction in its radius of gyration of up to approximately 30% and that the effective chain-chain interactions are strongly modified.

Comparison of the different types of surfactants for the effect on activity and structure of soybean peroxidase

In the pH 2.6 and 5.2 systems, soybean peroxidase (SBP) (isoelectric point, pI 3.9) has positive and negative charge, respectively. In order to acquire detailed knowledge on the role played by electrostatics in the denaturation of proteins, a comparison of anionic surfactant sodium dodecyl sulfate (SDS), nonionic surfactant nonaethylene glycol monododecyl ether [C12H25O(CH2CH2O)9H] (AEO9), and cationic surfactant cetyltrimethylammonium bromide (CTAB) for the influences on the activity and structure of soybean peroxidase (SBP) was carried out by measuring the activity, far-UV circular dichrosm, fluorescence, and electronic absorption spectra of SBP in the pH 2.6 and 5.2 systems at 30 degrees C. In the pH 2.6 systems, the interaction of SDS with SBP results in an increase in the fluorescence intensity with a red shift of the emission maximum of the tryptophan fluorescence and a blue shift of the Soret band. In the meantime, the alpha-helix of SBP is unfolded and the activity of SBP is lost irreversibly. In pH 5.2 systems, the fluorescence spectra features of SBP are similar to those in pH 2.6 systems with increasing SDS concentration, but a red shift of Soret band as well as an alteration of the tertiary structure of SBP occurs, and the lost activity is recoverable. The electrostatic interactions between SBP and SDS play an important role in the denaturation of SBP. The effects of AEO9 and CTAB in pH 2.6 and 5.2 systems on the activity and spectral features of SBP are similar to that of SDS in pH 5.2 systems, but AEO9 is prone to unfold the beta-sheet of SBP in pH 2.6 systems. The electrostatic interactions of CTAB with SBP are not the primary elements for denaturation of SBP, which distinctly differ from those of SDS. These results can be useful with respect to wide applications of the surfactants in the separation and purification of proteins.

Macromolecular crowding improves polymer encapsulation within giant lipid vesicles

We report the effect of macromolecular crowding on encapsulation efficiency of fluorescently labeled poly(ethylene glycol) (PEG) and dextran polymers within individual giant lipid vesicles (GVs). Low concentrations of the fluorescently labeled polymers (82 nM to 186 pM) were mixed with varying concentrations of nonfluorescent polymers that served as crowding agents during vesicle formation by gentle hydration. Encapsulation efficiency of the fluorescently labeled polymers in individual GVs (EEind) was determined via confocal fluorescence microscopy. EEind for high molecular weight polymers (e.g., fluorescein isothiocyanate (FITC)-dextran 500 and 2000 kDa) increased substantially in the presence of several weight percent unlabeled PEG or dextran. For example, when 0.24 microM FITC dextran 500 kDa was encapsulated, addition of 3% PEG 8 kDa improved the mean concentration in the GVs from 0.14 microM (+/-50%) to 0.24 microM (+/-12%). Light scattering data indicate reduced hydrodynamic radii for polymers as a function of increasing polymer concentration, suggesting that the improvements in EEind result from polymer condensation due to macromolecular crowding. Polymeric cosolutes did not significantly impact EEind for lower molecular weight polymers (e.g., Alexa Fluor 488-PEG 20 kDa), which already encapsulated efficiently (EEind to approximately 1). However, for both the higher and lower molecular weight labeled polymers, cosolutes led to improved uniformity in EEind for vesicles within a batch. Methods for improving the value and homogeneity of EEind for polymeric solutes in lipid vesicles are important in a variety of applications, including the use of vesicles as microreactors and as vehicles for drug delivery.

Cytoplasmic protein mobility in osmotically stressed Escherichia coli

Facile diffusion of globular proteins within a cytoplasm that is dense with biopolymers is essential to normal cellular biochemical activity and growth. Remarkably, Escherichia coli grows in minimal medium over a wide range of external osmolalities (0.03 to 1.8 osmol). The mean cytoplasmic biopolymer volume fraction ((phi)) for such adapted cells ranges from 0.16 at 0.10 osmol to 0.36 at 1.45 osmol. For cells grown at 0.28 osmol, a similar phi range is obtained by plasmolysis (sudden osmotic upshift) using NaCl or sucrose as the external osmolyte, after which the only available cellular response is passive loss of cytoplasmic water. Here we measure the effective axial diffusion coefficient of green fluorescent protein (D(GFP)) in the cytoplasm of E. coli cells as a function of (phi) for both plasmolyzed and adapted cells. For plasmolyzed cells, the median D(GFP) (D(GFP)(m)) decreases by a factor of 70 as (phi) increases from 0.16 to 0.33. In sharp contrast, for adapted cells, D(GFP)(m) decreases only by a factor of 2.1 as (phi) increases from 0.16 to 0.36. Clearly, GFP diffusion is not determined by (phi) alone. By comparison with quantitative models, we show that the data cannot be explained by crowding theory. We suggest possible underlying causes of this surprising effect and further experiments that will help choose among competing hypotheses. Recovery of the ability of proteins to diffuse in the cytoplasm after plasmolysis may well be a key determinant of the time scale of the recovery of growth.

The effects of macromolecular crowding on the mechanical stability of protein molecules

Macromolecular crowding, a common phenomenon in the cellular environments, can significantly affect the thermodynamic and kinetic properties of proteins. A single-molecule method based on atomic force microscopy (AFM) was used to investigate the effects of macromolecular crowding on the forces required to unfold individual protein molecules. It was found that the mechanical stability of ubiquitin molecules was enhanced by macromolecular crowding from added dextran molecules. The average unfolding force increased from 210 pN in the absence of dextran to 234 pN in the presence of 300 g/L dextran at a pulling speed of 0.25 microm/sec. A theoretical model, accounting for the effects of macromolecular crowding on the native and transition states of the protein molecule by applying the scaled-particle theory, was used to quantitatively explain the crowding-induced increase in the unfolding force. The experimental results and interpretation presented could have wide implications for the many proteins that experience mechanical stresses and perform mechanical functions in the crowded environment of the cell.

Influence of macromolecular crowding on protein-protein association rates--a Brownian dynamics study

The high total concentration of macromolecules, often referred to as macromolecular crowding, is one of the characteristic features of living cells. Macromolecular crowding influences interactions between many types of macromolecules, with consequent effects on, among others, the rates of reactions occurring in the cell. Simulations to study the influence of crowding on macromolecular association rate were performed using a modified Brownian dynamics protocol. The calculated values of the time-dependent self-diffusion coefficients in different crowding conditions are in a very good agreement with those obtained by other authors. Simulations of the complex formation between the monoclonal antibody HyHEL-5 and its antigen hen egg lysozyme, both represented at atomic level detail, show that the calculated association rates strongly depend on the volume excluded by crowding. The rate obtained for the highest concentration of crowding particles is greater than twofold higher than the rate for proteins without crowding.

Crowded, cell-like environment induces shape changes in aspherical protein

How the crowded environment inside cells affects the structures of proteins with aspherical shapes is a vital question because many proteins and protein-protein complexes in vivo adopt anisotropic shapes. Here we address this question by combining computational and experimental studies of a football-shaped protein (i.e., Borrelia burgdorferi VlsE) in crowded, cell-like conditions. The results show that macromolecular crowding affects protein-folding dynamics as well as overall protein shape. In crowded milieus, distinct conformational changes in VlsE are accompanied by secondary structure alterations that lead to exposure of a hidden antigenic region. Our work demonstrates the malleability of "native" proteins and implies that crowding-induced shape changes may be important for protein function and malfunction in vivo.

Macromolecular crowding and confinement: biochemical, biophysical, and potential physiological consequences

Expected and observed effects of volume exclusion on the free energy of rigid and flexible macromolecules in crowded and confined systems, and consequent effects of crowding and confinement on macromolecular reaction rates and equilibria are summarized. Findings from relevant theoretical/simulation and experimental literature published from 2004 onward are reviewed. Additional complexity arising from the heterogeneity of local environments in biological media, and the presence of nonspecific interactions between macromolecules over and above steric repulsion, are discussed. Theoretical and experimental approaches to the characterization of crowding- and confinement-induced effects in systems approaching the complexity of living organisms are suggested.

Guiding protein aggregation with macromolecular crowding

Macromolecular crowding is expected to have a significant effect on protein aggregation. In the present study we analyzed the effect of macromolecular crowding on fibrillation of four proteins, bovine S-carboxymethyl-alpha-lactalbumin (a disordered form of the protein with reduced three out of four disulfide bridges), human insulin, bovine core histones, and human alpha-synuclein. These proteins are structurally different, varying from natively unfolded (alpha-synuclein and core histones) to folded proteins with rigid tertiary and quaternary structures (monomeric and hexameric forms of insulin). All these proteins are known to fibrillate in diluted solutions, however their aggregation mechanisms are very divers and some of them are able to form different aggregates in addition to fibrils. We studied how macromolecular crowding guides protein between different aggregation pathways by analyzing the effect of crowding agents on the aggregation patterns under the variety of conditions favoring different aggregated end products in diluted solutions.

Intrinsic disorder in scaffold proteins: getting more from less

Regulation, recognition and cell signaling involve the coordinated actions of many players. Signaling scaffolds, with their ability to bring together proteins belonging to common and/or interlinked pathways, play crucial roles in orchestrating numerous events by coordinating specific interactions among signaling proteins. This review examines the roles of intrinsic disorder (ID) in signaling scaffold protein function. Several well-characterized scaffold proteins with structurally and functionally characterized ID regions are used here to illustrate the importance of ID for scaffolding function. These examples include scaffolds that are mostly disordered, only partially disordered or those in which the ID resides in a scaffold partner. Specific scaffolds discussed include RNase, voltage-activated potassium channels, axin, BRCA1, GSK-3beta, p53, Ste5, titin, Fus3, BRCA1, MAP2, D-AKAP2 and AKAP250. Among the mechanisms discussed are: molecular recognition features, fly-casting, ease of encounter complex formation, structural isolation of partners, modulation of interactions between bound partners, masking of intramolecular interaction sites, maximized interaction surface per residue, toleration of high evolutionary rates, binding site overlap, allosteric modification, palindromic binding, reduced constraints for alternative splicing, efficient regulation via posttranslational modification, efficient regulation via rapid degradation, protection of normally solvent-exposed sites, enhancing the plasticity of interaction and molecular crowding. We conclude that ID can enhance scaffold function by a diverse array of mechanisms. In other words, scaffold proteins utilize several ID-facilitated mechanisms to enhance function, and by doing so, get more functionality from less structure.

Residue-level interrogation of macromolecular crowding effects on protein stability

Theory predicts that macromolecular crowding affects protein behavior, but experimental confirmation is scant. Herein, we report the first residue-level interrogation of the effects of macromolecular crowding on protein stability. We observe up to a 100-fold increase in the stability, as measured by the equilibrium constant for folding, for the globular protein chymotrypsin inhibitor 2 (CI2) in concentrations of the cosolute poly(vinylpyrrolidone) (PVP) that mimic the protein concentration in cells. We show that the increased stability is caused by the polymeric nature of PVP and that the degree of stabilization depends on both the location of the individual residue in the protein structure and the PVP concentration. Our data reinforce the assertion that macromolecular crowding stabilizes the protein by destabilizing its unfolded states.

DeltaF508 mutation increases conformational flexibility of CFTR protein

BACKGROUND

The deletion of Phe508 in the first nucleotide-binding domain of the CFTR protein is the most common mutation leading to cystic fibrosis.

METHODS

We present a Molecular Dynamics study on the native and mutated domains, based on their recently published crystal structure.

RESULTS

DeltaF508 CFTR has much more conformational freedom compared to the wild-type, and exposes its hydrophobic interior to the solution.

CONCLUSIONS

The increased flexibility might be the reason for the recognition of mutated CFTR by the housekeeping proteins and its premature degradation. This, in turn results in reduction of population of functional channels at the epithelial cell surface and disease phenotype.

Structure of the nucleocapsid-binding domain from the mumps virus polymerase; an example of protein folding induced by crystallization

The human pathogen mumps virus, like all paramyxoviruses, encodes a polymerase responsible for virally directed RNA synthesis. The template for the polymerase is the nucleocapsid, a filamentous protein-RNA complex harboring the viral genome. Interaction of the polymerase and the nucleocapsid is mediated by a small domain tethered to the end of the phosphoprotein (P), one of the polymerase subunits. We report the X-ray crystal structure of this region of mumps virus P (the nucleocapsid-binding domain, or NBD, amino acids 343-391). The mumps P NBD forms a compact bundle of three alpha-helices within the crystal, a fold apparently conserved across the Paramyxovirinae. In solution, however, the domain exists in the molten globule state. This is demonstrated through application of differential scanning calorimetry, circular dichroism spectroscopy, NMR spectroscopy, and dynamic light scattering. While the mumps P NBD is compact and has persistent secondary structure, it lacks a well-defined tertiary structure under normal solution conditions. It can, however, be induced to fold by addition of a stabilizing methylamine cosolute. The domain provides a rare example of a molten globule that can be crystallized. The structure that is stabilized in the crystal represents the fully folded state of the domain, which must be transiently realized during binding to the viral nucleocapsid. While the intermolecular forces that govern the polymerase-nucleocapsid interaction appear to be different in measles, mumps, and Sendai viruses, for each of these viruses, polymerase translocation involves the coupled binding and folding of protein domains. In all cases, we suggest that this will result in a weak-affinity protein complex with a short lifetime, which allows the polymerase to take rapid steps forward.

Molecular crowding enhances native structure and stability of alpha/beta protein flavodoxin

To investigate the consequences of macromolecular crowding on the behavior of a globular protein, we performed a combined experimental and computational study on the 148-residue single-domain alpha/beta protein, Desulfovibrio desulfuricans apoflavodoxin. In vitro thermal unfolding experiments, as well as assessment of native and denatured structures, were probed by using far-UV CD in the presence of various amounts of Ficoll 70, an inert spherical crowding agent. Ficoll 70 has a concentration-dependent effect on the thermal stability of apoflavodoxin (DeltaT(m) of 20 degrees C at 400 mg/ml; pH 7). As judged by CD, addition of Ficoll 70 causes an increase in the amount of secondary structure in the native-state ensemble (pH 7, 20 degrees C) but only minor effects on the denatured state. Theoretical calculations, based on an off-lattice model and hard-sphere particles, are in good agreement with the in vitro data. The simulations demonstrate that, in the presence of 25% volume occupancy of spheres, native flavodoxin is thermally stabilized, and the free energy landscape shifts to favor more compact structures in both native and denatured states. The difference contact map reveals that the native-state compaction originates in stronger interactions between the helices and the central beta-sheet, as well as by less fraying in the terminal helices. This study demonstrates that macromolecular crowding has structural effects on the folded ensemble of polypeptides.

Effect of High Concentration of Inert Cosolutes on the Refolding of an Enzyme

The kinetics of refolding of carbonic anhydrase II following transfer from a buffer containing 5 m guanidinium chloride to a buffer containing 0.5 m guanidinium chloride were studied by measuring the time-dependent recovery of enzymatic activity. Experiments were carried out in buffer containing concentrations of two "inert" cosolutes, sucrose and Ficoll 70, a sucrose polymer, at concentrations up to 150 g/liter. Data analysis indicates that both cosolutes significantly accelerate the rate of refolding to native or compact near-native conformations, but decrease the fraction of catalytically active enzyme recovered in the limit of long time. According to the simplest model that fits the data, both cosolutes accelerate a competing side reaction yielding inactive compact species. Acceleration of the side reaction by Ficoll is significantly greater than that of sucrose at equal w/v concentrations.

Procollagen triple helix assembly: an unconventional chaperone-assisted folding paradigm

Fibers composed of type I collagen triple helices form the organic scaffold of bone and many other tissues, yet the energetically preferred conformation of type I collagen at body temperature is a random coil. In fibers, the triple helix is stabilized by neighbors, but how does it fold? The observations reported here reveal surprising features that may represent a new paradigm for folding of marginally stable proteins. We find that human procollagen triple helix spontaneously folds into its native conformation at 30-34 degrees C but not at higher temperatures, even in an environment emulating Endoplasmic Reticulum (ER). ER-like molecular crowding by nonspecific proteins does not affect triple helix folding or aggregation of unfolded chains. Common ER chaperones may prevent aggregation and misfolding of procollagen C-propeptide in their traditional role of binding unfolded polypeptide chains. However, such binding only further destabilizes the triple helix. We argue that folding of the triple helix requires stabilization by preferential binding of chaperones to its folded, native conformation. Based on the triple helix folding temperature measured here and published binding constants, we deduce that HSP47 is likely to do just that. It takes over 20 HSP47 molecules to stabilize a single triple helix at body temperature. The required 50-200 microM concentration of free HSP47 is not unusual for heat-shock chaperones in ER, but it is 100 times higher than used in reported in vitro experiments, which did not reveal such stabilization.

Effects of osmolytes on hexokinase kinetics combined with macromolecular crowding

We investigated the effect of compatible and non-compatible osmolytes in combination with macromolecular crowding on the kinetics of yeast hexokinase. This was motivated by the fact that almost all studies concerning the osmolyte effects on enzyme activity have been performed in diluted buffer systems, which are far from the physiological conditions within cells, where the cytosol contains several hundred mg protein ml(-1). Four organic (glycerol, betaine, TMAO and urea) and one inorganic (NaCl) osmolyte were tested. It was concluded that the effect of compatible osmolytes (glycerol, betaine and TMAO) on V(max) and K(M) was practically equivalent in pure buffer and in 200-250 mg BSA ml(-1) supporting the view that these small organic osmolytes do minimal perturbance on enzyme function in physiological solutions. The effect of urea on enzyme kinetics was not independent of protein concentration, since the presence of 250 mg BSA ml(-1) partly compensated the perturbing effect of urea. Even though the organic osmolytes glycerol, betaine and TMAO are generally considered compatible with enzyme function, especially glycerol did have a significant effect on hexokinase kinetics, decreasing both k(cat), K(M) and k(cat)/K(M). The osmolytes decreased k(cat)/K(M) in the order: NaCl>Urea>TMAO/glycerol>betaine. For the organic osmolytes this order correlates with the degree of exclusion from protein-water interfaces. Thus, the stronger the exclusion the weaker the perturbing effects on k(cat)/K(M).

The influence of macromolecular crowding on HIV-1 protease internal dynamics

High macromolecular concentrations, or crowded conditions, have been shown to affect a wide variety of molecular processes, including diffusion, association and dissociation, and protein folding and stability. Here, we model the effect of macromolecular crowding on the internal dynamics of a protein, HIV-1 protease, using Brownian dynamics simulations. HIV-1 protease possesses a pair of flaps which are postulated to open in the early stages of its catalytic mechanism. Compared to low concentrations, close-packed concentrations of repulsive crowding agents are found to significantly reduce the fraction of time that the protease flaps are open. Macromolecular crowding is likely to have a major effect on in vivo enzyme activity, and may play an important regulatory role in the viral life cycle.

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 10k(B)T 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.

Destabilised mutants of ubiquitin gain equal stability in crowded solutions

This paper investigates the thermodynamic and kinetic response of WT* ubiquitin (F45W) and three mutants to high concentrations of glucose, sucrose and dextran under physiological temperature and pH. WT* ubiquitin was stabilised by the same amount when comparing each cosolute on a weight to volume ratio, with cosolute effects largely independent of denaturant concentration. The energy difference between the mutants and WT* ubiquitin also remained the same in high concentrations of cosolute. An apparent decrease in transition-state surface burial in the presence of the cosolutes was attributed to increased compaction of the denatured state, and not to the Hammond effect. Together, these results suggest higher thermodynamic stabilities and folding rates for proteins in vivo compared to in vitro, in addition to more compact denatured states. Because the effects of mutation are the same in dilute solution and crowded conditions used to mimic the cellular environment, there is validity in using measurements of mutant stabilities made in dilute solutions to inform on how the mutations may affect stability in vivo.

Albumin is a redox-active crowding agent that promotes oxidative folding of cysteine-rich peptides

Oxidative folding that occurs in a crowded cellular milieu is characterized by multifaceted interactions that occur among nascent polypeptides and resident components of the endoplasmic reticulum (ER) lumen. Macromolecular crowding has been considered an essential factor in the folding of polypeptides, but the excluded volume effect has not been evaluated for small, disulfide-rich peptides. In the research presented, we examined how macromolecular crowding agents, such as albumin, ovalbumin, and polysaccharides, influenced the kinetics and thermodynamics of forming disulfide bonds in four model peptides of varying molecular size from 13 residues (1.4 kDa) to 58-residues (6.5 kDa): conotoxins: GI, PVIIA, r11a, and bovine pancreatic trypsin inhibitor. Our results indicate that the excluded volume effect does not significantly alter the folding rates nor equilibria for these peptides. In stark contrast, folding reactions were dramatically accelerated, when protein-based crowding agents were present at concentrations lower than those predicted to provide the excluded volume effect. Submillimolar albumin alone was as effective as glutathione in promoting the oxidative folding of GI conotoxin at concentrations typically found in the ER. To the best of our knowledge, this is the first report and quantitative characterization of oxidative folding of peptides mediated by other than thioredoxin-based protein disulfide bonds. Our work raises a possibility that concurrent secretory and ER-resident proteins may influence the oxidative folding of small, cysteine-rich peptides not as crowding agents, but as redox-active factors.

Highly Concentrated Monoclonal Antibody Solutions: Direct Analysis of Physical Structure and Thermal Stability

Virtually all current analytical methods employed in the development of highly concentrated monoclonal antibody (MAb) formulations require dilution of the sample before acquiring data. Thus, there is an unmet need for methods to study proteins directly at high concentration, since extrapolation of stability indicating parameters obtained from dilute studies may not be representative of the high concentration solution. Only slight or no modifications of biophysical methods including fluorescence, UV absorbance, circular dichroism, and FTIR (ATR and transmittance) spectroscopies as well as differential scanning calorimetry (DSC) are described here that permit the direct study of immunoglobulins (and other proteins) at high concentrations. Although FTIR spectra show differences that are dependent upon sampling geometry, other spectroscopic data from two different recombinant MAbs suggests that structure of each antibody exists in a physically similar state in the concentration range of 0.1-190 mg/mL in 40 mM pH 6 citrate-phosphate buffer. Upon thermally stressing these proteins, spectroscopic techniques that probe tertiary structure demonstrate a decrease in the apparent thermal melting temperature of approximately 5-20 degrees C of both proteins with increasing concentration. In contrast, DSC thermograms and CD thermal experiments suggest a minor degree of stabilization (approximately 2 degrees C) for both antibodies although protein association could be responsible for these observations. Empirical phase diagrams produced from spectroscopic data also suggest (1) the existence of similar structural states at low temperatures independent of concentration and (2) a decrease in the temperature at which phase changes are observed with increasing concentration. The decrease in structural stability observed in these studies is probably the result of aggregation or self-association of the recombinant MAbs upon heating in crowded solutions and not due to a decrease in the intrinsic structural stability of the MAbs.

Methods of Changing Biopolymer Volume Fraction and Cytoplasmic Solute Concentrations for In Vivo Biophysical Studies

In vitro changes in polymer volume fraction (macromolecular crowding) and changes in solute or salt concentration typically have large effects on protein and nucleic acid processes (e.g., folding, binding, assembly, precipitation, crystallization). However, the large changes in these concentration variables, which occur in vivo as part of cellular responses to osmotic stress, appear to have much less dramatic effects on cellular biopolymer processes. Methods of changing intracellular concentrations by varying the extracellular osmolality or the concentration of a permeable solute or by titrating cells with an impermeable solute (plasmolysis) under conditions where an active response is suppressed are reviewed. The first in vivo biophysical studies of protein folding and protein diffusion performed as a function of these variables are also discussed.

Mixed Macromolecular Crowding Accelerates the Refolding of Rabbit Muscle Creatine Kinase: Implications for Protein Folding in Physiological Environments

The effects of four single macromolecular crowding agents, Ficoll 70, dextran 70, polyethylene glycol (PEG) 2000, and calf thymus DNA (CT DNA), and three mixed crowding agents containing both CT DNA and polysaccharide (or PEG 2000) on the refolding of guanidine hydrochloride-denatured rabbit muscle creatine kinase (MM-CK) have been examined by activity assay. When the total concentration of the mixed crowding agent is 100 g/l, in which the weight ratio of CT DNA to Ficoll 70 is 1:9, the refolding yield of MM-CK after refolding for 3 h under these conditions increases 23% compared with that in the presence of 10 g/l CT DNA, 18% compared with 100 g/l Ficoll 70, and 19% compared with that in the absence of crowding agents. A remarkable increase in the refolding yield of MM-CK by a mixed crowding agent containing CT DNA and dextran 70 (or PEG 2000) is also observed. Further folding kinetics analyses show that these three mixed crowding agents remarkably accelerate the refolding of MM-CK, compared with single crowding agents. Aggregation of MM-CK in the presence of any of the three mixed crowding agents is less serious than that in the presence of a single crowding agent at the same concentration but more serious than that in the absence of crowding agents. Both the refolding yield and the refolding rate of MM-CK in mixtures of these agents are increased relative to the individual agents by themselves, indicating that mixed macromolecular crowding agents are more favorable to MM-CK folding and can be used to reflect the physiological environment more accurately than single crowding agents.

How can biochemical reactions within cells differ from those in test tubes?

Nonspecific interactions between individual macro-molecules and their immediate surroundings ("background interactions") within a medium as heterogeneous and highly volume occupied as the interior of a living cell can greatly influence the equilibria and rates of reactions in which they participate. Background interactions may be either repulsive, leading to preferential size-and-shape-dependent exclusion from highly volume-occupied elements of volume, or attractive, leading to nonspecific associations or adsorption. Nonspecific interactions with different constituents of the cellular interior lead to three classes of phenomena: macromolecular crowding, confinement and adsorption. Theory and experiment have established that predominantly repulsive background interactions tend to enhance the rate and extent of macromolecular associations in solution, whereas predominantly attractive background interactions tend to enhance the tendency of macromolecules to associate on adsorbing surfaces. Greater than order-of-magnitude increases in association rate and equilibrium constants attributable to background interactions have been observed in simulated and actual intracellular environments.