Relative solvent accessible surface area predicts protein conformational changes upon binding

Protein interactions are often accompanied by significant changes in conformation. We have analyzed the relationships between protein structures and the conformational changes they undergo upon binding. Based upon this, we introduce a simple measure, the relative solvent accessible surface area, which can be used to predict the magnitude of binding-induced conformational changes from the structures of either monomeric proteins or bound subunits. Applying this to a large set of protein complexes suggests that large conformational changes upon binding are common. In addition, we observe considerable enrichment of intrinsically disordered sequences in proteins predicted to undergo large conformational changes. Finally, we demonstrate that the relative solvent accessible surface area of monomeric proteins can be used as a simple proxy for protein flexibility. This reveals a powerful connection between the flexibility of unbound proteins and their binding-induced conformational changes, consistent with the conformational selection model of molecular recognition.     

An effective solvent theory connecting the underlying mechanisms of osmolytes and denaturants for protein stability

An all-atom Gō model of Trp-cage protein is simulated using discontinuous molecular dynamics in an explicit minimal solvent, using a single, contact-based interaction energy between protein and solvent particles. An effective denaturant or osmolyte solution can be constructed by making the interaction energy attractive or repulsive. A statistical mechanical equivalence is demonstrated between this effective solvent model and models in which proteins are immersed in solutions consisting of water and osmolytes or denaturants. Analysis of these studies yields the following conclusions: 1), Osmolytes impart extra stability to the protein by reducing the entropy of the unfolded state. 2), Unfolded states in the presence of osmolyte are more collapsed than in water. 3), The folding transition in osmolyte solutions tends to be less cooperative than in water, as determined by the ratio of van 't Hoff to calorimetric enthalpy changes. The decrease in cooperativity arises from an increase in native structure in the unfolded state, and thus a lower thermodynamic barrier at the transition midpoint. 4), Weak denaturants were observed to destabilize small proteins not by lowering the unfolded enthalpy, but primarily by swelling the unfolded state and raising its entropy. However, adding a strong denaturant destabilizes proteins enthalpically. 5), The folding transition in denaturant-containing solutions is more cooperative than in water. 6), Transfer to a concentrated osmolyte solution with purely hard-sphere steric repulsion significantly stabilizes the protein, due to excluded volume interactions not present in the canonical Tanford transfer model. 7), Although a solution with hard-sphere interactions adds a solvation barrier to native contacts, the folding is nevertheless less cooperative for reasons 1–3 above, because a hard-sphere solvent acts as a protecting osmolyte.     

How a vicinal layer of solvent modulates the dynamics of proteins

The dynamics of a folded protein is studied in water and glycerol at a series of temperatures below and above their respective dynamical transition. The system is modeled in two distinct states whereby the protein is decoupled from the bulk solvent at low temperatures, and communicates with it through a vicinal layer at physiological temperatures. A linear viscoelastic model elucidates the less-than-expected increase in the relaxation times observed in the backbone dynamics of the protein. The model further explains the increase in the flexibility of the protein once the transition takes place and the differences in the flexibility under the different solvent environments. Coupling between the vicinal layer and the protein fluctuations is necessary to interpret these observations. The vicinal layer is postulated to form once a threshold for the volumetric fluctuations in the protein to accommodate solvents of different sizes is reached. Compensation of entropic-energetic contributions from the protein-coupled vicinal layer quantifies the scaling of the dynamical transition temperatures in various solvents. The protein adapts different conformational routes for organizing the required coupling to a specific solvent, which is achieved by adjusting the amount of conformational jumps in the surface-group dihedrals.     

The relative order of helical propensity of amino acids changes with solvent environment

A model peptide of sequence Ac-Y-VAXAK-VAXAK-VAXAK-NH(2), where X is substituted with one of nineteen amino acids (P excluded), was synthesized and titrated with methanol to study helical propensity as a function of solvent environment. The CD spectra of these peptides are largely random coil in 2 mM sodium phosphate buffer (pH 5.5) and show a conformational change to alpha-helix with increasing methanol content. Singular value decomposition was used to correct the CD spectra for the absorbing side chains of W, Y, F, C, and M, and this correction can be substantial. With correction both W and F become good helix formers. The free energy for helix propagation was calculated using the Lifson-Roig statistical model for each of the nineteen amino acids at each point in their titration. The results show that the rank order of helical propensity for the nineteen amino acids changes with solvent environment. This result will be particularly important if proteins undergo hydrophobic collapse before secondary structures are formed, because amino acids can then see different solvent environments as the secondary structures are formed. Related amino acids are found to have interesting correlations in the shape of their titration curves. This finding provides one explanation for the limiting 70% accuracy in predicting secondary structure from sequence, since the helical propensities used are calculated for an average solvent environment. Proteins 2000;39:132-141.     

A model for solvent contributions to polypeptide and protein circular dichroism

The possibility of bound solvent contributing directly to the circular dichroism of polypeptides and proteins is discussed. The model presented is based on the requirement of a breakdown in the planar symmetry of the amide environment. This symmetry breakdown is described in terms of the conformational states of the chain, and leads to necessary, but not sufficient, conditions for observable solvent contributions. Application of the model leads to the conclusion that, while some chain conformations are intrinsically incapable of roviding the required breakdown in the symmetry of solvent perturbations, other conformations force such a breakdown, notably poly-L -proline II and disordered chains.     

Excluded volume approximation to protein-solvent interaction. The solvent contact model.

Important properties of globular proteins, such as the stability of its folded state, depend sensitively on interactions with solvent molecules. Existing methods for estimating these interactions, such as the geometrical surface model, are either physically misleading or too time consuming to be applied routinely in energy calculations. As an alternative, we derive here a simple model for the interactions between protein atoms and solvent atoms in the first hydration layer, the solvent contact model, based on the conservation of the total number of atomic contacts, a consequence of the excluded-volume effect. The model has the conceptual advantage that protein-protein contacts and protein-solvent contacts are treated in the same language and the technical advantage that the solvent term becomes a particularly simple function of interatomic distances. The model allows rapid calculation of any physical property that depends only on the number and type of protein-solvent nearest-neighbor contacts. We propose use of the method in the calculation of protein solvation energies, conformational energy calculations, and molecular dynamics simulations.     

Time-resolved structural investigation of regenerated silk fibroin nanofibers treated with solvent vapor

Nonwoven matrices of silk fibroin (SF) nanofibers were prepared by electrospinning a regenerated SF solution, followed by treatment with solvent vapor including water, methanol, ethanol, and propanol. Structural changes of solvent vapor-treated SF nanofibers were investigated in a time-resolved manner using IR spectroscopy. Conformational transitions of SF nanofibers from random coil to beta-sheet forms were dependent on the type of solvent vapor used, and their transition rates were strongly influenced by treatment temperatures. Consistent with previous findings, methanol vapor treatment provided a fast and effective means by which to alter the secondary structure of SF nanofibers. However, treatment with water vapor, as compared to treatment with alcohol vapor, was also useful for inducing structural changes in SF nanofibers. As demonstrated in the present study, our approach of controlling secondary structure formation of proteins by solvent vapor treatment and monitoring real-time conformational changes may be useful for the design and tailoring of materials for biomedical applications.     

Influence of isopropanol-water solvent mixtures on the conformation of poly-L-lysine

The helix–coil transition of poly-L -lysine (PLL) in water–isopropanol solvent mixtures has been investigated at room temperature by circular dichroism measurements. Within the range of 70%–80% isopropanol concentration (by volume), the polymer undergoes a sharp transition, characterized by the formation of a fully charged α-helical structure. On the basis of some experimental evidence the role of the organic component in solution appears more complicated than that of strengthening the intramolecular hydrogen bonds in the polymer. By analogy with the distribution of the components of alcohol–water mixtures in simple ionic systems, it is thought that only an high co-solvent concentration brings about an extensive and possible cooperative depletion of the clusters of firmly-bound water molecules in the domain of the polylelectrolyte, favoring the transition to the α-helical structure. On the other hand, CD spectral patterns show that the addition of NaCl in the alcohol-rich–water mixtures of charged poly-L -lysine gives rise to a transition from the α-helical to a β-structures conversion obeys a first-order rate law at all times, with a rate constant dependent on solvent composition and ionic strength. In these conditions, the rate of the process is close to that found for the thermally induced α–β transition. Higher polymer concentration and/or ionic strength cause a phase separation of β-PLL, suggesting that in this case interchain reactions (where hydrogen bonding should play the major role) predominate. Titration experiments on charged α-helical poly-L -lysine in 85% or 90% isopropanol mixtures confirm the occurrence of a conformational transition, which takes place within a degree of dissociation α of 0.2–0.75. The transition is accompanied by a visible turbidity, which increases as the titration proceeds. Implications of the solvent distribution around the macroion on the observed conformational phenomena are also discussed.     

Conformational transition of hyaluronic acid in aqueous-organic solvent monitored by vacuum ultraviolet circular dichroism

The chiroptical transition of hyaluronic acid (HA) in aqueous-organic solvent has been investigated by circular dichroism (CD) spectroscopy into the vacuum ultraviolet region. The CD of HA changes dramatically, monitoring a cooperative transition as the dielectric constant of an aqueous solution is reduced by adding organic solvents. This transition results in a high-intensity CD band at 188 nm, indicating an ordered structure in the mixed solvent. Heating HA in the mixed solvent also causes a cooperative transition, reducing the CD to that found for the polymer in aqueous solution. In contrast, heating HA in aqueous solution results in small, noncooperative changes in the CD spectrum. This indicates an unordered structure in aqueous solution. The CD as the dielectric constant is reduced exhibits isodichroic points, showing that there are only two environments for chromophores contributing to the CD. This is confirmed by singular value decomposition of CD spectra recorded as a function of solvent composition, which shows the spectra to contain only two principal components. The data describing the thermally induced transition of HA in mixed solvent are not consistent with infinite cooperativity. The van't Hoff relation yields thermodynamic parameters for the conformational transition in terms of the cooperative unit of -60 kcal mol-1 for delta H degrees and -180 eu mol-1 for delta S degrees.     

Simulations of the solvent structure for macromolecules. II. Structure of water solvating Na+-B-DNA at 300 K and a model for conformational transitions induced by solvent variations

The structure of water and its interaction energy with a fragment of B-DNA composed of 12 base pairs and of the corresponding 24 sugar and 22 phosphate units and Na⁺ ions (one at each phosphate group) are analyzed using Monte Carlo simulations. The sample of water molecules, at the simulated temperature of 300 K, is composed of 447 water molecules. The results are discussed either in terms of statistical analyses over the 2,000,000 simulated conformations (after equilibration) or with reference to an “average configuration.” Comparison is made to a simulation previously presented for the same system but without counterions. Isotherm at different relative humidity, hydration, and reactivity scales for different sites, the hydration number at each site, the structure of intraphosphate and interphosphate hydrogen-bonded filaments of water are reported and discussed. The stabilization of the B-conformation induced by the solvent with counterion (“ion-induced compression effect”) is analyzed on the base of the above findings. A preliminary model to predict conformational transition in DNA is presented. The analyses reported are very detailed to allow refined interpretations of spectroscopic (infrared, Raman, and nmr) and scattering (x-ray and neutron beam) data on DNA insolution.     

Specific protein dynamics near the solvent glass transition assayed by radiation-induced structural changes

The nature of the dynamical coupling between a protein and its surrounding solvent is an important, yet open issue. Here we used temperature-dependent protein crystallography to study structural alterations that arise in the enzyme acetylcholinesterase upon X-ray irradiation at two temperatures: below and above the glass transition of the crystal solvent. A buried disulfide bond, a buried cysteine, and solvent exposed methionine residues show drastically increased radiation damage at 155 K, in comparison to 100 K. Additionally, the irradiation-induced unit cell volume increase is linear at 100 K, but not at 155 K, which is attributed to the increased solvent mobility at 155 K. Most importantly, we observed conformational changes in the catalytic triad at the active site at 155 K but not at 100 K. These changes lead to an inactive catalytic triad conformation and represent, therefore, the observation of radiation-inactivation of an enzyme at the atomic level. Our results show that at 155 K, the protein has acquired--at least locally--sufficient conformational flexibility to adapt to irradiation-induced alterations in the conformational energy landscape. The increased protein flexibility may be a direct consequence of the solvent glass transition, which expresses as dynamical changes in the enzyme's environment. Our results reveal the importance of protein and solvent dynamics in specific radiation damage to biological macromolecules, which in turn can serve as a tool to study protein flexibility and its relation to changes in a protein's environment.     

Functional importance of short-range binding and long-range solvent interactions in helical antifreeze peptides

Short-range ice binding and long-range solvent perturbation both have been implicated in the activity of antifreeze proteins and antifreeze glycoproteins. We study these two mechanisms for activity of winter flounder antifreeze peptide. Four mutants are characterized by freezing point hysteresis (activity), circular dichroism (secondary structure), Förster resonance energy transfer (end-to-end rigidity), molecular dynamics simulation (structure), and terahertz spectroscopy (long-range solvent perturbation). Our results show that the short-range model is sufficient to explain the activity of our mutants, but the long-range model provides a necessary condition for activity: the most active peptides in our data set all have an extended dynamical hydration shell. It appears that antifreeze proteins and antifreeze glycoproteins have reached different evolutionary solutions to the antifreeze problem, utilizing either a few precisely positioned OH groups or a large quantity of OH groups for ice binding, assisted by long-range solvent perturbation.     

Intricacies of interactions,dynamics and solvent effects in enzyme catalysis: a computational perspective on cyclophilin A

The essential role of enzymes in biological processes has continually ignited sparks of interest in their mechanism of action. Fully understanding the mechanism of enzymes has broad implications in protein engineering and drug design. The more than five order of magnitude speed-up in the rate of peptidyl–prolyl cis–trans isomerisation by cyclophilin A (CypA) has been the target of intense research. CypA serves as a tractable model system, because it reversibly catalyses the rotation around peptidyl–prolyl bonds without any bond breakage or formation. Here, we discuss the results of recent computational approaches used to study the mechanism of CypA. We highlight the critical role of enzyme and substrate conformational dynamics in the developing interactions as the substrate approaches the transition state that results in an astonishing enhancement of isomerisation rate. The rate of isomerisation is affected by the intricate coupling between the dynamics of the substrate, enzyme and solvent. CypA binds its substrates via conformational selection, where rearrangements of key active site residues are necessary for substrate recognition. The conformational plasticity of the active site allows the enzyme to accommodate the most favourable interactions with the transition state that can be exploited for structure-based drug design.     

A critical analysis of continuum electrostatics: the screened Coulomb potential--implicit solvent model and the study of the alanine dipeptide and discrimination of misfolded structures of proteins

An analysis of the screened Coulomb potential--implicit solvent model (SCP--ISM) is presented showing that general equations for both the electrostatic and solvation free energy can be derived in a continuum approach, using statistical averaging of the polarization field created by the solvent around the molecule. The derivation clearly shows how the concept of boundary, usually found in macroscopic approaches, is eliminated when the continuum model is obtained from a microscopic treatment using appropriate averaging techniques. The model is used to study the alanine dipeptide in aqueous solution, as well as the discrimination of native protein structures from misfolded conformations. For the alanine dipeptide the free energy surface in the phi--psi space is calculated and compared with recently reported results of a detailed molecular dynamics simulation using an explicit representation of the solvent, and with other available data. The study showed that the results obtained using the SCP--ISM are comparable to those of the explicit water calculation and compares favorably to the FDPB approach. Both transition states and energy minima show a high correlation (r > 0.98) with the results obtained in the explicit water analysis. The study of the misfolded structures of proteins comprised the analysis of three standard decoy sets, namely, the EMBL, Park and Levitt, and Baker's CASP3 sets. In all cases the SCP--ISM discriminated well the native structures of the proteins, and the best-predicted structures were always near-native (cRMSD approximately 2 A).     

Long time dynamics of Met-enkephalin: comparison of explicit and implicit solvent models

Met-enkephalin is one of the smallest opiate peptides. Yet, its dynamical structure and receptor docking mechanism are still not well understood. The conformational dynamics of this neuron peptide in liquid water are studied here by using all-atom molecular dynamics (MD) and implicit water Langevin dynamics (LD) simulations with AMBER potential functions and the three-site transferable intermolecular potential (TIP3P) model for water. To achieve the same simulation length in physical time, the full MD simulations require 200 times as much CPU time as the implicit water LD simulations. The solvent hydrophobicity and dielectric behavior are treated in the implicit solvent LD simulations by using a macroscopic solvation potential, a single dielectric constant, and atomic friction coefficients computed using the accessible surface area method with the TIP3P model water viscosity as determined here from MD simulations for pure TIP3P water. Both the local and the global dynamics obtained from the implicit solvent LD simulations agree very well with those from the explicit solvent MD simulations. The simulations provide insights into the conformational restrictions that are associated with the bioactivity of the opiate peptide dermorphin for the delta-receptor.     

Hydrogen exchange and the dynamic structure of proteins

Summary In native proteins, buried, labile protons undergo isotope exchange with solvent hydrogens, but the kinetics of exchange are markedly slower than in unfolded polypeptides. This indicates that, whereas buried protein atoms are shielded from solvent, the protein fluctuates around the time average structure and occasionally exposes buried sites to solvent. Generally, hydrogen exchange studies are designed to characterize the nature of the fluctuations between conformational substates, to monitor the shift in conformational equilibria among protein substates due to ligand binding or other factors, or to monitor the major cooperative denaturation transition. In this article, we review the recent reports of hydrogen exchange in proteins, focusing on recent advances in methodology, especially with regard to the implications of the results for the mechanism of hydrogen exchange in folded proteins.     

Helix-coil transitions of a polypeptide in a two-component solvent

A microscopic model is considered of a helix-coil transition of polypeptides in a two-component solvent one of whose components competes for the formation of hydrogen bonds with the peptide group. It is shown that by a redetermination of the temperature parameter the model is reduced to a polypeptide chain without the solvent. Behavior of the transition parameters is calculated in relation to the solvent concentration competing for the formation of hydrogen bonds at different parameters of polypeptide-solvent interaction.     

A solvent model for simulations of peptides in bilayers. I. Membrane-promoting alpha-helix formation

We describe an efficient solvation model for proteins. In this model atomic solvation parameters imitating the hydrocarbon core of a membrane, water, and weak polar solvent (octanol) were developed. An optimal number of solvation parameters was chosen based on analysis of atomic hydrophobicities and fitting experimental free energies of gas-cyclohexane, gas-water, and octanol-water transfer for amino acids. The solvation energy term incorporated into the ECEPP/2 potential energy function was tested in Monte Carlo simulations of a number of small peptides with known energies of bilayer-water and octanol-water transfer. The calculated properties were shown to agree reasonably well with the experimental data. Furthermore, the solvation model was used to assess membrane-promoting alpha-helix formation. To accomplish this, all-atom models of 20-residue homopolypeptides-poly-Leu, poly-Val, poly-Ile, and poly-Gly in initial random coil conformation-were subjected to nonrestrained Monte Carlo conformational search in vacuo and with the solvation terms mimicking the water and hydrophobic parts of the bilayer. All the peptides demonstrated their largest helix-forming tendencies in a nonpolar environment, where the lowest-energy conformers of poly-Leu, Val, Ile revealed 100, 95, and 80% of alpha-helical content, respectively. Energetic and conformational properties of Gly in all environments were shown to be different from those observed for residues with hydrophobic side chains. Applications of the solvation model to simulations of peptides and proteins in the presence of membrane, along with limitations of the approach, are discussed.     

Protein molecular dynamics with the generalized Born/ACE solvent model

Implicit solvent models are increasingly important for the study of proteins in aqueous solution. Here, the generalized Born (GB) solvent polarization model as implemented in the analytical ACE potential [Schaefer and Karplus (1996) J Phys Chem 100:1578] is used to perform molecular dynamics simulations of two small, homologous proteins: the immunoglobulin-binding domain of streptococcal protein G and the Ras binding domain of Raf. Several model parameterizations are compared through more than 60 ns of simulation. Results are compared with two simpler solvent models-an accessible surface area model and a distant-dependent dielectric model, with finite-difference Poisson calculations, with existing explicit solvent simulations, and with experimental data. The simpler models yield stable but distorted structures. The best GB/ACE implementation uses a set of atomic Voronoi volumes reported recently, obtained by averaging over a large database of crystallographic protein structures. A 20% reduction is applied to the volumes, compensating in an average sense for an excessive de-screening of individual charges inherent in the ACE self-energy and for an undersolvation of dipolar groups inherent in the GB screening function. This GB/ACE parameterization yields stable trajectories on the 0.5-1-ns time scale that deviate moderately (approximately 1.5-2.5 A) from the X-ray structure, reproduce approximately the surface distribution of charged, polar, and hydrophobic groups, and reproduce accurately backbone flexibility as measured by amide NMR-order parameters. Over longer time scales (1.5-3 ns), some of the protein G runs escape from the native energy basin and deviate strongly (3 A) from the native structure. The conformations sampled during the transition out of the native energy basin are overstabilized by the GB/ACE solvation model, as compared with a numerical treatment of the full dielectric continuum model.