Macromolecular solvation energies derived from small molecule crystal morphology.

The morphology of small molecule crystals provides a model for evaluating surface solvation energies in a system with similar packing density to that observed for amino acid residues in proteins. The solvation energies associated with the transfer of methylene and carboxyl groups between vacuum and aqueous phases are estimated to be approx. $40 and -260 cal/A2, respectively, from an analysis of the morphology of succinic acid crystals. These solvation energies predict values for contact angles in reasonable agreement with measurements determined from macroscopic monolayer surfaces. Transfer free energies between vapor and water phases for a series of carboxylic acids are also predicted reasonably well by these solvation energies, provided the surface exposure of different groups is quantitated with the molecular surface area rather than the more traditional accessible surface area. In general, molecular surfaces and molecular surface areas are seen to have important advantages for characterizing the structure and energetics of macromolecular surfaces. Crystal faces of succinic acid with the lowest surface energies in aqueous solution are characteristically smooth. Increasing surface roughness and apolarity are associated with higher surface energies, which suggests an approach for modifying the surface properties of proteins and other macromolecules.     

Estimation of the maximum change in stability of globular proteins upon mutation of a hydrophobic residue to another of smaller size.

Although the hydrophobic effect is generally considered to be one of the most important forces in stabilizing the folded structure of a globular protein molecule, there is a lack of consensus on the precise magnitude of this effect. The magnitude of the hydrophobic effect is most directly measured by observing the change in stability of a protein molecule when an internal hydrophobic residue is mutated to another of smaller size. Results of such measurements have, however, been confusing because they vary greatly and are generally considerably larger than expected from the transfer free energies of corresponding small molecules. In this article, a thermodynamic argument is presented to show (1) that the variation is mainly due to that in the flexibility of the protein molecule at the site of mutation, (2) that the maximum destabilization occurs when the protein at the site of mutation is rigid, in which case the value of the destabilization is approximately given by the work of cavity formation in water, and (3) that the transfer free energy approximately gives the minimum of the range of variations. The best numerical agreements between the small molecule and the protein systems are obtained when the data from the small molecule system are expressed as the molarity-based standard free energies without other corrections.     

Hydration and conformational equilibria of simple hydrophobic and amphiphilic solutes.

We consider whether the continuum model of hydration optimized to reproduce vacuum-to-water transfer free energies simultaneously describes the hydration free energy contributions to conformational equilibria of the same solutes in water. To this end, transfer and conformational free energies of idealized hydrophobic and amphiphilic solutes in water are calculated from explicit water simulations and compared to continuum model predictions. As benchmark hydrophobic solutes, we examine the hydration of linear alkanes from methane through hexane. Amphiphilic solutes were created by adding a charge of +/-1e to a terminal methyl group of butane. We find that phenomenological continuum parameters fit to transfer free energies are significantly different from those fit to conformational free energies of our model solutes. This difference is attributed to continuum model parameters that depend on solute conformation in water, and leads to effective values for the free energy/surface area coefficient and Born radii that best describe conformational equilibrium. In light of these results, we believe that continuum models of hydration optimized to fit transfer free energies do not accurately capture the balance between hydrophobic and electrostatic contributions that determines the solute conformational state in aqueous solution.     

Stability scale and atomic solvation parameters extracted from 1023 mutation experiments

The stability scale of 20 amino acid residues is derived from a database of 1023 mutation experiments on 35 proteins. The resulting scale of hydrophobic residues has an excellent correlation with the octanol-to-water transfer free energy corrected with an additional Flory-Huggins molar-volume term (correlation coefficient r = 0.95, slope = 1.05, and a near zero intercept). Thus, hydrophobic contribution to folding stability is characterized remarkably well by transfer experiments. However, no corresponding correlation is found for hydrophilic residues. Both the hydrophilic portion and the entire scale, however, correlate strongly with average burial accessible surface (r = 0.76 and 0.97, respectively). Such a strong correlation leads to a near uniform value of the atomic solvation parameters for atoms C, S, O/N, O(-0.5), and N(+0.5,1). All are in the range of 12-28 cal x mol(-1) A(-2), close to the original estimate of hydrophobic contribution of 25-30 cal x mol(-1) A(-2) to folding stability. Without any adjustable parameters, the new stability scale and new atomic solvation parameters yielded an accurate prediction of protein-protein binding free energy for a separate database of 21 protein-protein complexes (r = 0.80 and slope = 1.06, and r = 0.83 and slope = 0.93, respectively).     

Intermolecular interactions between protein and other molecules including hydration effects

The structural aspects of protein functions, e.g., molecular recognition such as enzyme-substrate and antibody-antigen interactions, are elucidated in terms of dehydration and atomic interactions. When a protein interacts with some target molecule, water molecules at the interacting regions of both molecules are removed, with loss of the hydration free energy, but gaining atomic interactions between atoms of the contact sites in both molecules. The free energies of association originating from the dehydration and interactions between the atoms can be computed from changes in the accessible surface areas of the atoms involved. The free energy due to interactions between atomic groups at the contact sites is estimated as the sum of those estimated from the changes in the accessible surface area of 7 atomic groups, assuming that the interactions are proportional to the change of the area. The chain enthalpies and entropies evaluated from experimental thermodynamic properties and hydration quantities at the standard temperature for 10 proteins were available to determine the proportional constants for the atomic groups. This method was applied to the evaluation of association constants for the dimerization of proteins and the formation of proteolytic enzyme-inhibitor complexes, and the computed constants were in agreement with the experimental ones. However, the method is not accurate enough to account quantitatively for the change in the thermal stability of mutants of T4 lysozyme. Nevertheless, this method provides a way to elucidate the interactions between molecules in solution.     

Physico-chemical surface characteristics and adhesive properties of Streptococcus salivarius strains with defined cell surface structures

Physico-chemical surface characteristics and adhesive properties of a series of mutants of Streptococcus salivarius HB with defined cell surface structures were determined. Zeta potentials showed no relation either with the presence or absence of specific antigens on the bacterial cell surface, or with the adhesive properties of the cells. Hydrophobicity was assessed by surface free energy determination from measured contact angles, by adsorption to hexadecane and by hydrophobic interaction chromatography. Generally, the progressive removal of fibril subclasses from the cell surface resulted in a reduced hydrophobicity. However, specific fibrillar subclasses appeared to contribute to surface hydrophobicity to widely different extents. Bacterial adhesion to polymethylmethacrylate increased with increasing hydrophobicity of the mutants. However, adhesion to a more complex biological substratum, such as saliva-coated hydroxyapatite, correlated only partly with hydrophobicity. The organism, deprived of most of its fibrillar surface structures, clearly showed the least adhesion to hydrophobic ligands, to both polymethylmethacrylate and saliva-coated hydroxyapatite, and had a significantly higher surface free energy than the other mutants and the parent strain.     

Lipophorin transport of hydrocarbon during early vitellogenesis in the silkworm,Bombyx mori

Lipophorin transports the hydrophobic molecule from origin to destination in time specific manner. Here, we investigate the hydrocarbon composition in the lipophorin during day 2 of pupal silkworm, Bombyx mori. Lipophorin was isolated from hemolymph by immunoprecipitation; lipid extracted and analyzed in GC-MS, resulting in seventeen compounds including eight hydrocarbons. Which were searched with the Pherobase (Pheromone database) and functional roles analysed. All hydrocarbons denoted as a pheromone except pentatriacontane in lepidopteron insects. Other hand, hydrocarbons such as hexadecane, nonadecane, undecane and hexacosane specifically refer as an attractant, additionally heptacosane, octacosane and docosane indicate as an allomone in non-lepidopteron insects. As well as, docosane and undecane perform as kairomone. Identified pheromone interaction with lipophorin was analysed by molecular docking and shows the best binding score. All hydrocarbons bound in a lipid binding pocket, most of these sharing the same binding sites for hydrophobic interaction and hydrogen bonding. Overall findings elucidated that lipophorin associated with different hydrocarbons by hydrogen bonds and hydrophobic interactions, and each of the hydrocarbon having various functional roles.     

Surface free energy and interaction of Staphylococcus epidermidis with biomaterials

The adhesion of twenty nine Staphylococcus epidermidis strains to teflon, polyethylene, polycarbonate and bovine pericardium was studied in vitro and examined in relation to the surface free energies of both bacteria and biomaterials. All S. epidermidis strains had similar surface free energies, close to that of water, and adhered better to the materials with analogous surface free energies. There was a significant correlation (Kendall's Tau B = 1000) of biomaterial's surface free energy with the number of adhering bacteria. This correlation is inverse (Kendall's Tau B = -1000) when surface hydrophobicity is considered instead of surface free energy. This indicates that in Staphylococcus epidermidis adherence to biomaterials is inversely correlated to the surface hydrophobicity of the last, being so just the opposite of that occurring with other bacteria.     

An extended aqueous solvation model based on atom-weighted solvent accessible surface areas: SAWSA v2.0 model

A new method is proposed for calculating aqueous solvation free energy based on atom-weighted solvent accessible surface areas. The method, SAWSA v2.0, gives the aqueous solvation free energy by summing the contributions of component atoms and a correction factor. We applied two different sets of atom typing rules and fitting processes for small organic molecules and proteins, respectively. For small organic molecules, the model classified the atoms in organic molecules into 65 basic types and additionally. For small organic molecules we proposed a correction factor of hydrophobic carbon to account for the aggregation of hydrocarbons and compounds with long hydrophobic aliphatic chains. The contributions for each atom type and correction factor were derived by multivariate regression analysis of 379 neutral molecules and 39 ions with known experimental aqueous solvation free energies. Based on the new atom typing rules, the correlation coefficient (r) for fitting the whole neutral organic molecules is 0.984, and the absolute mean error is 0.40 kcal mol^–1, which is much better than those of the model proposed by Wang et al. and the SAWSA model previously proposed by us. Furthermore, the SAWSA v2.0 model was compared with the simple atom-additive model based on the number of atom types (NA). The calculated results show that for small organic molecules, the predictions from the SAWSA v2.0 model are slightly better than those from the atom-additive model based on NA. However, for macromolecules such as proteins, due to the connection between their molecular conformation and their molecular surface area, the atom-additive model based on the number of atom types has little predictive power. In order to investigate the predictive power of our model, a systematic comparison was performed on seven solvation models including SAWSA v2.0, GB/SA_1, GB/SA_2, PB/SA_1, PB/SA_2, AM1/SM5.2R and SM5.0R. The results showed that for organic molecules the SAWSA v2.0 model is better than the other six solvation models. For proteins, the model classified the atoms into 20 basic types and the predicted aqueous free energies of solvation by PB/SA were used for fitting. The solvation model based on the new parameters was employed to predict the solvation free energies of 38 proteins. The predicted values from our model were in good agreement with those from the PB/SA model and were much better than those given by the other four models developed for proteins.Figure The definition of hydrophobic carbons. Here CA, CB and CD are three carbon atoms; X represents a heteroatom. According to our definition, CB is a hydrophobic carbon, CA is not a hydrophobic carbon because a heteroatom is within four atoms and CD is not a hydrophobic carbon because CD is sp²- hydridized and in a six-member ring.Electronic Supplementary Material Supplementary material is available for this article at     

Hydrophobic regions on protein surfaces. Derivation of the solvation energy from their area distribution in crystallographic protein structures.

For the first time, a direct approach for the derivation of an atomic solvation parameter from macromolecular structural data alone is presented. The specific free energy of solvation for hydrophobic surface regions of proteins is delineated from the area distribution of hydrophobic surface patches. The resulting value is 18 cal/(mol.A2), with a statistical uncertainty of +/-2 cal/mol.A2) at the 5% significance level. It compares favorably with the parameters for carbon obtained by other authors who use the the crystal geometry of succinic acid or energies of transfer from hydrophobic solvent to water for small organic compounds. Thus, the transferability of atomic solvation parameters for hydrophobic atoms to macromolecules has been directly demonstrated. A careful statistical analysis demonstrates that surface energy parameters derived from thermodynamic data of protein mutation experiments are clearly less confident.     

A novel method reveals that solvent water favors polyproline II over beta-strand conformation in peptides and unfolded proteins: conditional hydrophobic accessible surface area (CHASA)

In aqueous solution, the ensemble of conformations sampled by peptides and unfolded proteins is largely determined by their interaction with water. It has been a long-standing goal to capture these solute-water energetics accurately and efficiently in calculations. Historically, accessible surface area (ASA) has been used to estimate these energies, but this method breaks down when applied to amphipathic peptides and proteins. Here we introduce a novel method in which hydrophobic ASA is determined after first positioning water oxygens in hydrogen-bonded orientations proximate to all accessible peptide/protein backbone N and O atoms. This conditional hydrophobic accessible surface area is termed CHASA. The CHASA method was validated by predicting the polyproline-II (P(II)) and beta-strand conformational preferences of non-proline residues in the coil library (i.e., non-alpha-helix, non-beta-strand, non-beta-turn library derived from X-ray elucidated structures). Further, the method successfully rationalizes the previously unexplained solvation energies in polyalanyl peptides and compares favorably with published experimentally determined P(II) residue propensities. We dedicate this paper to Frederic M. Richards.     

Anti-cooperativity and cooperativity in hydrophobic interactions: Three-body free energy landscapes and comparison with implicit-solvent potential functions for proteins

Potentials of mean force (PMFs) of three-body hydrophobic association are investigated to gain insight into similar processes in protein folding. Free energy landscapes obtained from explicit simulations of three methanes in water are compared with that predicted by popular implicit-solvent effective potentials for the study of proteins. Explicit-water simulations show that for an extended range of three-methane configurations, hydrophobic association at 25 degrees C under atmospheric pressure is mostly anti-cooperative, that is, less favorable than if the interaction free energies were pairwise additive. Effects of free energy nonadditivity on the kinetic path of association and the temperature dependence of additivity are explored by using a three-methane system and simplified chain models. The prevalence of anti-cooperativity under ambient conditions suggests that driving forces other than hydrophobicity also play critical roles in protein thermodynamic cooperativity. We evaluate the effectiveness of several implicit-solvent potentials in mimicking explicit water simulated three-body PMFs. The favorability of the contact free energy minimum is found to be drastically overestimated by solvent accessible surface area (SASA). Both the SASA and a volume-based Gaussian solvent exclusion model fail to predict the desolvation barrier. However, this barrier is qualitatively captured by the molecular surface area model and a recent "hydrophobic force field." None of the implicit-solvent models tested are accurate for the entire range of three-methane configurations and several other thermodynamic signatures considered.     

抗疟药物氯奎、阿的平、四氢-9-氨基(口了)啶与双链小牛胸腺DNA的结合

本文用体相微量量热计所得数据,估算了两种抗疟药物(antimalarial)分子和两种结构上相似的分子与DNA结合时的标准结合热焓。根据在不同离子强度下测定的表观结合常数获得了热力学结合常数。根据这些数据以及标准结合热焓计算出标准结合自由能、标准结合熵。结果发现凡与DNA结合的分子,具有线性芳环结构的,结合时主要取决于热焓的大小。具有脂肪链或脂肪环结构的,结合时主要取决于熵变。     

Interfacial free energies of intact and reconstituted erythrocyte surfaces: Implications for biological adhesion

Model cell surfaces consisting of phospholipids or phospholipids and the erythrocyte membrane glycoprotein glycophorin have been formed at an oil/water interface. Interfacial free energies have been estimated from surface wetting by both hydrophobic and hydrophilic test droplets on both the model surfaces and on intact erythrocytes. The use of a dense fluorocarbon oil to form the oil/water interface facilitates analysis by minimising surface deformation by the test drop. Hydrophobic test droplets (polar hydrocarbon oils) show increasing contact angles (decreasing wetting) with increasing hydrophilicity (decreasing interfacial free energy) of the model interface. Hydrophilic test droplets (phase separated aqueous polymer systems) show the opposite behaviour, spreading more as the interfacial free energy is decreased. Both systems give similar estimates of the interfacial free energy. Glycophorin reproduces the wetting properties of intact cell surfaces by reducing the lipid-water interfacial free energy from 5·10^?3 J·m^?2 to 1·10^?6 J·m^?2. From molecular considerations it is concluded that ‘cell surface free energy’ is an ambiguous term; its magnitude depends on the location of the interface in question. Thus, in a thermodynamic analysis of interactions at biosurfaces (such as cellular adhesion, chemotaxis or membrane fusion), the interfacial free energies may vary by more than three orders of magnitude depending on the location of the particular interface.     

Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons.

We demonstrate in this work that the surface tension, water-organic solvent, transfer-free energies and the thermodynamics of melting of linear alkanes provide fundamental insights into the nonpolar driving forces for protein folding and protein binding reactions. We first develop a model for the curvature dependence of the hydrophobic effect and find that the macroscopic concept of interfacial free energy is applicable at the molecular level. Application of a well-known relationship involving surface tension and adhesion energies reveals that dispersion forces play little or no net role in hydrophobic interactions; rather, the standard model of disruption of water structure (entropically driven at 25 degrees C) is correct. The hydrophobic interaction is found, in agreement with the classical picture, to provide a major driving force for protein folding. Analysis of the melting behavior of hydrocarbons reveals that close packing of the protein interior makes only a small free energy contribution to folding because the enthalpic gain resulting from increased dispersion interactions (relative to the liquid) is countered by the freezing of side chain motion. The identical effect should occur in association reactions, which may provide an enormous simplification in the evaluation of binding energies. Protein binding reactions, even between nearly planar or concave/convex interfaces, are found to have effective hydrophobicities considerably smaller than the prediction based on macroscopic surface tension. This is due to the formation of a concave collar region that usually accompanies complex formation. This effect may preclude the formation of complexes between convex surfaces.     

Energetics of protein folding

The energetics of protein folding determine the 3D structure of a folded protein. Knowledge of the energetics is needed to predict the 3D structure from the amino acid sequence or to modify the structure by protein engineering. Recent developments are discussed: major factors are reviewed and auxiliary factors are discussed briefly. Major factors include the hydrophobic factor (burial of non-polar surface area) and van der Waals interactions together with peptide hydrogen bonds and peptide solvation. The long-standing model for the hydrophobic factor (free energy change proportional to buried non-polar surface area) is contrasted with the packing-desolvation model and the approximate nature of the proportionality between free energy and apolar surface area is discussed. Recent energetic studies of forming peptide hydrogen bonds (gas phase) are reviewed together with studies of peptide solvation in solution. Closer agreement is achieved between the 1995 values for protein unfolding enthalpies in vacuum given by Lazaridis-Archontis-Karplus and Makhatadze-Privalov when the solvation enthalpy of the peptide group is taken from electrostatic calculations. Auxiliary factors in folding energetics include salt bridges and side-chain hydrogen bonds, disulfide bridges, and propensities to form alpha-helices and beta-structure. Backbone conformational entropy is a major energetic factor which is discussed only briefly for lack of knowledge.     

A CFF 91-based Continuum Solvation Model: Solvation Free Energies of Small Organic Molecules and Conformations of the Alanine Dipeptide in Solution

Abstract

For molecular mechanics simulations of solvated molecules, it is important to use a consistent approach for calculating both the force field energy and the solvation free energy. A continuum solvation model based upon the atomic charges provided with the CFF91 force field is derived. The electrostatic component of the solvation free energy is described by the Poisson-Bolzmann equation while the nonpolar comonent of the solvation energy is assumed to be proportional to the solvent accessible surface area of the solute. Solute atomic radii used to describe the interface between the solute and solvent are fitted to reproduce the energies of small organic molecules. Data for 140 compounds are presented and compared to experiment and to the results from the well-characterized quantum mechanical solvation model AM1-SM2. In particular, accurate results are obtained for amino acid neutral analogues (mean unsigned error of 0.3 kcal/mol). The conformational energetics of the solvated alanine dipeptide is discussed.     

Cell Surface Measurements in Hydrocarbon and Carbohydrate Fermentations

Acinetobacter calcoaceticus was grown in 11-liter batch fermentations with hexadecane or sodium citrate as the sole source of carbon. Surface and interfacial tension measurements of the microbial broth indicated that surface-active compounds were being produced only during growth on the hydrocarbon substrate. Contact angle measurements of an aqueous drop on a smooth lawn of cells in a hexadecane bath indicated a highly hydrophobic surface of the cells in the initial stages of the hydrocarbon fermentation (120° contact angle). At this stage, the entire cell population was bound to the hydrocarbon-aqueous interface. The contact angle dropped rapidly to approximately 45° after 14 h into the fermentation. This coincided with a shift of the cell population to the aqueous phase. Thus, the cells demonstrated more hydrophilic characteristics in the later stages of the fermentation. Contact angles on cells grown on sodium citrate ranged from 18 to 24° throughout the fermentation. The cells appear to be highly hydrophilic during growth on a soluble substrate. From the contact angle and aqueous-hydrocarbon interfacial tension, the surface free energy of the cells was calculated along with the cell-aqueous and cell-hydrocarbon interfacial tension. The results of these measurements were useful in quantitatively evaluating the hydrophobic nature of the cell surface during growth on hydrocarbons and comparing it with the hydrophilic nature of the cell surface during growth on a soluble substrate.