Computing the Thermodynamic Contributions of Interfacial Water

Accurateprediction of hydration free energies is a key objectiveof any free energy method that is applied to modeling and understandinginteractions in the aqueous phase. Inhomogeneous fluid solvation theory(IFST) is a statistical mechanical method for calculating solvationfree energies by quantifying the effect of a solute acting as a perturbationto bulk water. IFST has found wide application in understanding hydrationphenomena in biological systems, but quantitative applications havenot been comprehensively assessed. In this study, we report the hydrationfree energies of six simple solutes calculated using IFST and independentlyusing free energy perturbation (FEP). This facilitates a validationof IFST that is independent of the accuracy of the force field. Theresults demonstrate that IFST shows good agreement with FEP, withan R2 coefficient of determination of0.99 and a mean unsigned difference of 0.7 kcal/mol. However, samplingis a major issue that plagues IFST calculations and the results suggestthat a histogram method may require prohibitively long simulationsto achieve convergence of the entropies, for bin sizes which effectivelycapture the underlying probability distributions. Results also highlightthe sensitivity of IFST to the reference interaction energy of a watermolecule in bulk, with a difference of 0.01 kcal/mol changing thepredicted hydration free energies by approximately 2.4 kcal/mol forthe systems studied here. One of the major advantages of IFST overperturbation methods such as FEP is that the systems are spatiallydecomposed to consider the contribution of specific regions to thetotal solvation free energies. Visualizing these contributions canyield detailed insights into solvation thermodynamics. An insightfrom this work is the identification and explanation of regions withunfavorable free energy density relative to bulk water. These regionscontribute unfavorably to the hydration free energy. Further workis necessary before IFST can be extended to yield accurate predictionsof binding free energies, but the work presented here demonstratesits potential.

Hydration sites are locations of interest to water and they can be used to classify the behavior of water around chemical motifs commonly found on the surface of proteins. Inhomogeneous fluid solvation theory (IFST) is a method for calculating hydration free-energy changes from molecular dynamics (MD) trajectories. In this paper, hydration sites are identified from MD simulations of 380 diverse protein structures. The hydration free energies of the hydration sites are calculated using IFST and distributions of these free-energy changes are analyzed. The results show that for some hydration sites near features conventionally regarded as attractive to water, such as hydrogen bond donors, the water molecules are actually relatively weakly bound and are easily displaced. We also construct plots of the spatial density of hydration sites with high, medium, and low hydration free-energy changes which represent weakly and strongly bound hydration sites. It is found that these plots show consistent features around common polar amino acids for all of the proteins studied.

Inhomogeneous solvation theory (IST) and classical density functional theory (DFT) each provide a framework for relating distribution functions of solutions to their thermodynamic properties. As reviewed in this work, both IST and DFT can be formulated in a way that use two "end point" simulations, one of the pure solvent and the other of the solution, to determine the solute chemical potential and other thermodynamic properties of the solution and of subvolumes in regions local to the solute containing hydrating waters. In contrast to IST, where expressions for the excess energy and entropy of solution are the object of analysis, in the DFT end point formulation of the problem, the solute-solvent potential of mean force (PMF) plays a central role. The indirect part of the PMF corresponds to the lowest order (1-body) truncation of the IST expression. Because the PMF is a free energy function, powerful numerical methods can be used to estimate it. We show that the DFT expressions for the solute excess chemical potential can be written in a form which is local, involving integrals only over regions proximate to the solute. The DFT end point route to estimating solvation free energies provides an alternative path to that of IST for analyzing solvation effects on molecular recognition and conformational changes in solution, which can lead to new insights. In order to illustrate the kind of information that is contained in the solute-solvent PMF, we have carried out simulations of β-cyclodextrin in water. This solute is a well studied "host" molecule to which "guest" molecules bind; host-guest systems serve as models for molecular recognition. We illustrate the range of values the direct and indirect parts of the solute-solvent PMF can have as a water molecule is brought to the interface of β-cyclodextrin from the bulk; we discuss the "competition" between these two terms, and the role it plays in molecular recognition.

We have developed SSTMap, a software package for mapping structural and thermodynamic water properties in molecular dynamics trajectories. The package introduces automated analysis and mapping of local measures of frustration and enhancement of water structure. The thermodynamic calculations are based on Inhomogeneous Fluid Solvation Theory (IST), which is implemented using both site-based and grid-based approaches. The package also extends the applicability of solvation analysis calculations to multiple molecular dynamics (MD) simulation programs by using existing cross-platform tools for parsing MD parameter and trajectory files. SSTMap is implemented in Python and contains both command-line tools and a Python module to facilitate flexibility in setting up calculations and for automated generation of large data sets involving analysis of multiple solutes. Output is generated in formats compatible with popular Python data science packages. This tool will be used by the molecular modeling community for computational analysis of water in problems of biophysical interest such as ligand binding and protein function.

Cytochrome c oxidase is a redox-driven proton pump that creates a membrane proton gradient responsible for driving ATP synthesis in aerobic cells. The crystal structure of the enzyme has been recently solved; however, the details of the mechanism of its proton pumping remain unknown. The enzyme internal water molecules play a key role in proton translocation through the enzyme. Here, we examine the thermodynamic properties of internal water in a hydrophobic cavity around the catalytic center of the enzyme. The crystal structure does not show any water molecules in this region; it is believed, however, that, since protons are delivered to the catalytic center, where the reduction of molecular oxygen occurs, at least some water molecules must be present there. The goal of the present study was to examine how many water molecules are present in the catalytic center cavity and why these water molecules are not observed in the crystal structure of the enzyme. The behavior of water molecules is discussed in the context of redox-coupled proton translocation in the enzyme.

We have solved the 2.0-A resolution crystal structures of four cavity-creating Ile/Leu-->Ala mutations in the hydrophobic core of barnase and compare and contrast the structural responses to mutation with those found for Leu-->Ala mutations in T4 lysozyme. First, there are rearrangements of structure of barnase that cause the cavities to collapse partly, and there is an approximately linear relationship between the changes in stability and the volume of the cavity similar to that found for the mutants of T4 lysozyme. Second, although it is currently accepted that hydrophobic cavities formed on the mutation of large hydrophobic side chains to smaller ones are not occupied by water molecules, we found a buried water molecule in the crystal structure of the barnase mutant Ile76-->Ala. A single hydrogen bond is formed between the water molecule and a polar atom, the carbonyl oxygen of Phe7, in the hydrophobic cavity that is formed on mutation. A survey of hydrophobic cavities produced by similar mutations in different proteins reveals that they all contain a proportion of polar atoms in their linings. The availability of such polar sites has implications for understanding folding pathways because a solvated core is presumed present in the transition state for folding and unfolding. Notably, the hydrogen bond between the cavity-water and the carbonyl group of Phe7 is also a marked early feature of very recent molecular dynamics simulations of barnase denaturation [Caflisch, A., & Karplus, M. (1995) J. Mol. Biol. 252, 672-708]. It is possible that cavities engineered into the hydrophobic cores of other proteins may contain water molecules, even though they cannot be detected by crystallographic analysis.

The superlubricity mechanism of phospholipid molecules on biological surfaces and interfaces has been receiving much attention. Since the superlubricity can be achieved with a phosphoric acid aqueous solution, the interaction of the phosphate group with the water molecule is considered to be the key to bio‐lubrication. However, no direct evidence has been offered to distinctly interpret the underlying mechanism of superlubricity, due to the limitations in the method for the detection of interfacial molecules, especially water molecules on the interface. By using sum‐frequency generation (SFG) vibrational spectroscopy, which is extremely sensitive to interfacial molecules, the authors were able to explore the underlying microscopic mechanism for superlubricity in a phosphoric acid system, which might be related to interfacial water molecules. By trapping the phosphoric acid aqueous solution between silicon nitride and silica surfaces, they discovered that phosphoric acid could exercise a great influence on the ordered structure of interfacial water molecules, contributing to SFG spectral changes in the broad O–H bond stretching region. This work directly revealed the interfacial interaction between water and phosphoric acid molecules in liquid superlubricity interfaces, which could shed new light on the microscopic mechanism of liquid superlubricity.

: We present the first experimental measurements of the orientation and hydrogen bonding character of interfacial water molecules in their gaseous state in coexistence with the bulk liquid water. These interfacial vapor state molecules are distinct from the surface free OH and the interfacial liquid state water molecules and show a preferred orientation with their hydrogen atoms directed towards the liquid surface. The goal to develop a molecular level picture of water orientation and bonding at this vapor-liquid boundary where liquid phase water molecules coexist with vapor phase molecules has fascinated scientists for decades. Whereas most theoretical and experimental studies in recent years are converging on a consistent description of interfacial water on the liquid side of the interface, there is considerable disparity in the theoretical description of water molecules on the vapor side. A primary factor in this lack of consensus is the paucity of available data that unequivocally measures the properties of these interfacial vapor state molecules. As with theoretical efforts in this area, the low density of these vapor state interfacial water molecules is experimentally problematic. In this paper we present the first vibrational spectroscopic measurements of interfacial water vapor species in coexistence with their liquid phase. These detected vapor state molecules have a preferred orientation relative to the surface plane and have minimal hydrogen bonding to adjacent water molecules as manifested in the energy and linewidth of the spectral OH stretching modes examined. These molecules are distinctly different than the water molecules with a dangling bond into the vapor phase, or water in the liquid portion of the interface where hydrogen bonding between water molecules is strong.

We report the structure and dynamics of layered water structure near a bilayer heterosurface using classical molecular dynamics simulations and network graph theory. The heterosurfaces of our choice are technologically essential and well-studied hexagonal boron nitride (h-BN) and graphitic carbon nitride (g-C3N4). Starting with the water density distribution profile, we have studied different hydrogen bondings (HBs) associated with distance and angle distributions and correlated them with the HB count, followed by the investigations of dynamic properties. We realize the oddity while corresponding to the tetrahedral order parameter (TOP), HB donor/acceptor count, and HB lifetime. A quantitative gap is observed between the TOP and HB counts, and we perceive another structural factor playing a significant role. We observe a 2D sheetlike arrangement of hydrogen-bonded water molecules, namely, 2D-HB, in the interfacial layer instead of 3D tetrahedral arrangements. 2D-HB qualitatively acts as a key descriptor of the hydrophobicity of the interface. The probability of higher TOP among the interfacial layer water molecules is less for h-BN compared to g-C3N4. However, the per-water HBs for both the heterosurfaces remain indistinguishable, implying the existence of another significant physical factor related to HB. Hence, 2D-HB serves as a deciding factor. In the case of h-BN, water molecules in the first layer form extended 2D sheets compared to the second and bulk, which is not a scenario for g-C3N4. Following the network graph theory, we calculated the temporal evolution of the maximum number of water molecules connected in a single network. The layer 1 water molecules have slower orientational dynamics, higher HB lifetime, and consequently slower translational diffusion than layer 2 and bulk water molecules. The experimental studies suggested that the contact angle of water on h-BN can vary from 61.4 to 85.8°, higher than that of g-C3N4, depending on the surface stacking, support material, and exposure to air, which effectively makes h-BN more hydrophobic compared to g-C3N4. The interfacial water molecules have a smaller HB lifetime and a faster diffusion coefficient than g-C3N4. The HB lifetime of water molecules in bulk is less than that in the interface, irrespective of the surface. A slower reorientation lifetime, that is, 2.69 ps, for g-C3N4 interfacial water molecules is observed versus 2.20 ps for h-BN. Our results agree with the experimental observations and can help to understand the hydrophobicity of other relevant materials.

Bacteriophage T4 deoxycytidylate hydroxymethylase (EC 2.1.2.8), a homodimer of 246-residue subunits, catalyzes hydroxymethylation of the cytosine base in deoxycytidylate (dCMP) to produce 5-hydroxymethyl-dCMP. It forms part of a phage DNA protection system and appears to function in vivo as a component of a multienzyme complex called deoxyribonucleoside triphosphate (dNTP) synthetase. We have determined its crystal structure in the presence of the substrate dCMP at 1.6 A resolution. The structure reveals a subunit fold and a dimerization pattern in common with thymidylate synthases, despite low (approximately 20%) sequence identity. Among the residues that form the dCMP binding site, those interacting with the sugar and phosphate are arranged in a configuration similar to the deoxyuridylate binding site of thymidylate synthases. However, the residues interacting directly or indirectly with the cytosine base show a more divergent structure and the presumed folate cofactor binding site is more open. Our structure reveals a water molecule properly positioned near C-6 of cytosine to add to the C-7 methylene intermediate during the last step of hydroxymethylation. On the basis of sequence comparison and crystal packing analysis, a hypothetical model for the interaction between T4 deoxycytidylate hydroxymethylase and T4 thymidylate synthase in the dNTP-synthesizing complex has been built.

Hydration plays critical role in protein structure, stability, dynamics and function. Recent advancements in high-resolution crystallography have provided a clearer understanding of the hydration patterns in proteins and their complexes with nucleic acids. The high level of detail allows to observe hydration patterns that were previously unresolved. Water-mediated specific protein interaction with DNA were initially discovered for E. coli the tryptophan repressor (TrpR) operator complex. Fixed water molecules are strategically positioned to mediate interactions between the repressor and the DNA bases. Here we report determination of high- resolution structures of TrpR and its complexes from Francisella tularensis including: aporepressor, complexes with L-Trp (activator), indole propionic acid (IPA) (inhibitor) and with specific F. tularensis trp operator. Structure analysis shows conservation of ligand binding and specific repressor-DNA interactions, including water-mediated and suggests that the majority of these interactions may be preserved across TrpR family. This research highlights the crucial role that water molecules play in mediating interactions between the repressor protein and the DNA bases that define the operator's identity. Bound water molecules are likely underrepresented in models of the interface of many specific biological complexes either because of spatial disorder in the crystal or inadequate resolution. These water molecules are not just passive participants; they are actively involved in the stereospecific recognition process, forming a dynamic and reversible network that extends the functional surfaces of the macromolecules involved. While this study focuses on the TrpR/operator system, the findings may have broader implications for understanding other protein-nucleic acid interactions and macromolecular complexes.

The solvation of nonpolar molecules in water and that in simple liquids are compared and contrasted. First, solvation thermodynamics is reviewed in a way that focuses on how the enthalpy and entropy of solvation depend on the choice of microscopic volume change v in the solvation process--including special choices v being zero (fixed-volume condition) and v being the partial molecular volume of a solute molecule (fixed-pressure condition)--and how the solvation quantities are related with temperature derivatives of the solvation free energy. Second, the solvation free energy and the solvation enthalpy of a Lennard-Jones (LJ) atom in model water are calculated in the parameter space representing the solute size and the strength of the solute-solvent interaction, and the results are compared with those for an LJ atom in the LJ solvent. The solvation diagrams showing domains of different types of solvation in the parameter space are obtained both for the constant-volume condition and for the constant-pressure condition. Similarities between water and the simple liquid are found when the constant-volume solvation is considered while a significant difference manifests itself in the fixed-pressure solvation. The domain of solvation of hydrophobic character in the parameter space is large in the constant-volume solvation both for water and for the simple liquid. When switched to the constant-pressure condition accompanying a microscopic volume change, the hydrophobic domain remains large in water but it becomes significantly small in the simple liquid. The contrasting results are due to the smallness of the thermal pressure coefficient of water at low temperatures.

The structural properties and electronic structures of pentacoordinated uranyl complexes belonging to the [UO(2)F(n)(H(2)O)(5-n)](2-n) series have been studied in the gas and aqueous phases using density functionals with relativistic pseudopotentials and all-electron basis sets in the gas-phase calculations in combination with COSMO in the aqueous phase. In addition, the conformational orientation and structural and electronic properties of [UO(2)F(5)](3-) in the hydrophobic cavities of the right-handed coiled-coil (RHCC) protein of tetrabrachion have been determined using the hybrid QM/MM method. Although there is good agreement between the available experimental geometrical parameters and the values obtained in the aqueous phase using pseudopotentials or all-electron basis sets, variation of the uranyl U═O bond with the number of fluoride ligands is only truly captured after the inclusion of five water molecules in the second coordination sphere around the molecules. The docking procedure used in this work shows that there are only two possible orientations of the uranyl group of [UO(2)F(5)](3-) embedded in the hydrophobic cavities of the RHCC protein. The two orientations are exclusively along the axes perpendicular to the protein axial channel with no possible orientation of the uranyl group along the axial channel because of both steric effects and interaction with the alkyl chain of the isoleucine residues pointing into the axial channel. In addition, the embedded complex is always positioned nearer to the isoleucine residues at the N-terminal ends of the hydrophobic cavities. Energy analysis, however, reveals that both conformations can only be observed in cavity 2, the largest hydrophobic cavity. The structural and electronic properties of the ligand embedded in this cavity are very similar to those of the gas-phase structure. A comparable study of [Pt(CN)(6)](2-) and the anticancer drug cisplatin, [PtCl(2)(NH(3))(2)], in cavity 2, revealed the existence of just two orientations for the former, similar to the uranyl complex, and multiple orientations for the latter.

Water molecules influence molecular interactions in all biological systems, yet it is extremely difficult to understand their effects in precise atomic detail. Here we present evidence, based on highly refined atomic structures of the complexes of the L-arabinose-binding protein with L-arabinose, D-fucose and D-galactose, that bound water molecules, coupled with localized conformational changes, can govern substrate specificity and affinity. The atoms common to the three sugars are identically positioned in the binding site and the same nine strong hydrogen bonds are formed in all three complexes. Two hydrogen-bonded water molecules in the site contribute further to tight binding of L-arabinose but create an unfavourable interaction with the methyl group of D-fucose. Equally tight binding of D-galactose is attained by the replacement of one of the hydrogen-bonded water molecules by its--CH2OH group, coordinated with localized structural changes which include a shift and redirection of the hydrogen-bonding interactions of the other water molecule. These observations illustrate how ordered water molecules can contribute directly to the properties of proteins by influencing their interaction with ligands.

Many germ line antibodies have asparagine residues at specific sites to achieve specific antigen recognition. To study the role of asparagine residues in the stabilization of antigen-antibody complexes, we examined the interaction between hen egg white lysozyme (HEL) and the corresponding HyHEL-10 variable domain fragment (Fv). We introduced Ala and Asp substitutions into the Fv side chains of L-Asn-31, L-Asn-32, and L-Asn-92, which interact directly with residues in HEL via hydrogen bonding in the wild-type Fv-HEL complex, and we investigated the interactions between these mutant antibodies and HEL. Isothermal titration calorimetric analysis showed that all the mutations decreased the negative enthalpy change and decreased the association constants of the interaction. Structural analyses showed that the effects of the mutations on the structure of the complex could be compensated for by conformational changes and/or by gains in other interactions. Consequently, the contribution of two hydrogen bonds was minor, and their abolition by mutation resulted in only a slight decrease in the affinity of the antibody for its antigen. By comparison, the other two hydrogen bonds buried at the interfacial area had large enthalpic advantage, despite entropic loss that was perhaps due to stiffening of the interface by the bonds, and were crucial to the strength of the interaction. Deletion of these strong hydrogen bonds could not be compensated for by other structural changes. Our results suggest that asparagine can provide the two functional groups for strong hydrogen bond formation, and their contribution to the antigen-antibody interaction can be attributed to their limited flexibility and accessibility at the complex interface.