Solvation thermodynamics of biopolymers. II. Correlations between functional groups

Free-energy decomposition of salt effects on the solubilities of small molecules and the role of excluded-volume effects

The roles of cations and anions are different in the perturbation on solvation, and thus, the analyses of the separated contributions from cations and anions are useful to establish molecular pictures of ion-specific effects. In this work, we investigate the effects of cations, anions, and water separately in the solvation of n-alcohols and n-alkanes by free-energy decomposition. By utilising energy-representation theory of solvation, we address the contributions arising from the direct solute-solvent interactions and the excluded-volume effects. It is found that the change in solvation of n-alcohols and n-alkanes upon addition of salt depends primarily on the anion species. The direct interaction between the anion and solute is in agreement with the Setschenow coefficient in terms of the ranking of salting-in and salting-out for n-alkanes, which corresponds to the extent of accumulation of the anion on the solute surface. For each of the n-alcohols and n-alkanes examined, the excluded-volume component in the Setschenow coefficient is well correlated to the (total) Setschenow coefficient when the salt effects are concerned. The ranking of the excluded-volume component in the variation of the salt species is parallel to the water contribution, which is correlated further to the change in the water density upon the addition of the salt.

On the driving forces for protein-protein association

We analyze all the contributions to the standard free energy of association between two proteins. We find that the solvent-induced interactions between two (or more) hydrophilic groups can turn a highly unfavorable process of association into a highly favorable one. We therefore argue that in contrast to the generally accepted view, it is the hydrophilic rather than the hydrophobic effect that is dominant in biochemical processes such as protein-protein association, protein folding, and protein binding to DNA.

Osmolyte-induced changes in protein conformational equilibria

Examining solute-induced changes in protein conformational equilibria is a long-standing method for probing the role of water in maintaining protein stability. Interpreting the molecular details governing the solute-induced effects, however, remains controversial. We present experimental and theoretical data for osmolyte-induced changes in the stabilities of the A and N states of yeast iso-1-ferricytochrome c. Using polyol osmolytes of increasing size, we observe that osmolytes alone induce A-state formation from acid-denatured cytochrome c and N state formation from the thermally denatured protein. The stabilities of the A and N states increase linearly with osmolyte concentration. Interestingly, osmolytes stabilize the A state to a greater degree than the N state. To interpret the data, we divide the free energy for the reaction into contributions from nonspecific steric repulsions (excluded volume effects) and from binding interactions. We use scaled particle theory (SPT) to estimate the free energy contributions from steric repulsions, and we estimate the contributions from water-protein and osmolyte-protein binding interactions by comparing the SPT calculations to experimental data. We conclude that excluded volume effects are the primary stabilizing force, with changes in water-protein and solute-protein binding interactions making favorable contributions to stability of the A state and unfavorable contributions to the stability of the N state. The validity of our interpretation is strengthened by analysis of data on osmolyte-induced protein stabilization from the literature, and by comparison with other analyses of solute-induced changes in conformational equilibria.

Analysis of protein-protein interactions and the effects of amino acid mutations on their energetics. The importance of water molecules in the binding epitope

A modeling analysis has been conducted to assess the determinants of binding strength and specificity for three crystal complexes; the anti-hen egg white lysozyme antibody D1.3 complexed with hen egg white lysozyme (HEL), the D1.3 antibody complexed with the anti-lysozyme antibody E5.2, and barnase complexed with barstar. The strengths of individual binding components within these interfaces are evaluated using a model of binding free energy that is based on pairwise surface preferences. In all cases the energetics of binding are dominated by a relatively small number of interfacial residues that define the binding epitope. A precise geometric arrangement of these residues was not found; they were either localized to one region, or distributed throughout the binding interface. Surprisingly, interfacial crystal water molecules were calculated to contribute around 25% of the total calculated binding strength. Theoretical alanine mutations were completed by atomic deletions of the wild-type complexes. Strong correlations were observed between the calculated changes in binding free energy (deltadeltaG(calculated)) and the experimental values (deltadeltaG(observed)) for all but three of the 30 single residue mutations in the D1.3-HEL, D1.3-E5.2 and barnase-barstar systems and for all of the double mutations in the barnase-barstar system. This analysis finds that the observed differences in binding strength are consistent with a model that accounts for the changes in binding energy from the direct contacts between each member of the complex and indirect changes due to released crystallographic water molecules that are near the mutation site. The observed energy changes for double mutations in the barnase-barstar system is fully accounted for by considering water molecules bound jointly by each member of the complex.

A preference-based free-energy parameterization of enzyme-inhibitor binding. Applications to HIV-1-protease inhibitor design

The interface between protein receptor-ligand complexes has been studied with respect to their binary interatomic interactions. Crystal structure data have been used to catalogue surfaces buried by atoms from each member of a bound complex and determine a statistical preference for pairs of amino-acid atoms. A simple free energy model of the receptor-ligand system is constructed from these atom-atom preferences and used to assess the energetic importance of interfacial interactions. The free energy approximation of binding strength in this model has a reliability of about +/- 1.5 kcal/mol, despite limited knowledge of the unbound states. The main utility of such a scheme lies in the identification of important stabilizing atomic interactions across the receptor-ligand interface. Thus, apart from an overall hydrophobic attraction (Young L, Jernigan RL, Covell DG, 1994, Protein Sci 3:717-729), a rich variety of specific interactions is observed. An analysis of 10 HIV-1 protease inhibitor complexes is presented that reveals a common binding motif comprised of energetically important contacts with a rather limited set of atoms. Design improvements to existing HIV-1 protease inhibitors are explored based on a detailed analysis of this binding motif.

Stabilization of intermediate density states in globular proteins by homogeneous intramolecular attractive interactions

On-lattice simulations of two-dimensional self-avoiding chains subject to homogeneous intramolecular attractive interactions were performed as a model for studying various density regimes in globular proteins. For short chains of less than 15 units, all conformations were generated and classified by density. The range of intramolecular interactions was found to increase uniformly with density, and the average number of topological contacts is directly proportional to density. The uniform interaction energy increases the probability of high density states but does not necessarily lead to dominance of the highest density state. Typically, several large peaks appear in the probability distribution of packing densities, their location and amplitude being determined by the balance between entropic effects enhancing more expanded conformations and attractive interactions favoring compact forms. Also, the homogeneous interaction energy affects the distribution of most probable interacting points in favor of the longer range interactions over the short range ones, but in addition it introduces some more detailed preferences even among short range interactions. There are some implications about the characteristics of the intermediate density states and also for the likelihood that the native state does not correspond completely to the lowest energy conformation.

Solvation effects on the sequence variability of DNA double helical conformations

The role of solvation on the sequence dependent conformational variabilities in DNA has been studied by calculating hydration free energies from solvent accessible surface areas for several base steps, as a function of various helical parameters, roll, twist and propeller twist. The results of roll calculations suggest opposite trends for AA and GG steps, with the former tending to have a compressed minor groove and the latter a compressed major groove. These trends are consistent with the experimental findings on sequence preferences and the nature of anisotropic bending of DNA observed in nucleosomes (Drew, H.R. and Travers, A.A., J. Mol. Biol. 186, 773-790 (1985); Satchwell, S.C., Drew, H.R. and Travers, A.A., J. Mol. Biol. 191, 659-675 (1986)) and CAP-DNA interactions (Gartenberg, M.R. and Crothers, D.M., Nature 333, 824-829, (1988)). Solvation energy profiles also indicate preferences for the base pairs in GG and AA steps to adopt low and high propeller twists, respectively. Such agreements may either reflect a coincidence of solvation effects with other energy terms or a dominance of solvent effects. The results are discussed in the context of the crystallographic observations of structural tendencies.