Impact of interfacial curvature on molecular properties of aqueous interfaces

The curvature of soft interfaces plays a crucial role in determining their mechanical and thermodynamic properties, both at macroscopic and microscopic scales. In the case of air/water interfaces, particular attention has recently focused on water microdroplets, due to their distinctive chemical reactivity. However, the specific impact of curvature on the molecular properties of interfacial water and interfacial reactivity has so far remained elusive. Here, we use molecular dynamics simulations to determine the effect of curvature on a broad range of structural, dynamical, and thermodynamical properties of the interface. For a droplet, a flat interface, and a cavity, we successively examine the structure of the hydrogen-bond network and its relation to vibrational spectroscopy, the dynamics of water translation, rotation, and hydrogen-bond exchanges, and the thermodynamics of ion solvation and ion-pair dissociation. Our simulations show that curvature predominantly impacts the hydrogen-bond structure through the fraction of dangling OH groups and the dynamics of interfacial water molecules. In contrast, curvature has a limited effect on solvation and ion-pair dissociation thermodynamics. For water microdroplets, this suggests that the curvature alone cannot fully account for the distinctive reactivity measured in these systems, which are of great importance for catalysis and atmospheric chemistry.

Molecular Origin of Distinct Hydration Dynamics in Double Helical DNA and RNA Sequences

Water molecules are essential to determine the structure of nucleic acids and mediate their interactions with other biomolecules. Here, we characterize the hydration dynamics of analogous DNA and RNA double helices with unprecedented resolution and elucidate the molecular origin of their differences: first, the localization of the slowest hydration water molecules─in the minor groove in DNA, next to phosphates in RNA─and second, the markedly distinct hydration dynamics of the two phosphate oxygen atoms OR and OS in RNA. Using our Extended Jump Model for water reorientation, we assess the relative importance of previously proposed factors, including the local topography, water bridges, and the presence of ions. We show that the slow hydration dynamics at RNA OR sites is not due to bridging water molecules but is caused by both the larger excluded volume and the stronger initial H-bond next to OR, due to the different phosphate orientations in A-form double helical RNA.

Scrutinizing the protein hydration shell from molecular dynamics simulations against consensus small-angle scattering data

Biological macromolecules in solution are surrounded by a hydration shell, whose structure differs from the structure of bulk solvent. While the importance of the hydration shell for numerous biological functions is widely acknowledged, it remains unknown how the hydration shell is regulated by macromolecular shape and surface composition, mainly because a quantitative probe of the hydration shell structure has been missing. We show that small-angle scattering in solution using X-rays (SAXS) or neutrons (SANS) provide a protein-specific probe of the protein hydration shell that enables quantitative comparison with molecular simulations. Using explicit-solvent SAXS/SANS predictions, we derived the effect of the hydration shell on the radii of gyration Rg of five proteins using 18 combinations of protein force field and water model. By comparing computed Rg values from SAXS relative to SANS in D2O with consensus SAXS/SANS data from a recent worldwide community effort, we found that several but not all force fields yield a hydration shell contrast in remarkable agreement with experiments. The hydration shell contrast captured by Rg values depends strongly on protein charge and geometric shape, thus providing a protein-specific footprint of protein-water interactions and a novel observable for scrutinizing atomistic hydration shell models against experimental data.

Water molecule ordering on the surface of an intrinsically disordered protein

The dynamics and local structure of the hydration water on surfaces of folded proteins have been extensively investigated. However, our knowledge of the hydration of intrinsically disordered proteins (IDPs) is more limited. Here, we compare the local structure of water molecules hydrating a globular protein, lysozyme, and the intrinsically disordered N-terminal of c-Src kinase (SH4UD) using molecular dynamics simulation. The radial distributions from the protein surface of the first and the second hydration shells are similar for the folded protein and the IDP. However, water molecules in the first hydration shell of both the folded protein and the IDP are perturbed from the bulk. This perturbation involves a loss of tetrahedrality, which is, however, significantly more marked for the folded protein than the IDP. This difference arises from an increase in the first hydration shell of the IDP of the fraction of hydration water molecules interacting with oxygen. The water ordering is independent of the compactness of the IDP. In contrast, the lifetimes of water molecules in the first hydration shell increase with IDP compactness, indicating a significant impact of IDP configuration on water surface pocket kinetics, which here is linked to differential pocket volumes and polarities.

Coarse-Graining Waters: Unveiling The Effective Hydrophilicity/Hydrophobicity of Individual Protein Atoms and The Roles of Waters' Hydrogens

There have been many coarse-graining methods developed that aim to reduce the sizes of simulated systems and their computational costs. In this work, we develop a new coarse-graining method, called coarse-graining-delta (or δ-CG in short), that reduces the degrees of freedom of the potential energy surface by coarse-graining relative locations of atoms from their unit centers. Our method extends and generalizes the methods used in the coarse-grained normal mode analysis and enables us to study the roles of the individual removed atoms in a system, which have been difficult to study in molecular dynamics simulations. By applying δ-CG to coarse-grain three-point water molecules into single-point solvent particles, we successfully identify the effective hydrophilicity and hydrophobicity of all the individual protein atom types, which collectively correlate well with the known hydrophilic, hydrophobic, and amphipathic characteristics of amino acids. Moreover, our investigation shows that water's hydrogens have two roles in interacting with protein atoms. First, water molecules adjust their poses around different amino acids and their atoms, and the statistical preferences of the hydrogen poses near the atoms determine the effective hydrophilicity and hydrophobicity of the atoms, which have not been successfully addressed before. Second, the collective dynamics of the hydrogens assist the water molecules in escaping from the potential energy wells of the hydrophilic atoms. Our method also shows that coarse-graining a system mathematically leads to breaking antisymmetry of the nonbonded interactions; as a result, two interacting coarse-grained units exert different forces on each other. Our study indicates that the accuracy of coarse-grained force fields, such as the MARTINI force field and the UNRES force field, can be improved in two ways: (i) refining their potential energy functions and coefficients by analyzing the coarse-grained potential energy surface using δ-CG, and (ii) introducing non-antisymmetric interactions.

Competing Nuclear Quantum Effects and Hydrogen-Bond Jumps in Hydrated Kaolinite

Recent work has shown that the dynamics of hydrogen bonds in pure clays are affected by nuclear quantum fluctuations, with different effects for the hydrogen bonds holding different layers of the clay together and for those within the same layer. At the clay-water interface there is an even wider range of types of hydrogen bond, suggesting that the quantum effects may be yet more varied. We apply classical and thermostated ring polymer molecular dynamics simulations to show that nuclear quantum effects accelerate hydrogen-bond dynamics to varying degrees. By interpreting the results in terms of the extended jump model of hydrogen-bond switching, we can understand the origins of these effects in terms of changes in the quantum kinetic energy of hydrogen atoms during an exchange. We also show that the extended jump mechanism is applicable not only to the hydrogen bonds involving water, but also those internal to the clay.

The significance of bioelectricity on all levels of organization of an organism. Part 1: From the subcellular level to cells

Bioelectricity plays an essential role in the structural and functional organization of biological organisms. In this first article of our three-part series, we summarize the importance of bioelectricity for the basic structural level of biological organization, i.e. from the subcellular level (charges, ion channels, molecules and cell organelles) to cells.

Number of Hydrogen Bonds per Unit Solvent Accessible Surface Area: A Descriptor of Functional States of Proteins

Proteins function close to native and near-native conformations. These states are evolutionarily selected to ensure the effect of mutations is minimized. The structural organization of a protein is hierarchical and modular, which reduces the dimensionality of the configurational space of the native states. Thus, finding appropriate descriptors that define the native state among all possible states of a protein is a problem of immense interest. The present study explores the correlation between solvent accessible surface areas (SASAs) and different intraprotein as well as protein-water hydrogen bonds of 55 single-chain globular proteins from four different structural classes (all α, all β, α+β, and α/β), 16 multichain proteins, and 4 macromolecular complexes. A systematic analysis of the solvent accessible surface area and intraprotein and protein-water hydrogen bonds suggests a linear relationship between SASAs and hydrogen bonds. The number of protein-water hydrogen bonds per unit SASA ranges from 3 to 4 for all the different structural protein classes. In contrast, the number of intramolecular hydrogen bonds per unit SASA, including the mainchain-mainchain, mainchain-sidechain, and sidechain-sidechain, varies between 0.75 to 2. The solvation free energy of a protein linearly decreases with SASA. Our study also shows that the solvation free energy/SASA varies from -75 to -105 kJ mol^-1 nm^-2 across all the native states studied here. The number conservancy of intraprotein hydrogen bonds per unit SASA possibly imparts structural stability to the native structure. On the other hand, 3-4 protein-water hydrogen bonds per unit SASA are possibly required to maintain a balance between the solubility and functionality of the native states. This study provides a basis for synthetic biologists to design new folds with improved functionality.

Distinct Hydrogen Bonding Dynamics Underlies the Microheterogeneity in DMF-Water Mixtures

The hydrogen bonding interaction between the amide functional group and water is fundamental to understanding the liquid-liquid heterogeneity in biological systems. Herein, the structure and dynamics of the N,N-dimethylformamide (DMF)-water mixtures have been investigated by linear and nonlinear IR spectroscopies, using the hydroxyl stretch and extrinsic probe of thiocyanate as local vibrational reporters. According to vibrational relaxation dynamics measurements, the orientational dynamics of water is not directly tied to those of DMF molecules. Wobbling-in-a-cone analysis demonstrates that the water molecules have varying degrees of angular restriction depending on their composition due to the formation of specific water-DMF networks. Because of the preferential solvation by DMF molecules, the rotational dynamics of the extrinsic probe is slowed significantly, and its rotational time constants are correlated to the change of solution viscosity. The unique structural dynamics observed in the DMF-water mixtures is expected to provide important insights into the underlying mechanism of microscopic heterogeneity in binary mixtures.

The protein-stabilizing effects of TMAO in aqueous and non-aqueous conditions

We present a new water-dependent molecular mechanism for the widely-used protein stabilizing osmolyte, trimethylamine N-oxide (TMAO), whose mode of action has remained controversial. Classical interpretations, such as osmolyte exclusion from the vicinity of protein, cannot adequately explain the behavior of this osmolyte and were challenged by recent data showing the direct interactions of TMAO with proteins, mainly via hydrophobic binding. Solvent effect theories also fail to propose a straightforward mechanism. To explore the role of water and the hydrophobic association, we disabled osmolyte-protein hydrophobic interactions by replacing water with hexane and using lipase enzyme as an anhydrous-stable protein. Biocatalysis experiments showed that under this non-aqueous condition, TMAO does not act as a stabilizer, but strongly deactivates the enzyme. Molecular dynamics (MD) simulations reveal that TMAO accumulates near the enzyme and makes many hydrogen bonds with it, like denaturing osmolytes. Some TMAO molecules even reach the active site and interact strongly with the catalystic traid. In aqueous solvent, the enzyme functions well: the extent of TMAO interactions is reduced and can be divided into both polar and non-polar terms. Structural analysis shows that in water, some TMAO molecules bind to the enzyme surface like a surfactant. We show that these interactions limit water-protein hydrogen bonds and unfavorable water-hydrophobic surface contacts. Moreover, a more hydrophobic environment is formed in the solvation layer, which reduces water dynamics and subsequently, rigidifies the backbone in aqueous solution. We show that osmolyte amphiphilicity and protein surface heterogeneity can address the weaknesses of exclusion and solvent effect theories about the TMAO mechanism.

Environmentally sensitive fluorescent nucleoside analogues as probes for nucleic acid - protein interactions: molecular design and biosensing applications

Fluorescent nucleoside analogues (FNAs) are indispensable in studying the interactions of nucleic acids with nucleic acid-binding proteins. By replacing one of the poorly emissive natural nucleosides, FNAs enable real-time optical monitoring of the binding interactions in solutions, under physiologically relevant conditions, with high sensitivity. Besides that, FNAs are widely used to probe conformational dynamics of biomolecular complexes using time-resolved fluorescence methods. Because of that, FNAs are tools of high utility for fundamental biological research, with potential applications in molecular diagnostics and drug discovery. Here I review the structural and physical factors that can be used for the conversion of the molecular binding events into a detectable fluorescence output. Typical environmentally sensitive FNAs, their properties and applications, and future challenges in the field are discussed.

A Critical Review on the Sensing, Control, and Manipulation of Single Molecules on Optofluidic Devices

Single-molecule techniques have shifted the paradigm of biological measurements from ensemble measurements to probing individual molecules and propelled a rapid revolution in related fields. Compared to ensemble measurements of biomolecules, single-molecule techniques provide a breadth of information with a high spatial and temporal resolution at the molecular level. Usually, optical and electrical methods are two commonly employed methods for probing single molecules, and some platforms even offer the integration of these two methods such as optofluidics. The recent spark in technological advancement and the tremendous leap in fabrication techniques, microfluidics, and integrated optofluidics are paving the way toward low cost, chip-scale, portable, and point-of-care diagnostic and single-molecule analysis tools. This review provides the fundamentals and overview of commonly employed single-molecule methods including optical methods, electrical methods, force-based methods, combinatorial integrated methods, etc. In most single-molecule experiments, the ability to manipulate and exercise precise control over individual molecules plays a vital role, which sometimes defines the capabilities and limits of the operation. This review discusses different manipulation techniques including sorting and trapping individual particles. An insight into the control of single molecules is provided that mainly discusses the recent development of electrical control over single molecules. Overall, this review is designed to provide the fundamentals and recent advancements in different single-molecule techniques and their applications, with a special focus on the detection, manipulation, and control of single molecules on chip-scale devices.

Comparative analysis of hydration layer reorientation dynamics of antifreeze protein and protein cytochrome P450

Antifreeze proteins (AFPs) inhibit ice re-crystallization by a mechanism remaining largely elusive. Dynamics of AFPs’ hydration water and its involvement in the antifreeze activity have not been identified conclusively. We herein, by simulation and theory, examined the water reorientation dynamics in the first hydration layer of an AFP from the spruce budworm, Choristoneura fumiferana, compared with a protein cytochrome P450 (CYP). The increase of potential acceptor water molecules around donor water molecules leads to the acceleration of hydrogen bond exchange between water molecules. Therefore, the jump reorientation of water molecules around the AFP active region is accelerated. Due to the mutual coupling and excitation of hydrogen bond exchange, with the acceleration of hydrogen bond exchange, the rearrangement of the hydrogen bond network and the frame reorientation of water are accelerated. Therefore, the water reorientation dynamics of AFP is faster than that of CYP. The results of this study provide a new physical image of antifreeze protein and a new understanding of the antifreeze mechanism of antifreeze proteins.

Salicornia europaea L. Functional Traits Indicate Its Optimum Growth

Salicornia europaea L. grows in areas periodically flooded by salty or brackish water. It has potential economic value, because it can be used as food, forage, or biofuel, and has potential in pharmaceuticals and cosmetics. Increasing interest in S. europaea is due to its extreme salt tolerance and well growth in marginal saline soils. However, the variation in its functional traits in response to environmental conditions is still poorly studied. There are still questions regarding the optimal level of salinity for different traits. Therefore, we worked to address the question if S. europaea traits from different scales are controlled by salinity level. Based on performed pot experiment, we found that almost all traits are salinity dependent but affected in different ways. We demonstrated that morphological, biomass, and anatomical properties indicate optimum growth between 200 and 400 mM NaCl and growth limitations at 0, 800, and 1000 mM NaCl. Moreover, we found the most affected traits which include photosynthetic pigments and protein content, plant surface area, peroxidase activity, and anatomic traits related to cell shape. Our results significantly expanded the knowledge about S. europaea functional traits variation in response to salinity, which can be important for discovering regulating processes and for possible future agricultural applications.

An efficient algorithm calculating common solvent accessible volume

The solvent accessible surface area and the solvent accessible volume are measurements commonly used in implicit solvent models to include the effect of forces exerted by solvents on the protein surfaces (or the atoms on protein surfaces). The two measurements have limitations in describing interactions between proteins (or proteins’ atoms) mediated/bridged by solvents. This is because describing the interactions between proteins should be able to capture the chain of protein-solvent-protein interactions while the solvent accessible surface area or the solvent accessible volume can capture only protein-solvent interactions. If we represent the solvent as a continuous medium, we can consider an atom of a protein can effectively interact with the solvent within a certain distance from its surface (or its own solvent-interacting sphere). In this case, the protein-solvent-protein interactions can be measured by the amount of solvent interacting with two proteins’ atoms at the same time (or the volume shared by the two atoms’ solvent-interacting spheres excluding the volumes occupied by proteins’ atoms). We call the shared volume as the common solvent accessible volume (CSAV); there has been no method developed to determine the CSAV. In this work, we propose a new sweep-line-based method that efficiently calculates the common solvent accessible volume. The performance and accuracy of the proposed sweep-line-based method are compared with those of the naïve voxel-based method. The proposed method takes log-linear time to the number of atoms involved in a CSAV calculation and linear time to the resolution. Our results, tested with 52 protein structures of various sizes, show that the proposed sweep-line-based method is superior to the voxel-based method in both computational efficiency and accuracy.

Fast and Accurate Quantum Mechanical Modeling of Large Molecular Systems Using Small Basis Set Hartree-Fock Methods Corrected with Atom-Centered Potentials

There has been significant interest in developing fast and accurate quantum mechanical methods for modeling large molecular systems. In this work, by utilizing a machine learning regression technique, we have developed new low-cost quantum mechanical approaches to model large molecular systems. The developed approaches rely on using one-electron Gaussian-type functions called atom-centered potentials (ACPs) to correct for the basis set incompleteness and the lack of correlation effects in the underlying minimal or small basis set Hartree-Fock (HF) methods. In particular, ACPs are proposed for ten elements common in organic and bioorganic chemistry (H, B, C, N, O, F, Si, P, S, and Cl) and four different base methods: two minimal basis sets (MINIs and MINIX) plus a double-ζ basis set (6-31G*) in combination with dispersion-corrected HF (HF-D3/MINIs, HF-D3/MINIX, HF-D3/6-31G*) and the HF-3c method. The new ACPs are trained on a very large set (73 832 data points) of noncovalent properties (interaction and conformational energies) and validated additionally on a set of 32 048 data points. All reference data are of complete basis set coupled-cluster quality, mostly CCSD(T)/CBS. The proposed ACP-corrected methods are shown to give errors in the tenths of a kcal/mol range for noncovalent interaction energies and up to 2 kcal/mol for molecular conformational energies. More importantly, the average errors are similar in the training and validation sets, confirming the robustness and applicability of these methods outside the boundaries of the training set. In addition, the performance of the new ACP-corrected methods is similar to complete basis set density functional theory (DFT) but at a cost that is orders of magnitude lower, and the proposed ACPs can be used in any computational chemistry program that supports effective-core potentials without modification. It is also shown that ACPs improve the description of covalent and noncovalent bond geometries of the underlying methods and that the improvement brought about by the application of the ACPs is directly related to the number of atoms to which they are applied, allowing the treatment of systems containing some atoms for which ACPs are not available. Overall, the ACP-corrected methods proposed in this work constitute an alternative accurate, economical, and reliable quantum mechanical approach to describe the geometries, interaction energies, and conformational energies of systems with hundreds to thousands of atoms.

The Structural and Dynamical Properties of the Hydration of SNase Based on a Molecular Dynamics Simulation

The dynamics of protein–water fluctuations are of biological significance. Molecular dynamics simulations were performed in order to explore the hydration dynamics of staphylococcal nuclease (SNase) at different temperatures and mutation levels. A dynamical transition in hydration water (at ~210 K) can trigger larger-amplitude fluctuations of protein. The protein–water hydrogen bonds lost about 40% in the total change from 150 K to 210 K, while the Mean Square Displacement increased by little. The protein was activated when the hydration water in local had a comparable trend in making hydrogen bonds with protein– and other waters. The mutations changed the local chemical properties and the hydration exhibited a biphasic distribution, with two time scales. Hydrogen bonding relaxation governed the local protein fluctuations on the picosecond time scale, with the fastest time (24.9 ps) at the hydrophobic site and slowest time (40.4 ps) in the charged environment. The protein dynamic was related to the water’s translational diffusion via the relaxation of the protein–water’s H-bonding. The structural and dynamical properties of protein–water at the molecular level are fundamental to the physiological and functional mechanisms of SNase.

Identifying hydrophobic protein patches to inform protein interaction interfaces

Interactions between proteins lie at the heart of numerous biological processes and are essential for the proper functioning of the cell. Although the importance of hydrophobic residues in driving protein interactions is universally accepted, a characterization of protein hydrophobicity, which informs its interactions, has remained elusive. The challenge lies in capturing the collective response of the protein hydration waters to the nanoscale chemical and topographical protein patterns, which determine protein hydrophobicity. To address this challenge, here, we employ specialized molecular simulations wherein water molecules are systematically displaced from the protein hydration shell; by identifying protein regions that relinquish their waters more readily than others, we are then able to uncover the most hydrophobic protein patches. Surprisingly, such patches contain a large fraction of polar/charged atoms and have chemical compositions that are similar to the more hydrophilic protein patches. Importantly, we also find a striking correspondence between the most hydrophobic protein patches and regions that mediate protein interactions. Our work thus establishes a computational framework for characterizing the emergent hydrophobicity of amphiphilic solutes, such as proteins, which display nanoscale heterogeneity, and for uncovering their interaction interfaces.

Water Structure, Dynamics, and Sum-Frequency Generation Spectra at Electrified Graphene Interfaces

The properties of water at an electrified graphene electrode are studied via classical molecular dynamics simulations with a constant potential approach. We show that the value of the applied electrode potential has dramatic effects on the structure and dynamics of interfacial water molecules. While a positive potential slows down the reorientational and translational dynamics of water, an increasing negative potential first accelerates the interfacial water dynamics before a deceleration at very large magnitude potential values. Further, our spectroscopic calculations indicate that the water rearrangements induced by electrified interfaces can be probed experimentally. In particular, the calculated water vibrational sum-frequency generation (SFG) spectra show that SFG specifically reports on the first two water layers at 0 V but that at larger magnitude applied potentials the resulting static field induces long-range contributions to the spectrum. Electrified graphene interfaces provide promising paradigm systems for comprehending both short- and long-range neighboring aqueous system impacts.

Determining terahertz resonant peaks of biomolecules in aqueous environment

The resonant peaks of biomolecules provide information on the molecules' physical and chemical properties. Although many biomolecules have resonant peaks in the terahertz region, it is difficult to observe their specific signals in aqueous environments. Hence, this paper proposes a method for determining these peaks. We found the specific resonant peaks of a modified nucleoside, 5-methlycytidine and modified HEK293T DNA in an aqueous solution through baseline correction. We evaluated the consistency of various fitting functions used for determining the peaks with various parameters. We separated two resonance peaks of 5-methlycytidine at 1.59 and 1.97 THz and for artificially methylated HEK293T DNA at 1.64 and 2.0 THz.

Assembly of peptides in mica-graphene nanocapillaries controlled by confined water

Water in nanoscale-confined geometries has unique physicochemical properties in contrast to bulk water, and is believed to play important roles in biological processes although there is less direct information available in the literature. Here, we report the self-assembly behaviors of a neurodegenerative disease related peptide termed GAV-9 encapsulated in mica-graphene nanocapillaries interacting with water nanofilms condensed under ambient conditions, based on atomic force microscopy (AFM) imaging and molecular dynamics (MD) simulations. The results revealed that, upon increase in the humidity, the GAV-9 peptide monomers adsorbed the confined water molecules and transitioned to unexpected hydrogel-like structures. Our MD simulations also suggested that in the confined mica-graphene nanocapillaries, the GAV-9 peptide monomers would indeed form water-rich hydrogel structures instead of highly ordered nanofilaments. The interfacial water confined in the mica-graphene nanocapillary is found to be crucial for such a transition. Moreover, the distribution of confined water layers largely depended on the locations of the preformed peptide nanofilaments, and the peptide nanofilaments further assembled into nanosheets with the water layer increasing, but depolymerized to amorphous peptide assemblies with the water layer decreasing. The polymerization and depolymerization of the peptide nanofilaments could be controlled in a reversible manner. Our results have supplied a simplified model system to uncover the effects of the confined interfacial water on the biological process at the molecular level.

Protein Solvent Shell Structure Provides Rapid Analysis of Hydration Dynamics

The solvation layer surrounding a protein is clearly an intrinsic part of protein structure-dynamics-function, and our understanding of how the hydration dynamics influences protein function is emerging. We have recently reported simulations indicating a correlation between regional hydration dynamics and the structure of the solvation layer around different regions of the enzyme Candida antarctica lipase B, wherein the radial distribution function (RDF) was used to calculate the pairwise entropy, providing a link between dynamics (diffusion) and thermodynamics (excess entropy) known as Rosenfeld scaling. Regions with higher RDF values/peaks in the hydration layer (the first peak, within 6 Å of the protein surface) have faster diffusion in the hydration layer. The finding thus hinted at a handle for rapid evaluation of hydration dynamics at different regions on the protein surface in molecular dynamics simulations. Such an approach may move the analysis of hydration dynamics from a specialized venture to routine analysis, enabling an informatics approach to evaluate the role of hydration dynamics in biomolecular function. This paper first confirms that the correlation between regional diffusive dynamics and hydration layer structure (via water center of mass around protein side-chain atom RDF) is observed as a general relationship across a set of proteins. Second, it seeks to devise an approach for rapid analysis of hydration dynamics, determining the minimum amount of information and computational effort required to get a reliable value of hydration dynamics from structural data in MD simulations based on the protein-water RDF. A linear regression model using the integral of the hydration layer in the water-protein RDF was found to provide statistically equivalent apparent diffusion coefficients at the 95% confidence level for a set of 92 regions within five different proteins. In summary, RDF analysis of 10 ns of data after simulation convergence is sufficient to accurately map regions of fast and slow hydration dynamics around a protein surface. Additionally, it is anticipated that a quick look at protein-water RDFs, comparing peak heights, will be useful to provide a qualitative ranking of regions of faster and slower hydration dynamics at the protein surface for rapid analysis when investigating the role of solvent dynamics in protein function.

Counterion Effect on Vibrational Relaxation and the Rotational Dynamics of Interfacial Water and an Anionic Vibrational Probe in the Confined Reverse Micelles Environment

Vibrational relaxation and the rotational dynamics of water molecules encapsulated in reverse micelles (RMs) have been investigated by ultrafast infrared (IR) spectroscopy and two-dimensional IR (2D IR) spectroscopy. By changing the counterion of the hydrophilic headgroup in the RMs formed by Aerosol-OT (AOT) from Na⁺ to K⁺, Cs⁺ and Ca²⁺, we could determine the specific counterion effects on the rotational dynamics of water molecules. The orientational relaxation time constant of water decreases in the order Ca²⁺ > Na⁺ > K⁺ > Cs⁺. The SCN^- anionic probe and counterion can form ion pairs at the interfacial region of the RMs. The rotational dynamics of SCN^- anion significantly decreases because of the synergistic effects of confinement and the surface interactions in the interfacial region of the RMs. The results can provide a new understanding of the cationic Hofmeister effect at the molecular level observed in biological studies.

Hydration Structure and Dynamics of Inhibitor-Bound HIV-1 Protease

Water is essential in many biological processes, and the hydration structure plays a critical role in facilitating protein folding, dynamics, and ligand binding. A variety of biophysical spectroscopic techniques have been used to probe the water solvating proteins, often complemented with molecular dynamics (MD) simulations to resolve the spatial and dynamic features of the hydration shell, but comparing relative water structure is challenging. In this study 1 μs MD simulations were performed to identify and characterize hydration sites around HIV-1 protease bound to an inhibitor, darunavir (DRV). The water density, hydration site occupancy, extent and anisotropy of fluctuations, coordinated water molecules, and hydrogen bonds were characterized and compared to the properties of bulk water. The water density of the principal hydration shell was found to be higher than bulk, dependent on the topology and physiochemical identity of the biomolecular surface. The dynamics of water molecules occupying principal hydration sites was highly dependent on the number of water-water interactions and inversely correlated with hydrogen bonds to the protein-inhibitor complex. While many waters were conserved following the symmetry of homodimeric HIV protease, the asymmetry induced by DRV resulted in asymmetric lower-occupancy hydration sites at the concave surface of the active site. Key interactions between water molecules and the protease, that stabilize the protein in the inhibited form, were altered in a drug resistant variant of the protease indicating that modulation of solvent-solute interactions might play a key role in conveying drug resistance. Our analysis provides insights into the interplay between an enzyme inhibitor complex and the hydration shell and has implications in elucidating water structure in a variety of biological processes and applications including ligand binding, inhibitor design, and resistance.

Physico-chemical properties of aqueous drug solutions: From the basic thermodynamics to the advanced experimental and simulation results

The physical chemical properties of aqueous solutions of model compounds are illustrated in relation to hydration and solubility issues by using three perspectives: thermodynamic, spectroscopic and molecular dynamics simulations. The thermodynamic survey of the fundamental backgrounds of concentration dependence and experimental solubility results show some peculiar behavior of aqueous solutions with several types of similar solutes. Secondly, the use of a variety of experimental spectroscopic devices, operating under different experimental conditions of dimension and frequency, has produced a large amount of structural and dynamic data on aqueous solutions showing the richness of the information produced, depending on where and how the experiment is carried out. Finally, the use of molecular dynamics computational work is presented to highlight how the different types of solute functional groups and surface topologies organize adjacent water molecules differently. The highly valuable contribution of computer simulation studies in providing molecular explanations for experimental deductions, either of a thermodynamic or spectroscopic nature, is shown to have changed the current knowledge of many aqueous solution processes. While this paper is intended to provide a collective view on the latest literature results, still the presentation aims at a tutorial explanation of the potentials of the three methodologies in the field of aqueous solutions of pharmaceutical molecules.

The impact of water on the ambivalent behavior and paradoxical phenomenon of the amyloid-β fibril protein

The crucial role of water in amyloid-β(Aβ) fibril proteins is evaluated in several ways including the water's thermodynamic and kinetic solvation effects. As regards the water's character, its hindered-rotation barriers are also considered. The following protein molecules considered here are: the Aβ40 (PDB ID: 2LMN), Aβ42 (PDB ID: 5KK3 and 2NAO) and the double-layered Aβ17-42 fibril. We discuss: (i) extracellular Aβ40 and Aβ42 fibril monomers exhibit an ambivalent propensity to transform into a helical form toward the N-term region and a β-strand-like form near the C-terminal; (ii) interfacial water molecules play a crucial role in protein-protein interactions, as molecular dynamics simulations have shown a significant impact on the protein-protein binding; (iii) it is shown that the spontaneous dimerization process of the Aβ42 fibril protein in water occurs via a two-step nucleation-accommodation mechanism; (iv) MD simulations of the double-layered Aβ17-42 fibril model show that the C↔C interface appears more energetically favorable than the N↔N interface due to large hydrophobic contacts; (v) the water's role in the HET-s prion and in the Aβ fibrillar aggregates; (vi) it was found that the monomer-oligomer equilibrium spontaneously dissociates into stable monomeric species when they are incubated up to 3 μm for a longer time (>1 week) in a physiological buffer.

Water Dynamics in the Hydration Shells of Biomolecules

The structure and function of biomolecules are strongly influenced by their hydration shells. Structural fluctuations and molecular excitations of hydrating water molecules cover a broad range in space and time, from individual water molecules to larger pools and from femtosecond to microsecond time scales. Recent progress in theory and molecular dynamics simulations as well as in ultrafast vibrational spectroscopy has led to new and detailed insight into fluctuations of water structure, elementary water motions, electric fields at hydrated biointerfaces, and processes of vibrational relaxation and energy dissipation. Here, we review recent advances in both theory and experiment, focusing on hydrated DNA, proteins, and phospholipids, and compare dynamics in the hydration shells to bulk water.

In Silico Studies of Small Molecule Interactions with Enzymes Reveal Aspects of Catalytic Function

Small molecules, such as solvent, substrate, and cofactor molecules, are key players in enzyme catalysis. Computational methods are powerful tools for exploring the dynamics and thermodynamics of these small molecules as they participate in or contribute to enzymatic processes. In-depth knowledge of how small molecule interactions and dynamics influence protein conformational dynamics and function is critical for progress in the field of enzyme catalysis. Although numerous computational studies have focused on enzyme-substrate complexes to gain insight into catalytic mechanisms, transition states and reaction rates, the dynamics of solvents, substrates, and cofactors are generally less well studied. Also, solvent dynamics within the biomolecular solvation layer play an important part in enzyme catalysis, but a full understanding of its role is hampered by its complexity. Moreover, passive substrate transport has been identified in certain enzymes, and the underlying principles of molecular recognition are an area of active investigation. Enzymes are highly dynamic entities that undergo different conformational changes, which range from side chain rearrangement of a residue to larger-scale conformational dynamics involving domains. These events may happen nearby or far away from the catalytic site, and may occur on different time scales, yet many are related to biological and catalytic function. Computational studies, primarily molecular dynamics (MD) simulations, provide atomistic-level insight and site-specific information on small molecule interactions, and their role in conformational pre-reorganization and dynamics in enzyme catalysis. The review is focused on MD simulation studies of small molecule interactions and dynamics to characterize and comprehend protein dynamics and function in catalyzed reactions. Experimental and theoretical methods available to complement and expand insight from MD simulations are discussed briefly.

Spectrum of Slow and Super-Slow (Picosecond to Nanosecond) Water Dynamics around Organic and Biological Solutes

Water dynamics in the solvation shell of solutes plays a very important role in the interaction of biomolecules and in chemical reaction dynamics. However, a selective spectroscopic study of the solvation shell is difficult because of the interference of the solute dynamics. Here we report on the observation of heavily slowed down water dynamics in the solvation shell of different solutes by measuring the low-frequency spectrum of solvation water, free from the contribution of the solute. A slowdown factor of ∼50 is observed even for relatively low concentrations of the solute. We go on to show that the effect can be generalized to different solutes including proteins.

Molecular couplings and energy exchange between DNA and water mapped by femtosecond infrared spectroscopy of backbone vibrations

Molecular couplings between DNA and water together with the accompanying processes of energy exchange are mapped via the ultrafast response of DNA backbone vibrations after OH stretch excitation of the water shell. Native salmon testes DNA is studied in femtosecond pump-probe experiments under conditions of full hydration and at a reduced hydration level with two water layers around the double helix. Independent of their local hydration patterns, all backbone vibrations in the frequency range from 940 to 1120 cm^-1 display a quasi-instantaneous reshaping of the spectral envelopes of their fundamental absorption bands upon excitation of the water shell. The subsequent reshaping kinetics encompass a one-picosecond component, reflecting the formation of a hot ground state of the water shell, and a slower contribution on a time scale of tens of picoseconds. Such results are benchmarked by measurements with resonant excitation of the backbone modes, resulting in distinctly different absorption changes. We assign the fast changes of DNA absorption after OH stretch excitation to structural changes in the water shell which couple to DNA through the local electric fields. The second slower process is attributed to a flow of excess energy from the water shell into DNA, establishing a common heated ground state in the molecular ensemble. This interpretation is supported by theoretical calculations of the electric fields exerted by the water shell at different temperatures.

WatAA: Atlas of Protein Hydration. Exploring synergies between data mining and ab initio calculations

Water molecules represent an integral part of proteins and a key determinant of protein structure, dynamics and function. WatAA is a newly developed, web-based atlas of amino-acid hydration in proteins. The atlas provides information about the ordered first hydration shell of the most populated amino-acid conformers in proteins. The data presented in the atlas are drawn from two sources: experimental data and ab initio quantum-mechanics calculations. The experimental part is based on a data-mining study of a large set of high-resolution protein crystal structures. The crystal-derived data include 3D maps of water distribution around amino-acids and probability of occurrence of each of the identified hydration sites. The quantum mechanics calculations validate and extend this primary description by optimizing the water position for each hydration site, by providing hydrogen atom positions and by quantifying the interaction energy that stabilizes the water molecule at the particular hydration site position. The calculations show that the majority of experimentally derived hydration sites are positioned near local energy minima for water, and the calculated interaction energies help to assess the preference of water for the individual hydration sites. We propose that the atlas can be used to validate water placement in electron density maps in crystallographic refinement, to locate water molecules mediating protein-ligand interactions in drug design, and to prepare and evaluate molecular dynamics simulations. WatAA: Atlas of Protein Hydration is freely available without login at .

Nuclear Quantum Effects in Water Reorientation and Hydrogen-Bond Dynamics

We combine classical and ring polymer molecular dynamics simulations with the molecular jump model to provide a molecular description of the nuclear quantum effects (NQEs) on water reorientation and hydrogen-bond dynamics in liquid H₂O and D₂O. We show that while the net NQE is negligible in D₂O, it leads to a ∼13% acceleration in H₂O dynamics compared to a classical description. Large angular jumps-exchanging hydrogen-bond partners-are the dominant reorientation pathway (just as in a classical description); the faster reorientation dynamics arise from the increased jump rate constant. NQEs do not change the jump amplitude distribution, and no significant tunneling is found. The faster jump dynamics are quantitatively related to decreased structuring of the OO radial distribution function when NQEs are included. This is explained, via a jump model analysis, by competition between the effects of water's librational and OH stretch mode zero-point energies on the hydrogen-bond strength.

Revisiting the droplet simulation approach to derive force-field parameters for water on molybdenum disulfide from wetting angle measurements

Owing to its peculiar electronic properties, molybdenum disulfide (MoS₂) has been the subject of a growing number of studies in the recent years. In applications, this material and other transition metal dichalcogenides (TMDs) may have to interact with a liquid or polymer phase as well as solutions of biomolecules. It is therefore of primary importance to understand the wetting and adhesion properties of TMDs. Starting from existing models, we derive Lennard-Jones parameters for the interaction between water and the basal plane of MoS₂ that are consistent with recent wetting experiments. Molecular dynamics simulations indicate that a stack of only two MoS₂ monolayers is necessary to capture the wetting behavior of bulk MoS₂. It is found that the Coulomb interaction between water and monolayer and bilayer MoS₂ plays no role in the related interfacial thermodynamics. Calculations with the optimized parameters show that the depth of the well of the interaction potential between water and bulk MoS₂ is of the order of 8.2 kJ/mol. Such a value is comparable with what was found for graphite and consistent with the fact that the wetting angles of water on graphite and MoS₂ are almost equal. The derivation of the force-field parameters is performed using a methodology which, contrary to previous studies, makes a consistent use of droplet calculations. The results of our work should find application in further simulation studies on the wetting behavior of TMDs and other dispersive materials.

Reaction Path Averaging: Characterizing the Structural Response of the DNA Double Helix to Electron Transfer

A polarizable environment, prominently the solvent, responds to electronic changes in biomolecules rapidly. The knowledge of conformational relaxation of the biomolecule itself, however, may be scarce or missing. In this work, we describe in detail the structural changes in DNA undergoing electron transfer between two adjacent nucleobases. We employ an approach based on averaging of tens to hundreds of thousands of nonequilibrium trajectories generated with molecular dynamics simulation, and a reduction of dimensionality suitable for DNA. We show that the conformational response of the DNA proceeds along a single collective coordinate that represents the relative orientation of two consecutive base pairs, namely, a combination of helical parameters shift and tilt. The structure of DNA relaxes on time scales reaching nanoseconds, contributing marginally to the relaxation of energies, which is dominated by the modes of motion of the aqueous solvent. The concept of reaction path averaging (RPA), conveniently exploited in this context, makes it possible to filter out any undesirable noise from the nonequilibrium data, and is applicable to any chemical process in general.

The opposite effects of sodium and potassium cations on water dynamics

Water rotational dynamics in NaSCN and KSCN solutions at a series of concentrations are investigated using femtosecond infrared spectroscopy and theory. Femtosecond infrared measurements, consistent with previous NMR observations, detect that sodium slows down while potassium accelerates the water O-H bond rotation. Results of reported neutron scattering measurements, on the other hand, suggested that these two cations have similar structure-breaking effects on water, and therefore should both accelerate water rotation through the presumably dominating large-amplitude angular jump component. To explain this discrepancy, theoretical studies with both classical and ab initio models were carried out, which indicate that both ions indeed accelerate the large-amplitude angular jump rotation of the water molecules, while the observed cation specific effect originates from the non-negligible opposite impact of the sodium and potassium cations on the diffusive rotation of water molecules.