RNA Hairpin Folding in the Crowded Cell

Precise secondary and tertiary structure formation is critically important for the cellular functionality of ribonucleic acids (RNAs). RNA folding studies were mainly conducted in vitro, without the possibility of validating these experiments inside cells. Here, we directly resolve the folding stability of a hairpin‐structured RNA inside live mammalian cells. We find that the stability inside the cell is comparable to that in dilute physiological buffer. On the contrary, the addition of in vitro artificial crowding agents, with the exception of high‐molecular‐weight PEG, leads to a destabilization of the hairpin structure through surface interactions and reduction in water activity. We further show that RNA stability is highly variable within cell populations as well as within subcellular regions of the cytosol and nucleus. We conclude that inside cells the RNA is subject to (localized) stabilizing and destabilizing effects that lead to an on average only marginal modulation compared to diluted buffer.     

Inactivation of Recombinant Human Brain-Type Creatine Kinase During Denaturation by Guanidine Hydrochloride in a Macromolecular Crowding System

In this study, we quantitatively examined the effects of the macromolecular crowding agents, polyethylene glycol 2000 (PEG 2000) and dextran 70, on guanidine hydrochloride (GdnHCl)-induced denaturation of recombinant human brain-type creatine kinase (rHBCK). Our results showed that both PEG 2000 and dextran 70 had a protective effect on the inactivation of rHBCK induced by 0.5 M GdnHCl at 25 °C. The presence of 200 g/L PEG 2000 resulted in the retention of 35.33 % of rHBCK activity after 4 h of inactivation, while no rHBCK activity was observed after denaturation in the absence of macromolecular crowding agents. The presence of PEG 2000 and dextran 70 at a concentration of 100 g/L could decelerate the k ₂ value of the slow track to 21 and 33 %, respectively, in comparison to values obtained in the absence of crowding agents. Interestingly, inactivation of rHBCK in the presence of 200 g/L PEG 2000 followed first-order monophasic kinetics, with an apparent rate constant of 8?×?10^?5?s^?1. The intrinsic fluorescence results showed that PEG 2000 was better than dextran 70 at stabilizing rHBCK conformation. In addition, the results of the phase diagram indicate that more intermediates may be captured when rHBCK is denatured in a macromolecular crowding system. Mixed crowding agents did not produce better results than single crowding agents, but the protective effects of PEG 2000 on the inactivation and unfolding of rHBCK tended to increase as the ratio of PEG 2000 increased in the mixed crowding agent solution. Though it is not clear which crowding agents more accurately simulated the intracellular environment, this study could lead to a better understanding of protein unfolding in the intracellular environment.     

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.     

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.     

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.     

Cost‐effective imprinting combining macromolecular crowding and a dummy template for the fast purification of punicalagin from pomegranate husk extract

The combination of molecular crowding and virtual imprinting was employed to develop a cost‐effective method to prepare molecularly imprinted polymers. By using linear polymer polystyrene as a macromolecular crowding agent, an imprinted polymer recognizable to punicalagin had been successfully synthesized with punicalin as the dummy template. The resulting punicalin‐imprinted polymer presented a remarkable selectivity to punicalagin with an imprinting factor of 3.17 even at extremely low consumption of the template (template/monomer ratio of 1:782). In contrast, the imprinted polymer synthesized without crowding agent, did not show any imprinting effect at so low template amount. The imprinted polymers made by combination of molecular crowding and virtual imprinting can be utilized for the fast separation of punicalagin from pomegranate husk extract after optimizing the protocol of solid‐phase extraction with the recovery of 85.3 ± 1.2%.     

Misfolding of amyloidogenic proteins at membrane surfaces: the impact of macromolecular crowding

The presence of inert macromolecular crowding agents mimics the situation in vivo where amyloidogenic proteins are released into an aqueous, congested intracellular environment. By using the amphiphatic Alzheimer Abeta-protein as the model system, the presence of a three-dimensional macromolecular crowding environment enhanced significantly its misfolding behavior if charged membrane surfaces as two-dimensional aggregation templates were present.     

Toward realistic modeling of dynamic processes in cell signaling: quantification of macromolecular crowding effects

One of the major factors distinguishing molecular processes in vivo from biochemical experiments in vitro is the effect of the environment produced by macromolecular crowding in the cell. To achieve a realistic modeling of processes in the living cell based on biochemical data, it becomes necessary, therefore, to consider such effects. We describe a protocol based on Brownian dynamics simulation to characterize and quantify the effect of various forms of crowding on diffusion and bimolecular association in a simple model of interacting hard spheres. We show that by combining the elastic collision method for hard spheres and the mean field approach for hydrodynamic interaction (HI), our simulations capture the correct dynamics of a monodisperse system. The contributions from excluded volume effect and HI to the crowding effect are thus quantified. The dependence of the results on size distribution of each component in the system is illustrated, and the approach is applied as well to the crowding effect on electrostatic-driven association in both neutral and charged environments; values for effective diffusion constants and association rates are obtained for the specific conditions. The results from our simulation approach can be used to improve the modeling of cell signaling processes without additional computational burdens.     

Enzyme Entrapped in Polymer‐Modified Nanopores: The Effects of Macromolecular Crowding and Surface Hydrophobicity

Macromolecular crowding is an ubiquitous phenomenon in living cells that significantly affects the function of enzymes in vivo. However, this effect has not been paid much attention in the research of the immobilization of enzymes onto mesoporous silica. Herein, we report the combined effects of macromolecular crowding and surface hydrophobicity on the performance of an immobilized enzyme by accommodating lipase molecules into a series of mesoporous silicas with different amounts of inert poly(methacrylate) (PMA) covalently anchored inside the nanopores. The incorporation of the PMA polymer into the nanopores of mesoporous silica enables the fabrication of a crowded and hydrophobic microenvironment for the immobilized enzyme and the variation in polymer content facilitates an adjustment of the degree of crowding and surface properties of this environment. Based on this system, the catalytic features of immobilized lipase were investigated as a function of polymer content in nanopores and the results indicated that the catalytic efficiency, thermostability, and reusability of immobilized lipase could all be improved by taking advantage of the macromolecular crowding effect and surface hydrophobicity. These findings provide insight into the possible functions of the macromolecular crowding effect, which should be considered and integrated into the fabrication of suitable mesoporous silicas to improve enzyme immobilization.     

Kinetic Insights into the Elongation Reaction of Actin Filaments as a Function of Temperature,Pressure, and Macromolecular Crowding

Actin polymerization is an essential process in eukaryotic cells that provides a driving force for motility and mechanical resistance for cell shape. By using preformed gelsolin–actin nuclei and applying stopped‐flow methodology, we quantitatively studied the elongation kinetics of actin filaments as a function of temperature and pressure in the presence of synthetic and protein crowding agents. We show that the association of actin monomers to the pointed end of double‐stranded helical actin filaments (F‐actin) proceeds via a transition state that requires an activation energy of 56 kJ mol^?1 for conformational and hydration rearrangements, but exhibits a negligible activation volume, pointing to a compact transition state that is devoid of packing defects. Macromolecular crowding causes acceleration of the F‐actin elongation rate and counteracts the deteriorating effect of pressure. The results shed new light on the combined effect of these parameters on the polymerization process of actin, and help us understand the temperature and pressure sensitivity of actin polymerization under extreme conditions.     

Difference between Extra‐ and Intracellular T1 Values of Carboxylic Acids Affects the Quantitative Analysis of Cellular Kinetics by Hyperpolarized NMR

Incomplete knowledge of the longitudinal relaxation time constant (T₁) leads to incorrect assumptions in quantitative kinetic models of cellular systems, studied by hyperpolarized real‐time NMR. Using an assay that measures the intracellular signal of small carboxylic acids in living cells, the intracellular T₁ of the carboxylic acid moiety of acetate, keto‐isocaproate, pyruvate, and butyrate was determined. The intracellular T₁ is shown to be up to four‐fold shorter than the extracellular T₁. Such a large difference in T₁ values between the inside and the outside of the cell has significant influence on the quantification of intracellular metabolic activity. It is expected that the significantly shorter T₁ value of the carboxylic moieties inside cells is a result of macromolecular crowding. An artificial cytosol has been prepared and applied to predict the T₁ of other carboxylic acids. We demonstrate the value of this prediction tool.     

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.     

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.     

Macromolecular crowding tunes folding landscape of parallel α/β protein, apoflavodoxin

Proteins normally fold in crowded cellular environments. Here we use a set of Desulfovibrio desulfuricans apoflavodoxin variants to assess--with residue-specific resolution--how apoflavodoxin's folding landscape is tuned by macromolecular crowding. We find that, under crowded conditions, initial topological frustration is reduced, subsequent folding requires less ordering in the transition state, and β-strand 1 becomes more important in guiding the process. We propose that conditions more closely mimicking the cellular environment make the ensemble of unfolded conformations less expanded, resulting in a folding funnel that is smoother and narrower.     

Macromolecular Crowding and the Sizes of Neutral Flexible Polymer Chains: The Role of Colloids Sizes and Concentrations

In the present work, we revisit the effect of macromolecular crowding on the sizes of flexible neutral polymer chains. Motivated by recent experimental measurements on crowding effects on neutral flexible polymers chains, we perform Monte Carlo simulations on a model system consisting of hard spheres (HS) and a neutral flexible polymer chain. We find that, depending on the ratio of the sizes of the colloidal particles to the sizes of the polymer chain, and thus, on the extent of the colloid partitioning among the chain segments and the solution, the flexible polymeric coil may be either continuously compressed, or initially compressed followed by a reswelling at high enough colloid concentration. The chain behavior is thus nonmonotonic, a point which, apart from the work of Khalatur et al., has not so far been stressed in simulations of flexible polymer chains under crowding conditions. A thermodynamic model for the polymer–colloid interactions based on the Gibbs–Duhem equation and on a “Flory‐type” argument is also presented, emphasizing the indirect influence of macromolecular crowding on the monomers chemical potential. We show explicitly that under crowding conditions, the colloids are driven into the most compact coil states. These analytical results are compared with the results of the potential of mean force between the chain center of mass and the colloids obtained from the Monte Carlo simulations, and a reasonable agreement is found. The implications of the aforementioned results are further discussed in the context of biological systems, specially those for which macromolecular crowding is supposed to play the important role of including preferentially other (charged) macromolecules into the colloid‐compressed polymer phase.

     

Enhancement of enantioselectivity in chiral capillary electrophoresis using hydroxypropyl‐beta‐cyclodextrin as chiral selector under molecular crowding conditions induced by dextran or dextrin

Molecular crowding is a new approach to enhance the retention properties and selectivity of molecularly imprinted polymers. In this work, this concept was first applied to chiral CE to enhance its enantioselectivity. A model system, enantioseparation of salbutamol using hydroxypropyl‐beta‐cyclodextrin as chiral selector in the presence of dextran or dextrin as crowding‐inducing agents, was chosen to demonstrate its potency. Some parameters, especially the concentration of crowding‐inducing agents and cyclodextrins were investigated intensively. Moreover, based on fluorescence spectroscopy and affinity CE, it was found that the presence of crowding‐inducing agents could promote the association of enantiomers with cyclodextrins and intensify the interacting differences of two enantiomers with cyclodextrins. As a result, the essential concentration of cyclodextrins to make the enantiomers reach baseline separation was significantly decreased with the aid of molecular crowding. This study shows that molecular crowding is an effective strategy to enhance the enantioselectivity of cyclodextrin in chiral CE.     

Macromolecular crowding effects on reactions of TePixD (Tll0078)

To reveal macromolecular crowding effects on a chemical reaction of a BLUF (sensors of blue light using FAD) protein (PixD from a thermophilic cyanobacterium Thermosynechococcus elongatus BP-1 [TePixD, Tll0078]), the photoreaction was studied at various concentrations of the macromolecule Ficoll-70 by UV/Vis absorption spectroscopy and the pulsed laser-induced transient grating (TG) method. The absorption spectrum did not change with varying concentration of Ficoll-70. The crowding did not affect the quantum yield of the spectral red shift reaction, recovery rate of the product, rate constant of the volume change reaction and the magnitude of the volume change. However, the magnitude of the TG signal representing the diffusion-sensitive conformation change significantly increased on addition of Ficoll-70. This dependence was attributed to the crowding effect on the TePixD decamer-pentamer equilibrium in the solution. This result indicates that the TePixD reaction is more efficient in cellular than in in vitro conditions.     

Translational Dynamics of Lipidated Ras Proteins in the Presence of Crowding Agents and Compatible Osmolytes

Ras proteins are small GTPases and are involved in transmitting signals that control cell growth, differentiation, and proliferation. Since the cell cytoplasm is crowded with different macromolecules, understanding the translational dynamics of Ras proteins in crowded environments is crucial to yielding deeper insight into their reactivity and function. Herein, the translational dynamics of lipidated N‐Ras and K‐Ras4B is studied in the bulk and in the presence of a macromolecular crowder (Ficoll) and the compatible osmolyte and microcrowder sucrose by fluorescence correlation spectroscopy. The results reveal that N‐Ras forms dimers due to the presence of its lipid moiety in the hypervariable region, whereas K‐Ras4B remains in its monomeric form in the bulk. Addition of a macromolecular crowding agent gradually favors clustering of the Ras proteins. In 20 wt % Ficoll N‐Ras forms trimers and K‐Ras4B dimers. Concentrations of sucrose up to 10 wt % foster formation of N‐Ras trimers and K‐Ras dimers as well. The results can be rationalized in terms of the excluded‐volume effect, which enhances the association of the proteins, and, for the higher concentrations, by limited‐hydration conditions. The results of this study shed new light on the association state of these proteins in a crowded environment. This is of particular interest for the Ras proteins, because their solution state—monomeric or clustered—influences their membrane‐partitioning behavior and their interplay with cytosolic interaction partners.     

Effects of quenched and annealed macromolecular crowding elements on a simple model for signaling in T lymphocytes

Biochemical reactions in cells occur in an environment that is crowded in the sense that various macromolecular species and organelles occupy much of the space. The effects of molecular crowding on biochemical reactions have usually been studied in the past in a spatially homogeneous environment. However, signal transduction in cells is often initiated by the binding of receptors and ligands in two apposed cell membranes, and the pertinent biochemical reactions occur in a spatially inhomogeneous environment. We have studied the effects of crowding on biochemical reactions that involve both membrane proteins and cytosolic molecules by investigating a simplified version of signaling in T lymphocytes using a Monte Carlo algorithm. We find that, if signal transduction occurs on time scales that are slow compared to the motility of the molecules and organelles that constitute the crowding elements, the effects of crowding are qualitatively the same as in a homogeneous three-dimensional (3D) medium. In contrast, if signal transduction occurs on a time scale that is much faster than the time over which the crowding elements move, then the effects of varying the extent of crowding are very different when reactions occur in both 2- and 3D space. We discuss these differences and their origin. Since many signaling reactions are fast, our results may be useful for diverse situations in cell biology.