Empirical Optimization of Interactions between Proteins and Chemical Denaturants in Molecular Simulations

The Action of Chemical Denaturants: From Globular to Intrinsically Disordered Proteins

Proteins perform their many functions by adopting either a minimal number of strictly similar conformations, the native state, or a vast ensemble of highly flexible conformations. In both cases, their structural features are highly influenced by the chemical environment. Even though a plethora of experimental studies have demonstrated the impact of chemical denaturants on protein structure, the molecular mechanism underlying their action is still debated. In the present review, after a brief recapitulation of the main experimental data on protein denaturants, we survey both classical and more recent interpretations of the molecular basis of their action. In particular, we highlight the differences and similarities of the impact that denaturants have on different structural classes of proteins, i.e., globular, intrinsically disordered (IDP), and amyloid-like assemblies. Particular attention has been given to the IDPs, as recent studies are unraveling their fundamental importance in many physiological processes. The role that computation techniques are expected to play in the near future is illustrated.

Single-molecule Detection of Ultrafast Biomolecular Dynamics with Nanophotonics

Single-molecule Förster resonance energy transfer (FRET) is a versatile technique for probing the structure and dynamics of biomolecules even in heterogeneous ensembles. However, because of the limited fluorescence brightness per molecule and the relatively long fluorescence lifetimes, probing ultrafast structural dynamics in the nanosecond time scale has thus far been very challenging. Here, we demonstrate that nanophotonic fluorescence enhancement in zero-mode waveguides enables measurements of previously inaccessible low-nanosecond dynamics by dramatically improving time resolution and reduces data acquisition times by more than an order of magnitude. As a prototypical example, we use this approach to probe the dynamics of a short intrinsically disordered peptide that were previously inaccessible with single-molecule FRET measurements. We show that we are now able to detect the low-nanosecond correlations in this peptide, and we obtain a detailed interpretation of the underlying distance distributions and dynamics in conjunction with all-atom molecular dynamics simulations, which agree remarkably well with the experiments. We expect this combined approach to be widely applicable to the investigation of very rapid biomolecular dynamics.

Integrating single-molecule spectroscopy and simulations for the study of intrinsically disordered proteins

Over the last two decades, intrinsically disordered proteins and protein regions (IDRs) have emerged from a niche corner of biophysics to be recognized as essential drivers of cellular function. Various techniques have provided fundamental insight into the function and dysfunction of IDRs. Among these techniques, single-molecule fluorescence spectroscopy and molecular simulations have played a major role in shaping our modern understanding of the sequence-encoded conformational behavior of disordered proteins. While both techniques are frequently used in isolation, when combined they offer synergistic and complementary information that can help uncover complex molecular details. Here we offer an overview of single-molecule fluorescence spectroscopy and molecular simulations in the context of studying disordered proteins. We discuss the various means in which simulations and single-molecule spectroscopy can be integrated, and consider a number of studies in which this integration has uncovered biological and biophysical mechanisms.

Atomic view of cosolute-induced protein denaturation probed by NMR solvent paramagnetic relaxation enhancement

The cosolvent effect arises from the interaction of cosolute molecules with a protein and alters the equilibrium between native and unfolded states. Denaturants shift the equilibrium toward the latter, while osmolytes stabilize the former. The molecular mechanism whereby cosolutes perturb protein stability is still the subject of considerable debate. Probing the molecular details of the cosolvent effect is experimentally challenging as the interactions are very weak and transient, rendering them invisible to most conventional biophysical techniques. Here, we probe cosolute-protein interactions by means of NMR solvent paramagnetic relaxation enhancement together with a formalism we recently developed to quantitatively describe, at atomic resolution, the energetics and dynamics of cosolute-protein interactions in terms of a concentration normalized equilibrium average of the interspin distance, [Formula: see text], and an effective correlation time, τ_c The system studied is the metastable drkN SH3 domain, which exists in dynamic equilibrium between native and unfolded states, thereby permitting us to probe the interactions of cosolutes with both states simultaneously under the same conditions. Two paramagnetic cosolute denaturants were investigated, one neutral and the other negatively charged, differing in the presence of a carboxyamide group versus a carboxylate. Our results demonstrate that attractive cosolute-protein backbone interactions occur largely in the unfolded state and some loop regions in the native state, electrostatic interactions reduce the [Formula: see text] values, and temperature predominantly impacts interactions with the unfolded state. Thus, destabilization of the native state in this instance arises predominantly as a consequence of interactions of the cosolutes with the unfolded state.

Molecular detection of Mycobacterium tuberculosis in blood stained sputum samples using GeneXpert PCR assay

This study investigated the possibility of detecting Mycobacterium tuberculosis (MTB) in blood-stained sputa with GeneXpert assay (Xpert MTB/Rif G4 v.5) using appropriate blood lysing (distilled water and distilled water/carbon tetrachloride) and protein denaturing (guanidinium chloride and heat) agents. Blood free sputa were collected from individuals infected with MTB. Various levels of blood-spiked sputa (0%-50%) were prepared and subsequently assayed with GeneXpert analyzer. GeneXpert was found to be reproducible at less than 2% blood contamination. However, beyond 5% blood contamination, GeneXpert was unreliable with absolute PCR inhibition at 20% of blood contamination. Boiling at 95°C for 5 minutes was able to recover MTB DNA in previously undetectable levels as well as in 57% of patients' sputa with blood stains with previous negative GeneXpert results.

Extended Experimental Inferential Structure Determination Method in Determining the Structural Ensembles of Disordered Protein States

Proteins with intrinsic or unfolded state disorder comprise a new frontier in structural biology, requiring the characterization of diverse and dynamic structural ensembles. We introduce a comprehensive Bayesian framework, the Extended Experimental Inferential Structure Determination (X-EISD) method, that calculates the maximum log-likelihood of a disordered protein ensemble. X-EISD accounts for the uncertainties of a range of experimental data and back-calculation models from structures, including NMR chemical shifts, J-couplings, Nuclear Overhauser Effects (NOEs), paramagnetic relaxation enhancements (PREs), residual dipolar couplings (RDCs), hydrodynamic radii (R h ), single molecule fluorescence Förster resonance energy transfer (smFRET) and small angle X-ray scattering (SAXS). We apply X-EISD to the joint optimization against experimental data for the unfolded drkN SH3 domain and find that combining a local data type, such as chemical shifts or J-couplings, paired with long-ranged restraints such as NOEs, PREs or smFRET, yields structural ensembles in good agreement with all other data types if combined with representative IDP conformers.

Emerging consensus on the collapse of unfolded and intrinsically disordered proteins in water

Establishing the degree of collapse of unfolded or disordered proteins is a fundamental problem in biophysics, because of its relation to protein folding and to the function of intrinsically disordered proteins. However, until recently, different experiments gave qualitatively different results on collapse and there were large discrepancies between experiments and all-atom simulations. New methodology introduced in the past three years has helped to resolve the differences between experiments, and improvements in simulations have closed the gap between experiment and simulation. These advances have led to an emerging consensus on the collapse of disordered proteins in water.

Distinct and Nonadditive Effects of Urea and Guanidinium Chloride on Peptide Solvation

Using enhanced-sampling replica exchange fully atomistic molecular dynamics simulations, we show that, individually, urea and guanidinium chloride (GdmCl) denature the Trpcage protein, but remarkably, the helical segment ¹NLYIQWL⁷ of the protein is stabilized in mixed denaturant solutions. GdmCl induces protein denaturation via a combination of direct and indirect effects involving dehydration of the protein and destabilization of stabilizing salt bridges. In contrast, urea denatures the protein through favorable protein-urea preferential interactions, with peptide-specific indirect effects of urea on the water structure around the protein. In the case of the helical segment of Trpcage, urea "oversolvates" the peptide backbone by reorganizing water molecules from the peptide side chains to the peptide backbone. An intricate nonadditive thermodynamic balance between GdmCl-induced dehydration of the peptide and the urea-induced changes in solvation structure triggers partial counteraction to urea denaturation and stabilization of the helix.

Evolution of All-Atom Protein Force Fields to Improve Local and Global Properties

Experimental studies on intrinsically disordered and unfolded proteins have shown that in isolation they typically have low populations of secondary structure and exhibit distance scalings suggesting that they are at near-theta-solvent conditions. Until recently, however, all-atom force fields failed to reproduce these fundamental properties of intrinsically disordered proteins (IDPs). Recent improvements by refining against ensemble-averaged experimental observables for polypeptides in aqueous solution have addressed deficiencies including secondary structure bias, global conformational properties, and thermodynamic parameters of biophysical reactions such as folding and collapse. To date, studies utilizing these improved all-atom force fields have mostly been limited to a small set of unfolded or disordered proteins. Here, we present data generated for a diverse library of unfolded or disordered proteins using three progressively improved generations of Amber03 force fields, and we explore how global and local properties are affected by each successive change in the force field. We find that the most recent force field refinements significantly improve the agreement of the global properties such as radii of gyration and end-to-end distances with experimental estimates. However, these global properties are largely independent of the local secondary structure propensity. This result stresses the need to validate force fields with reference to a combination of experimental data providing information about both local and global structure formation.

The combined force field-sampling problem in simulations of disordered amyloid-β peptides

Molecular dynamics simulations of intrinsically disordered proteins (IDPs) can provide high resolution structural ensembles if the force field is accurate enough and if the simulation sufficiently samples the conformational space of the IDP with the correct weighting of sub-populations. Here, we investigate the combined force field-sampling problem by testing a standard force field as well as newer fixed charge force fields, the latter specifically motivated for better description of unfolded states and IDPs, and comparing them with a standard temperature replica exchange (TREx) protocol and a non-equilibrium Temperature Cool Walking (TCW) sampling algorithm. The force field and sampling combinations are used to characterize the structural ensembles of the amyloid-beta peptides Aβ42 and Aβ43, which both should be random coils as shown recently by experimental nuclear magnetic resonance (NMR) and 2D Förster resonance energy transfer (FRET) experiments. The results illustrate the key importance of the sampling algorithm: while the standard force field using TREx is in poor agreement with the NMR J-coupling and nuclear Overhauser effect and 2D FRET data, when using the TCW method, the standard and optimized protein-water force field combinations are in very good agreement with the same experimental data since the TCW sampling method produces qualitatively different ensembles than TREx. We also discuss the relative merit of the 2D FRET data when validating structural ensembles using the different force fields and sampling protocols investigated in this work for small IDPs such as the Aβ42 and Aβ43 peptides.

Atomistic Force Fields for Proteins

All-atom, classical force fields for protein molecular dynamics (MD) simulations currently occupy a sweet spot in the universe of computational models, sufficiently detailed to be of predictive value in many cases, yet also simple enough that some biologically relevant time scales (microseconds or more) can now be sampled via specialized hardware or enhanced sampling methods. However, due to their long evolutionary history, there is now a myriad of force field branches in current use, which can make it hard for those entering the simulation field to know which would be the best set of parameters for a given application. In this chapter, I try to give an overview of the historical motivation for the different force fields available, suggestions for how to determine the most appropriate model and what to do if the results are in conflict with experimental evidence.

Contrasting Effects of Guanidinium Chloride and Urea on the Activity and Unfolding of Lysozyme

Cosolvents play an important role in regulating the stability and function of proteins present in the cell. We studied the role of cosolvents, urea and guanidinium chloride (GdmCl), which act as protein denaturants, in the catalytic activity and structural stability of the protein lysozyme using activity measurements, spectroscopy, and molecular dynamics simulations. We find that the activity of lysozyme increases on the addition of urea, whereas it decreases sharply on the addition of GdmCl. At low GdmCl concentrations ([GdmCl] < 4 M), the activity of lysozyme decreases, even though there is no significant perturbation in the structure of the lysozyme folded state. We find that this is due to the strong interaction of the Gdm⁺ ion with the residues Asp52 and Glu35, which are present in the lysozyme catalytic site. In contrast, urea interacts with Trp63 present in the loop region present near the active site of lysozyme, inducing minor conformational changes in lysozyme, which can increase the activity of lysozyme. At higher denaturant concentrations, experiments show that GdmCl completely denatures the protein, whereas the folded state is stable in the presence of urea. We further show that GdmCl denatures lysozyme with the disulfide bonds intact in the protein, whereas urea denatures the protein only when the disulfide bonds are broken using reducing agents.

Perspective: Chain dynamics of unfolded and intrinsically disordered proteins from nanosecond fluorescence correlation spectroscopy combined with single-molecule FRET

The dynamics of unfolded proteins are important both for the process of protein folding and for the behavior of intrinsically disordered proteins. However, methods for investigating the global chain dynamics of these structurally diverse systems have been limited. A versatile experimental approach is single-molecule spectroscopy in combination with Förster resonance energy transfer and nanosecond fluorescence correlation spectroscopy. The concepts of polymer physics offer a powerful framework both for interpreting the results and for understanding and classifying the properties of unfolded and intrinsically disordered proteins. This information on long-range chain dynamics can be complemented with spectroscopic techniques that probe different length scales and time scales, and integration of these results greatly benefits from recent advances in molecular simulations. This increasing convergence between the experiment, theory, and simulation is thus starting to enable an increasingly detailed view of the dynamics of disordered proteins.

Inferring properties of disordered chains from FRET transfer efficiencies

Förster resonance energy transfer (FRET) is a powerful tool for elucidating both structural and dynamic properties of unfolded or disordered biomolecules, especially in single-molecule experiments. However, the key observables, namely, the mean transfer efficiency and fluorescence lifetimes of the donor and acceptor chromophores, are averaged over a broad distribution of donor-acceptor distances. The inferred average properties of the ensemble therefore depend on the form of the model distribution chosen to describe the distance, as has been widely recognized. In addition, while the distribution for one type of polymer model may be appropriate for a chain under a given set of physico-chemical conditions, it may not be suitable for the same chain in a different environment so that even an apparently consistent application of the same model over all conditions may distort the apparent changes in chain dimensions with variation of temperature or solution composition. Here, we present an alternative and straightforward approach to determining ensemble properties from FRET data, in which the polymer scaling exponent is allowed to vary with solution conditions. In its simplest form, it requires either the mean FRET efficiency or fluorescence lifetime information. In order to test the accuracy of the method, we have utilized both synthetic FRET data from implicit and explicit solvent simulations for 30 different protein sequences, and experimental single-molecule FRET data for an intrinsically disordered and a denatured protein. In all cases, we find that the inferred radii of gyration are within 10% of the true values, thus providing higher accuracy than simpler polymer models. In addition, the scaling exponents obtained by our procedure are in good agreement with those determined directly from the molecular ensemble. Our approach can in principle be generalized to treating other ensemble-averaged functions of intramolecular distances from experimental data.

Precise estimation of transfer free energies for ionic species between similar media

Two-dimensional umbrella sampling is combined with molecular dynamics to calculate correction-free estimates of transfer properties for individual ions.

Molecular recognition and packing frustration in a helical protein

Biomolecular recognition entails attractive forces for the functional native states and discrimination against potential nonnative interactions that favor alternate stable configurations. The challenge posed by the competition of nonnative stabilization against native-centric forces is conceptualized as frustration. Experiment indicates that frustration is often minimal in evolved biological systems although nonnative possibilities are intuitively abundant. Much of the physical basis of minimal frustration in protein folding thus remains to be elucidated. Here we make progress by studying the colicin immunity protein Im9. To assess the energetic favorability of nonnative versus native interactions, we compute free energies of association of various combinations of the four helices in Im9 (referred to as H1, H2, H3, and H4) by extensive explicit-water molecular dynamics simulations (total simulated time > 300 μs), focusing primarily on the pairs with the largest native contact surfaces, H1-H2 and H1-H4. Frustration is detected in H1-H2 packing in that a nonnative packing orientation is significantly stabilized relative to native, whereas such a prominent nonnative effect is not observed for H1-H4 packing. However, in contrast to the favored nonnative H1-H2 packing in isolation, the native H1-H2 packing orientation is stabilized by H3 and loop residues surrounding H4. Taken together, these results showcase the contextual nature of molecular recognition, and suggest further that nonnative effects in H1-H2 packing may be largely avoided by the experimentally inferred Im9 folding transition state with native packing most developed at the H1-H4 rather than the H1-H2 interface.

Biomolecules need to recognize one another with high specificity: promoting “native” functional intermolecular binding events while avoiding detrimental “nonnative” bound configurations; i.e., “frustration”—the tendency for nonnative interactions—has to be minimized. Folding of globular proteins entails a similar discrimination. To gain physical insight, we computed the binding affinities of helical structures of the protein Im9 in various native or nonnative configurations by atomic simulations, discovering that partial packing of the Im9 core is frustrated. This frustration is overcome when the entire core of the protein is assembled, consistent with experiment indicating no significant kinetic trapping in Im9 folding. Our systematic analysis thus reveals a subtle, contextual aspect of biomolecular recognition and provides a general approach to characterize folding frustration.

Probing the Action of Chemical Denaturant on an Intrinsically Disordered Protein by Simulation and Experiment

Chemical denaturants are the most commonly used agents for unfolding proteins and are thought to act by better solvating the unfolded state. Improved solvation is expected to lead to an expansion of unfolded chains with increasing denaturant concentration, providing a sensitive probe of the denaturant action. However, experiments have so far yielded qualitatively different results concerning the effects of chemical denaturation. Studies using Förster resonance energy transfer (FRET) and other methods found an increase in radius of gyration with denaturant concentration, but most small-angle X-ray scattering (SAXS) studies found no change. This discrepancy therefore challenges our understanding of denaturation mechanism and more generally the accuracy of these experiments as applied to unfolded or disordered proteins. Here, we use all-atom molecular simulations to investigate the effect of urea and guanidinium chloride on the structure of the intrinsically disordered protein ACTR, which can be studied by experiment over a wide range of denaturant concentration. Using unbiased molecular simulations with a carefully calibrated denaturant model, we find that the protein chain indeed swells with increasing denaturant concentration. This is due to the favorable association of urea or guanidinium chloride with the backbone of all residues and with the side-chains of almost all residues, with denaturant-water transfer free energies inferred from this association in reasonable accord with experimental estimates. Interactions of the denaturants with the backbone are dominated by hydrogen bonding, while interactions with side-chains include other contributions. By computing FRET efficiencies and SAXS intensities at each denaturant concentration, we show that the simulation trajectories are in accord with both experiments on this protein, demonstrating that there is no fundamental inconsistency between the two types of experiment. Agreement with experiment also supports the picture of chemical denaturation described in our simulations, driven by weak association of denaturant with the protein. Our simulations support some assumptions needed for each experiment to accurately reflect changes in protein size, namely, that the commonly used FRET chromophores do not qualitatively alter the results and that possible effects such as preferential solvent partitioning into the interior of the chain do not interfere with the determination of radius of gyration from the SAXS experiments.

Consistent View of Polypeptide Chain Expansion in Chemical Denaturants from Multiple Experimental Methods

There has been a long-standing controversy regarding the effect of chemical denaturants on the dimensions of unfolded and intrinsically disordered proteins: A wide range of experimental techniques suggest that polypeptide chains expand with increasing denaturant concentration, but several studies using small-angle X-ray scattering (SAXS) have reported no such increase of the radius of gyration (Rg). This inconsistency challenges our current understanding of the mechanism of chemical denaturants, which are widely employed to investigate protein folding and stability. Here, we use a combination of single-molecule Förster resonance energy transfer (FRET), SAXS, dynamic light scattering (DLS), and two-focus fluorescence correlation spectroscopy (2f-FCS) to characterize the denaturant dependence of the unfolded state of the spectrin domain R17 and the intrinsically disordered protein ACTR in two different denaturants. Standard analysis of the primary data clearly indicates an expansion of the unfolded state with increasing denaturant concentration irrespective of the protein, denaturant, or experimental method used. This is the first case in which SAXS and FRET have yielded even qualitatively consistent results regarding expansion in denaturant when applied to the same proteins. To more directly illustrate this self-consistency, we used both SAXS and FRET data in a Bayesian procedure to refine structural ensembles representative of the observed unfolded state. This analysis demonstrates that both of these experimental probes are compatible with a common ensemble of protein configurations for each denaturant concentration. Furthermore, the resulting ensembles reproduce the trend of increasing hydrodynamic radius with denaturant concentration obtained by 2f-FCS and DLS. We were thus able to reconcile the results from all four experimental techniques quantitatively, to obtain a comprehensive structural picture of denaturant-induced unfolded state expansion, and to identify the most likely sources of earlier discrepancies.

Probing the Action of Chemical Denaturant on an Intrinsically Disordered Protein by Simulation and Experiment

Chemical denaturants are the most commonly used agents for unfolding proteins and are thought to act by better solvating the unfolded state. Improved solvation is expected to lead to an expansion of unfolded chains with increasing denaturant concentration, providing a sensitive probe of the denaturant action. However, experiments have so far yielded qualitatively different results concerning the effects of chemical denaturation. Studies using Förster resonance energy transfer (FRET) and other methods found an increase in radius of gyration with denaturant concentration, but most small-angle X-ray scattering (SAXS) studies found no change. This discrepancy therefore challenges our understanding of denaturation mechanism and more generally the accuracy of these experiments as applied to unfolded or disordered proteins. Here, we use all-atom molecular simulations to investigate the effect of urea and guanidinium chloride on the structure of the intrinsically disordered protein ACTR, which can be studied by experiment over a wide range of denaturant concentration. Using unbiased molecular simulations with a carefully calibrated denaturant model, we find that the protein chain indeed swells with increasing denaturant concentration. This is due to the favorable association of urea or guanidinium chloride with the backbone of all residues and with the side-chains of almost all residues, with denaturant-water transfer free energies inferred from this association in reasonable accord with experimental estimates. Interactions of the denaturants with the backbone are dominated by hydrogen bonding, while interactions with side-chains include other contributions. By computing FRET efficiencies and SAXS intensities at each denaturant concentration, we show that the simulation trajectories are in accord with both experiments on this protein, demonstrating that there is no fundamental inconsistency between the two types of experiment. Agreement with experiment also supports the picture of chemical denaturation described in our simulations, driven by weak association of denaturant with the protein. Our simulations support some assumptions needed for each experiment to accurately reflect changes in protein size, namely, that the commonly used FRET chromophores do not qualitatively alter the results and that possible effects such as preferential solvent partitioning into the interior of the chain do not interfere with the determination of radius of gyration from the SAXS experiments.