Water structure around dipeptides in aqueous solutions

The structure of water: A historical perspective

Attempts to understand the molecular structure of water were first made well over a century ago. Looking back at the various attempts, it is illuminating to see how these were conditioned by the state of knowledge of chemistry and physics at the time and the experimental and theoretical tools then available. Progress in the intervening years has been facilitated by not only conceptual and theoretical advances in physics and chemistry but also the development of experimental techniques and instrumentation. Exploitation of powerful computational methods in interpreting what at first sight may seem impenetrable experimental data has led us to the consistent and detailed picture we have today of not only the structure of liquid water itself and how it changes with temperature and pressure but also its interactions with other molecules, in particular those relevant to water's role in important chemical and biological processes. Much remains to be done in the latter areas, but the experimental and computational techniques that now enable us to do what might reasonably be termed "liquid state crystallography" have opened the door to make possible further advances. Consequently, we now have the tools to explore further the role of water in those processes that underpin life itself-the very prospect that inspired Bernal to develop his ideas on the structure of liquids in general and of water in particular.

The influence of the hydrogen-bond network on the structure and dynamics of the RAPRKKG heptapeptide and its mutants

The structural behaviour of the RAPRKKG heptapeptide after individual or multiple mutations was inspected through molecular dynamics simulation. The nature of the mutations provided information on the flexibility of the heptapeptide and on how water molecules establish hydrogen bonds with it. The structural behaviour of the wild-type and the mutated structures were measured through the analysis of protein‒protein and protein‒solvent hydrogen bonds. The conformational behaviours of the different structures were analysed through free energy landscape analysis. The flexibility characteristics of the mutants seem to depend on the reorganization of water molecules and their static or dynamic behaviour around amino acid side chains.

Walking on water: revisiting the role of water in articular cartilage biomechanics in relation to tissue engineering and regenerative medicine

The importance, and the difficulty, of generating biosynthetic articular cartilage is widely recognized. Problems arise from obtaining sufficient stiffness, toughness and longevity in the material and integration of new material into existing cartilage and bone. Much work has been done on chondrocytes and tissue macromolecular components while water, which comprises the bulk of the tissue, is largely seen as a passive component; the ‘solid matrix’ is believed to be the main load-bearing element most of the time. Water is commonly seen as an inert filler whose restricted flow through the tissue is believed to be sufficient to generate the properties measured. We propose that this model should be turned on its head. Water comprises 70–80% of the matrix and has a bulk modulus considerably greater than that of cartilage. We suggest that the macromolecular components structure the water to support the loads applied. Here, we shall examine the structure and organization of the main macromolecules, collagen, aggrecan and hyaluronan, and explore how water interacts with their polyelectrolyte nature. This may inform the biosynthetic process by identifying starting points to enable developing tissue properties to guide the cells into producing the appropriate macromolecular composition and structure.

On the Solute-Induced Structure-Making/Breaking Effect: Rigorous Links among Microscopic Behavior, Solvation Properties, and Solution Non-Ideality

We studied the solute-induced perturbation of the solvent environment around a solute species from a microscopic viewpoint and propose a novel approach to the understanding of the structure-making/breaking process, regardless of the type and nature of the solute-solvent interactions. Based on the Kirkwood-Buff fluctuation formalism, we present a rigorous statistical mechanics description of the evolution of the solvent structure around the solute, analyze its response to small perturbations of the ( TP) state conditions and composition of the system, and make direct connections between a few equivalent micro- and macroscopic manifestations as probes for, and targets of, experimental measurements. We illustrate the analysis with theoretical results from integral equation calculations of model fluids and experimental evidence from available data for a variety of aqueous electrolyte and nonelectrolyte real fluid solutions. Finally, we provide a critical discussion about the inadequacy underlying a widely used de facto criterion for the classification of structure-making/breaking solutes.

Structural evidence for solvent-stabilisation by aspartic acid as a mechanism for halophilic protein stability in high salt concentrations

Halophilic organisms have adapted to survive in high salt environments, where mesophilic organisms would perish. One of the biggest challenges faced by halophilic proteins is the ability to maintain both the structure and function at molar concentrations of salt. A distinct adaptation of halophilic proteins, compared to mesophilic homologues, is the abundance of aspartic acid on the protein surface. Mutagenesis and crystallographic studies of halophilic proteins suggest an important role for solvent interactions with the surface aspartic acid residues. This interaction, between the regions of the acidic protein surface and the solvent, is thought to maintain a hydration layer around the protein at molar salt concentrations thereby allowing halophilic proteins to retain their functional state. Here we present neutron diffraction data of the monomeric zwitterionic form of aspartic acid solutions at physiological pH in 0.25 M and 2.5 M concentration of potassium chloride, to mimic mesophilic and halophilic-like environmental conditions. We have used isotopic substitution in combination with empirical potential structure refinement to extract atomic-scale information from the data. Our study provides structural insights that support the hypothesis that carboxyl groups on acidic residues bind water more tightly under high salt conditions, in support of the residue-ion interaction model of halophilic protein stabilisation. Furthermore our data show that in the presence of high salt the self-association between the zwitterionic form of aspartic acid molecules is reduced, suggesting a possible mechanism through which protein aggregation is prevented.

Water-peptide site-specific interactions: a structural study on the hydration of glutathione

Water-peptide interactions play an important role in determining peptide structure and function. Nevertheless, a microscopic description of these interactions is still incomplete. In this study we have investigated at the atomic scale length the interaction between water and the tripeptide glutathione. The rationale behind this work, based on the combination between a neutron diffraction experiment and a computer simulation, is twofold. It extends previous studies on amino acids, addressing issues such as the perturbation of the water network brought by a larger biomolecule in solution. In addition, and more importantly, it seeks a possible link between the atomic length scale description of the glutathione-water interaction with the specific biological functionality of glutathione, an important intracellular antioxidant. Results indicate a rather weak hydrogen bond between the thiol (-SH) group of cysteine and its first neighbor water molecule. This -SH group serves as a proton donor, is responsible for the biological activity of glutathione, and it is involved in the formation of glutathione disulfide, the oxidized form of glutathione. Moreover, the hydration shell of the chemically identical carboxylate group on the glutamic acid residue and on the glycine residue shows an intriguing different spatial location of water molecules and coordination numbers around the two CO2(-) groups.

Dipeptide Aggregation in Aqueous Solution from Fixed Point-Charge Force Fields

The description of aggregation processes with molecular dynamics simulations is a playground for testing biomolecular force fields, including a new generation of force fields that explicitly describe electronic polarization. In this work, we study a system consisting of 50 glycyl-l-alanine (Gly-Ala) dipeptides in solution with 1001 water molecules. Neutron diffraction experiments have shown that at this concentration, Gly-Ala aggregates into large clusters. However, general-purpose force fields in combination with established water models can fail to correctly describe this aggregation process, highlighting important deficiencies in how solute-solute and solute-solvent interactions are parametrized in these force fields. We found that even for the fully polarizable AMOEBA force field, the degree of association is considerably underestimated. Instead, a fixed point-charge approach based on the newly developed IPolQ scheme [Cerutti et al. J. Phys. Chem.2013, 117, 2328] allows for the correct modeling of the dipeptide aggregation in aqueous solution. This result should stimulate interest in novel fitting schemes that aim to improve the description of the solvent polarization effect within both explicitly polarizable and fixed point-charge frameworks.

Alteration of water structure by peptide clusters revealed by neutron scattering in the small-angle region (below 1 Å(-1))

Solution scattering of neutrons and x-rays can provide direct information on local interactions of importance for biomolecular folding and structure. Here, neutron scattering experiments are combined with molecular-dynamics simulation to interpret the scattering signal of a series of dipeptides with varying degrees of hydrophobicity (GlyAla, GlyPro, and AlaPro) in concentrated aqueous solution (1:20 solute/water ratio) in which the peptides form large segregates (up to 50-60 amino acids). Two main results are found: 1), the shift to lower Q of the so-called water-ring peak (Q ≈ 2 Å(-1)) arises mainly from an overlap of water-peptide and peptide-peptide correlations in the region of 1.3 <Q< 2 Å(-1), rather than from a shift of the water signal induced by the presence of the clusters; and 2), in the low-Q region (Q ≈ 0.6 Å(-1)) a positive peak is observed originating from both the solute-solute correlations and changes in the water structure induced by the formation of the clusters. In particular, the water molecules are found to be more connected than in the bulk with hydrogen-bonding directions tangential to the exposed hydrophobic surfaces, and this effect increases with increasing peptide hydrophobicity. This work demonstrates that important information on the (hydrophobic) hydration of biomolecules can be obtained in the very-small-angle region.

A bulk water-dependent desolvation energy model for analyzing the effects of secondary solutes on biological equilibria

A new phenomenological model for interpreting the effects of solutes on biological equilibria is presented. The model attributes changes in equilibria to differences in the desolvation energy of the reacting species that, in turn, reflect changes in the free energy of the bulk water upon addition of secondary solutes. The desolvation approach differs notably from that of other solute models by treating the free energy of bulk water as a variable and by not ascribing the observed shifts in reaction equilibria to accumulation or depletion of solutes next to the surfaces of the reacting species. On the contrary, the partitioning of solutes is viewed as a manifestation of the different subpopulations of water that arise in response to the surface boundary conditions. A thermodynamic framework consistent with the proposed model is used to derive a relationship for a specific reaction, an aqueous solubility equilibrium, in two or more solutions. The resulting equation reconciles some potential issues with the transfer free energy model of Tanford. Application of the desolvation energy model to the analysis of a two-state protein folding equilibrium is discussed and contrasted to the application of two other solute models developed by Timasheff and by Parsegian. Future tabulation of solvation energies and bulk water energies may allow biophysical chemists to confirm the mechanism by which secondary solutes influence binding and conformational equilibria and may provide a common ground on which experimentalists and theoreticians can compare and evaluate their results.

Hydration water and bulk water in proteins have distinct properties in radial distributions calculated from 105 atomic resolution crystal structures

Water plays a critical role in the structure and function of proteins, although the experimental properties of water around protein structures are not well understood. The water can be classified by the separation from the protein surface into bulk water and hydration water. Hydration water interacts closely with the protein and contributes to protein folding, stability, and dynamics, as well as interacting with the bulk water. Water potential functions are often parametrized to fit bulk water properties because of the limited experimental data for hydration water. Therefore, the structural and energetic properties of the hydration water were assessed for 105 atomic resolution ( Collapse

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MESH Headings

• Crystallization
• Crystallography, X-Ray
• Proteins/chemistry
• Water/chemistry

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Grants

• P20 GM065762 NIGMS NIH HHS
• U01 GM062920 NIGMS NIH HHS
• R01 GM062920 NIGMS NIH HHS
• P20 GM065762-03 NIGMS NIH HHS
• R01 GM062920-09 NIGMS NIH HHS
• GM062920 NIGMS NIH HHS
• GM065762 NIGMS NIH HHS

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Affiliation(s)

Xianfeng Chen Department of Biology, Georgia State University, Atlanta, Georgia 30302–4010, USA
Irene Weber Department of Biology, Georgia State University, Atlanta, Georgia 30302–4010, USA
Robert W. Harrison Department of Biology, Georgia State University, Atlanta, Georgia 30302–4010, USA Department of Computer Science, Georgia State University, Atlanta, Georgia 30302–4010, USA

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