Diffusion of solvent around biomolecular solutes: a molecular dynamics simulation study

Diffusion and Viscosity in Mixed Protein Solutions

The viscosity and diffusion properties of crowded protein systems were investigated with molecular dynamics simulations of SH3 mixtures with different crowders, and results were compared with experimental data. The simulations accurately reproduced experimental trends across a wide range of protein concentrations, including highly crowded environments up to 300 g/L. Notably, viscosity increased with crowding but varied little between different crowder types, while diffusion rates were significantly reduced depending on protein-protein interaction strength. Analysis using the Stokes-Einstein relation indicated that the reduction in diffusion exceeded what was expected from viscosity changes alone, with the additional slow-down attributable to transient cluster formation driven by weakly attractive interactions. Contact kinetics analysis further revealed that longer-lived interactions contributed more significantly to reduced diffusion rates than short-lived interactions. This study also highlights the accuracy of current computational methodologies for capturing the dynamics of proteins in highly concentrated solutions and provides insights into the molecular mechanisms affecting protein mobility in crowded environments.

Diffusion and Viscosity in Mixed Protein Solutions

The viscosity and diffusion properties of crowded protein systems were investigated with molecular dynamics simulations of SH3 mixtures with different crowders, and results were compared with experimental data. The simulations accurately reproduced experimental trends across a wide range of protein concentrations, including highly crowded environments up to 300 g/L. Notably, viscosity increased with crowding but varied little between different crowder types, while diffusion rates were significantly reduced depending on protein-protein interaction strength. Analysis using the Stokes-Einstein relation indicated that the reduction in diffusion exceeded what was expected from viscosity changes alone, with the additional slow-down attributable to transient cluster formation driven by weakly attractive interactions. Contact kinetics analysis further revealed that longer-lived interactions contributed more significantly to reduced diffusion rates than short-lived interactions. This study also highlights the accuracy of current computational methodologies for capturing the dynamics of proteins in highly concentrated solutions and provides insights into the molecular mechanisms affecting protein mobility in crowded environments.

Optimization of Extraction Conditions for Biological Attributes of Newly Developed NARC-G1 Garlic Using Response Surface Methodology and Its GC-MS Characterization

The present paper is a comprehensive study on the optimization of ultrasonic assisted extraction and characterization of valued components from the newly developed garlic cultivar NARC-G1. The response surface methodology was employed to optimize the extraction time, solvent-to-solid ratio and extraction temperature, for optimal total phenolic contents (TPC), DPPH radical scavenging activity, α-amylase inhibition, and α-glucosidase inhibition. Under the optimized conditions (23 min extraction time, 60 °C temperature, and 39 : 1 solvent-to-solute ratio) the optimal TPC (13.76 mg GAE/g), DPPH radical scavenging activity (62.76 %), α-amylase inhibition (71.43 %), and α-glucosidase inhibition (79.43 %) were obtained. Significant correlations were observed between actual values and predicted values for the selected responses. Gas chromatography-mass spectrometry (GC-MS), revealed 26 high-value bioactives, with diallyl disulphide being the most abundant (16.22 %), followed by 2,3-dihydro-3,5-dihydroxy-6-methyl, 4H-pyran-4-one and 5-Hydroxymethylfurfural. Additionally, in silico investigation indicated that stigmasterol, arbutin, squalene, α-tocopherol and linoleic acid were responsible for antihyperglycemic potential. Moreover, antimicrobial activity revealed that S. mutans (19.25±1.98 mm) and L. monocytogenes (19.34±2.04 mm) were the most sensitive, while P. aeruginosa was the least sensitive bacterial strains against the optimized NARC-G1 garlic extract. This research effectively explains the optimal recovery of high-valued components from NARC-G1 and may contribute to nutra-pharmaceutical and functional food developments.

SPEADI: Accelerated Analysis of IDP-Ion Interactions from MD-Trajectories

The disordered nature of Intrinsically Disordered Proteins (IDPs) makes their structural ensembles particularly susceptible to changes in chemical environmental conditions, often leading to an alteration of their normal functions. A Radial Distribution Function (RDF) is considered a standard method for characterizing the chemical environment surrounding particles during atomistic simulations, commonly averaged over an entire or part of a trajectory. Given their high structural variability, such averaged information might not be reliable for IDPs. We introduce the Time-Resolved Radial Distribution Function (TRRDF), implemented in our open-source Python package SPEADI, which is able to characterize dynamic environments around IDPs. We use SPEADI to characterize the dynamic distribution of ions around the IDPs Alpha-Synuclein (AS) and Humanin (HN) from Molecular Dynamics (MD) simulations, and some of their selected mutants, showing that local ion-residue interactions play an important role in the structures and behaviors of IDPs.

The Effects of Flexibility on dsDNA–dsDNA Interactions

A detailed understanding of the physical mechanism of ion-mediated dsDNA interactions is important in biological functions such as DNA packaging and homologous pairing. We report the potential of mean force (PMF) or the effective solvent mediated interactions between two parallel identical dsDNAs as a function of interhelical separation in 0.15 M NaCl solution. Here, we study the influence of flexibility of dsDNAs on the effective interactions by comparing PMFs between rigid models and flexible ones. The role of flexibility of dsDNA pairs in their association is elucidated by studying the energetic properties of Na⁺ ions as well as the fluctuations of ions around dsDNAs. The introduction of flexibility of dsDNAs softens the vdW contact wall and induces more counterion fluctuations around dsDNAs. In addition, flexibility facilitates the Na⁺ ions dynamics affecting their distribution. The results quantify the extent of attraction influenced by dsDNA flexibility and further emphasize the importance of non-continuum solvation approaches.

Contributions of higher-order proximal distribution functions to solvent structure around proteins

The proximal distribution function (pDF) quantifies the probability of finding a solvent molecule in the vicinity of solutes. The approach constitutes a hierarchically organized theory for constructing approximate solvation structures around solutes. Given the assumption of universality of atom cluster-specific solvation, reconstruction of the solvent distribution around arbitrary molecules provides a computationally convenient route to solvation thermodynamics. Previously, such solvent reconstructions usually considered the contribution of the nearest-neighbor distribution only. We extend the pDF reconstruction algorithm to terms including next-nearest-neighbor contribution. As a test, small molecules (alanine and butane) are examined. The analysis is then extended to include the protein myoglobin in the P6 crystal unit cell. Molecular dynamics simulations are performed, and solvent density distributions around the solute molecules are compared with the results from different pDF reconstruction models. It is shown that the next-nearest-neighbor modification significantly improves the reconstruction of the solvent number density distribution in concave regions and between solute molecules. The probability densities are then used to calculate the solute-solvent non-bonded interaction energies including van der Waals and electrostatic, which are found to be in good agreement with the simulated values.

Protein Transport through Nanopores Illuminated by Long-Time-Scale Simulations

The transport of molecules through nanoscale confined space is relevant in biology, biosensing, and industrial filtration. Microscopically modeling transport through nanopores is required for a fundamental understanding and guiding engineering, but the short duration and low replica number of existing simulation approaches limit statistically relevant insight. Here we explore protein transport in nanopores with a high-throughput computational method that realistically simulates hundreds of up to seconds-long protein trajectories by combining Brownian dynamics and continuum simulation and integrating both driving forces of electroosmosis and electrophoresis. Ionic current traces are computed to enable experimental comparison. By examining three biological and synthetic nanopores, our study answers questions about the kinetics and mechanism of protein transport and additionally reveals insight that is inaccessible from experiments yet relevant for pore design. The discovery of extremely frequent unhindered passage can guide the improvement of biosensor pores to enhance desired biomolecular recognition by pore-tethered receptors. Similarly, experimentally invisible nontarget adsorption to pore walls highlights how to improve recently developed DNA nanopores. Our work can be expanded to pressure-driven flow to model industrial nanofiltration processes.

Computational and experimental assessment of pH and specific ions on the solute solvent interactions of clay-biochar composites towards tetracycline adsorption: Implications on wastewater treatment

Experimental and computational investigations have been conducted in this study to assess the influence of municipal waste pyrolyzed biochar impregnated clay composites on antibiotic removal as a material for wastewater treatment and simultaneous value-addition for waste. The surface potential (zeta potential) of the pristine biochar and composite samples are found to be within the range ~10 to ~ -40 mV in the pH range 2-10. The presence of different inorganic salt solutions influences the electrophoretic mobility of the dispersed phase in a suspension, as well as its zeta potential. In addition of Na⁺ salt solutions, the Na⁺ ions undergo electrostatic interaction with the negatively charged biochar samples and form a double layer at the interface of biochar and ionic salt solution. Molecular dynamics simulations have been employed to understand experimental findings, ions adsorption and solute-solvent interactions at the molecular level of two biochar B7 (seven benzene rings, one methoxy, one aldehyde and two hydroxyls groups) and B17 (seventeen benzene rings, one methoxy, two hydroxyls and two carboxylic acid groups) in salts aqueous solutions. The results confirm that hydroxyls and carboxylate groups of biochar are responsible for solute-solvent interactions. Successful removal of tetracycline antibiotics is observed with 26 mg/g maximum adsorption capacity with montmorillonite biochar composite. This study confirms that interactions between amide and hydroxyl groups of tetracycline with hydroxyl and carboxylate groups of biochar play the key role in the adsorption process. The solution pH and presence of different background electrolytes effectively influence the process of solute-solvent interactions as well as adsorption efficacy towards tetracycline adsorption.

Accurate modeling of a biological nanopore with an extended continuum framework

Despite the broad success of biological nanopores as powerful instruments for the analysis of proteins and nucleic acids at the single-molecule level, a fast simulation methodology to accurately model their nanofluidic properties is currently unavailable. This limits the rational engineering of nanopore traits and makes the unambiguous interpretation of experimental results challenging. Here, we present a continuum approach that can faithfully reproduce the experimentally measured ionic conductance of the biological nanopore Cytolysin A (ClyA) over a wide range of ionic strengths and bias potentials. Our model consists of the extended Poisson-Nernst-Planck and Navier-Stokes (ePNP-NS) equations and a computationally efficient 2D-axisymmetric representation for the geometry and charge distribution of the nanopore. Importantly, the ePNP-NS equations achieve this accuracy by self-consistently considering the finite size of the ions and the influence of both the ionic strength and the nanoscopic scale of the pore on the local properties of the electrolyte. These comprise the mobility and diffusivity of the ions, and the density, viscosity and relative permittivity of the solvent. Crucially, by applying our methodology to ClyA, a biological nanopore used for single-molecule enzymology studies, we could directly quantify several nanofluidic characteristics difficult to determine experimentally. These include the ion selectivity, the ion concentration distributions, the electrostatic potential landscape, the magnitude of the electro-osmotic flow field, and the internal pressure distribution. Hence, this work provides a means to obtain fundamental new insights into the nanofluidic properties of biological nanopores and paves the way towards their rational engineering.

Rotational and Translational Diffusion of Proteins as a Function of Concentration

Atomistic simulations of three different proteins at different concentrations are performed to obtain insight into protein mobility as a function of protein concentration. We report on simulations of proteins from diluted to the physiological water concentration (about 70% of the mass). First, the viscosity was computed and found to increase by a factor of 7-9 going from pure water to the highest protein concentration, in excellent agreement with in vivo nuclear magnetic resonance results. At a physiological concentration of proteins, the translational diffusion is found to be slowed down to about 30% of the in vitro values. The slow-down of diffusion found here using atomistic models is slightly more than that of a hard sphere model that neglects the electrostatic interactions. Interestingly, rotational diffusion of proteins is slowed down somewhat more (by about 80-95% compared to in vitro values) than translational diffusion, in line with experimental findings and consistent with the increased viscosity. The finding that rotation is retarded more than translation is attributed to solvent-separated clustering. No direct interactions between the proteins are found, and the clustering can likely be attributed to dispersion interactions that are stronger between proteins than between protein and water. Based on these simulations, we can also conclude that the internal dynamics of the proteins in our study are affected only marginally under crowding conditions, and the proteins become somewhat more stable at higher concentrations. Simulations were performed using a force field that was tuned for dealing with crowding conditions by strengthening the protein-water interactions. This force field seems to lead to a reproducible partial unfolding of an α-helix in one of the proteins, an effect that was not observed in the unmodified force field.

Dynamics of TMAO and urea in the hydration shell of the protein SNase

Using all-atom molecular dynamics simulations of aqueous solutions of the globular protein SNase, the dynamic behavior of water molecules and cosolvents (trimethylamine-N-oxide (TMAO) and urea) in the hydration shell of the protein was studied for different solvent compositions. TMAO is a potent protein-stabilizing osmolyte, whereas urea is known to destabilize proteins. For molecules that are initially located in successive narrow layers at a given distance from the protein, the mean displacements and the distribution of displacements for short time intervals are calculated. For molecules that are initially located in solvation shells of a given thickness around the protein, the characteristic residence times in these shells are determined to characterize the dynamic behavior of the solvent molecules as a function of the distance to the protein. A combined consideration of these characteristics allows to reveal additional features of the dynamics of the cosolvents. It is shown that TMAO molecules leave the nearest vicinity of the protein faster than urea molecules, despite the fact that the mobility of TMAO molecules, measured by their mean displacements, is lower than that of urea. Moreover, we show that the rate of release of TMAO molecules from the hydration shell is lower in ternary (TMAO + urea + H₂O) solvent mixtures than in the binary ones. This is consistent with a recent observation that the fraction of TMAO near the protein decreases in the presence of urea. From the analysis of the decay of the number of particles initially located in the region of the first peak of the distribution function of solvent molecules around the protein, we estimated that about 20 water molecules and 6-7 urea molecules stay near the protein for more than 1000 ps.

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.

Structure and Dynamics of the Hydration Shell: Spatially Decomposed Time Correlation Approach

Molecular simulations provide insight into solvation structures and dynamics with unparalleled spatial and temporal resolution. Here, we take advantage of this fact and develop a set of generally applicable computational tools for a detailed analysis of the hydration shell around an ionic or molecular solute. These tools allow us to quantify and visualize orientationally resolved radial distribution functions as well as distance-resolved orientational time-correlation functions of water molecules surrounding the solute. Such a detailed view of the hydration shells allows us to unravel important structural and dynamical features, which are not accessible when employing standard analysis techniques.

How proteins modify water dynamics

Much of biology happens at the protein-water interface, so all dynamical processes in this region are of fundamental importance. Local structural fluctuations in the hydration layer can be probed by ¹⁷O magnetic relaxation dispersion (MRD), which, at high frequencies, measures the integral of a biaxial rotational time correlation function (TCF)-the integral rotational correlation time. Numerous ¹⁷O MRD studies have demonstrated that this correlation time, when averaged over the first hydration shell, is longer than in bulk water by a factor 3-5. This rotational perturbation factor (RPF) has been corroborated by molecular dynamics simulations, which can also reveal the underlying molecular mechanisms. Here, we address several outstanding problems in this area by analyzing an extensive set of molecular dynamics data, including four globular proteins and three water models. The vexed issue of polarity versus topography as the primary determinant of hydration water dynamics is resolved by establishing a protein-invariant exponential dependence of the RPF on a simple confinement index. We conclude that the previously observed correlation of the RPF with surface polarity is a secondary effect of the correlation between polarity and confinement. Water rotation interpolates between a perturbed but bulk-like collective mechanism at low confinement and an exchange-mediated orientational randomization (EMOR) mechanism at high confinement. The EMOR process, which accounts for about half of the RPF, was not recognized in previous simulation studies, where only the early part of the TCF was examined. Based on the analysis of the experimentally relevant TCF over its full time course, we compare simulated and measured RPFs, finding a 30% discrepancy attributable to force field imperfections. We also compute the full ¹⁷O MRD profile, including the low-frequency dispersion produced by buried water molecules. Computing a local RPF for each hydration shell, we find that the perturbation decays exponentially with a decay "length" of 0.3 shells and that the second and higher shells account for a mere 3% of the total perturbation measured by ¹⁷O MRD. The only long-range effect is a weak water alignment in the electric field produced by an electroneutral protein (not screened by counterions), but this effect is negligibly small for ¹⁷O MRD. By contrast, we find that the ¹⁷O TCF is significantly more sensitive to the important short-range perturbations than the other two TCFs examined here.

Signatures of Solvation Thermodynamics in Spectra of Intermolecular Vibrations

This study explores the thermodynamic and vibrational properties of water in the three-dimensional environment of solvated ions and small molecules using molecular simulations. The spectrum of intermolecular vibrations in liquid solvents provides detailed information on the shape of the local potential energy surface, which in turn determines local thermodynamic properties such as the entropy. Here, we extract this information using a spatially resolved extension of the two-phase thermodynamics method to estimate hydration water entropies based on the local vibrational density of states (3D-2PT). Combined with an analysis of solute–water and water–water interaction energies, this allows us to resolve local contributions to the solvation enthalpy, entropy, and free energy. We use this approach to study effects of ions on their surrounding water hydrogen bond network, its spectrum of intermolecular vibrations, and resulting thermodynamic properties. In the three-dimensional environment of polar and nonpolar functional groups of molecular solutes, we identify distinct hydration water species and classify them by their characteristic vibrational density of states and molecular entropies. In each case, we are able to assign variations in local hydration water entropies to specific changes in the spectrum of intermolecular vibrations. This provides an important link for the thermodynamic interpretation of vibrational spectra that are accessible to far-infrared absorption and Raman spectroscopy experiments. Our analysis provides unique microscopic details regarding the hydration of hydrophobic and hydrophilic functional groups, which enable us to identify interactions and molecular degrees of freedom that determine relevant contributions to the solvation entropy and consequently the free energy.

Distinct Protein Hydration Water Species Defined by Spatially Resolved Spectra of Intermolecular Vibrations

In this molecular dynamics simulation study, we analyze intermolecular vibrations in the hydration shell of a solvated enyzme, the membrane type 1–matrix metalloproteinase, with high spatial resolution. Our approach allows us to characterize vibrational signatures of the local hydrogen bond network, the translational mobility of water molecules, as well as the molecular entropy, in specific local environments. Our study demonstrates the heterogeneity of water properties within the hydration shell of a complex biomolecule. We define a classification scheme based on the vibrational density of states that allows us to distinguish separate classes of hydration water species and facilitates the description of hydration water properties at distinct hydration sites. The results demonstrate that no single characteristic of the protein surface is sufficient to determine the properties of nearby water. The protein surface geometry, quantified here by the number of protein atoms in the vicinity of a hydration water molecule, as well as the chemical nature of a solvated protein functional group, influences dynamic and thermodynamic properties of solvating water molecules.

Enthalpic and Entropic Contributions to Hydrophobicity

Hydrophobic hydration plays a key role in a vast variety of biological processes, ranging from the formation of cells to protein folding and ligand binding. Hydrophobicity scales simplify the complex process of hydration by assigning a value describing the averaged hydrophobic character to each amino acid. Previously published scales were not able to calculate the enthalpic and entropic contributions to the hydrophobicity directly. We present a new method, based on Molecular Dynamics simulations and Grid Inhomogeneous Solvation Theory, that calculates hydrophobicity from enthalpic and entropic contributions. Instead of deriving these quantities from the temperature dependence of the free energy of hydration or as residual of the free energy and the enthalpy, we directly obtain these values from the phase space occupied by water molecules. Additionally, our method is able to identify regions with specific enthalpic and entropic properties, allowing to identify so-called "unhappy water" molecules, which are characterized by weak enthalpic interactions and unfavorable entropic constraints.

Investigation of changes in the arrangement of water molecules and salt ions surrounding different atoms of the DNA molecule during the melting process: a molecular dynamics simulation study

A molecular dynamics simulation was performed on a B-DNA duplex (CGCGAATTGCGC) at different temperatures. The DNA was immerged in a saltwater medium with 1 mol/L NaCl concentration. The arrangements of water molecules and cations around the different atoms of DNA on the melting pathway were investigated. Almost for all atoms of the DNA by double helix → single-stranded transition, the water molecules released from the DNA duplex and cations were close to single-stranded DNA, but this behavior was not clearly seen at melting temperatures. Therefore, release of water molecules and cations approaching the DNA by the increase of temperature does not have any effect on the sharpness of the transition curve. Most of the water molecules and cations were found to be around the negatively charged phosphate oxygen atoms. The number of water molecules released from the first shell hydration upon melting in the minor groove was higher than in the major groove, and intrusion of cations into the minor groove after melting was higher than into the major groove. The hydrations of imino protons were different from each other and were dependent on DNA bases.

Shape dependence of the radial distribution function of hydration water around proteins

The characterization of hydration water in proteins is important to understand their structure, function and folding properties. A calculation of the shape parameters reveals considerable asymmetry in the shapes of globular proteins. The present study suggests a generalized approach for the calculation of radial distribution of hydration water by accounting for the shape asymmetry in proteins. The surface and radial distribution function is analyzed for three groups of high resolution globular proteins and nonglobular proteins. This generalized approach depicts a considerable difference in the hydration water distribution pattern around aspherical proteins as compared to the earlier method and this difference is more pronounced for nonglobular proteins. The peaks for normalized RDF are found to be sharper compared to those of bulk water. The normalized RDF of hydration water exactly coincides with that of the bulk beyond 8.0 Å. The radial distribution of hydration water as a function of the water-protein distance matches with the experimentally observed distribution of hydration water around myoglobin. The results reveal that the distribution of hydration water is dependent on the shapes of proteins and hence a generalized approach should be used for the calculation of hydration water distribution around proteins, especially for nonglobular proteins.

Diffusion of water and selected atoms in DMPC lipid bilayer membranes

Molecular dynamics simulations have been used to determine the diffusion of water molecules as a function of their position in a fully hydrated freestanding 1,2-dimyristoyl-sn-glycero-3-phosphorylcholine (DMPC) bilayer membrane at 303 K and 1 atm. The diffusion rate of water in a ∼10 Å thick layer just outside the membrane surface is reduced on average by a factor of ∼2 relative to bulk. For water molecules penetrating deeper into the membrane, there is an increasing reduction in the average diffusion rate with up to one order of magnitude decrease for those deepest in the membrane. A comparison with the diffusion rate of selected atoms in the lipid molecules shows that ∼6 water molecules per lipid molecule move on the same time scale as the lipids and may therefore be considered to be tightly bound to them. The quasielastic neutron scattering functions for water and selected atoms in the lipid molecule have been simulated and compared to observed quasielastic neutron scattering spectra from single-supported bilayer DMPC membranes.

Transition of the hydration state of a surfactant accompanying structural transitions of self-assembled aggregates

What role does water play in the self-assembly of soft materials? To understand the correlation between the hydration state and the various self-assembled structures of a nonionic surfactant, terahertz time-domain spectroscopy has been performed for a C(12)E(5) solution with complementary use of small-angle x-ray scattering. Precise observations of the hydration state show clearly that transitions of the hydration state are accompanied by structural phase transitions of the surfactant from hexagonal to micelle to lamellae. These transitions of hydration state suggest that water is not a homogeneous solvent, and the interaction between water and the soft material is important for self-assembly.

Hydrophobicity of proteins and interfaces: insights from density fluctuations

Macroscopic characterizations of hydrophobicity (e.g., contact angle measurements) do not extend to the surfaces of proteins and nanoparticles. Molecular measures of hydrophobicity of such surfaces need to account for the behavior of hydration water. Theory and state-of-the-art simulations suggest that water density fluctuations provide such a measure; fluctuations are enhanced near hydrophobic surfaces and quenched with increasing surface hydrophilicity. Fluctuations affect conformational equilibria and dynamics of molecules at interfaces. Enhanced fluctuations are reflected in enhanced cavity formation, more favorable binding of hydrophobic solutes, increased compressibility of hydration water, and enhanced water-water correlations at hydrophobic surfaces. These density fluctuation-based measures can be used to develop practical methods to map the hydrophobicity/philicity of heterogeneous surfaces including those of proteins. They highlight that the hydrophobicity of a group is context dependent and is significantly affected by its environment (e.g., chemistry and topography) and especially by confinement. The ability to include information about hydration water in mapping hydrophobicity is expected to significantly impact our understanding of protein-protein interactions as well as improve drug design and discovery methods and bioseparation processes.

Protein crowding affects hydration structure and dynamics

The effect of protein crowding on the structure and dynamics of water was examined from explicit solvent molecular dynamics simulations of a series of protein G and protein G/villin systems at different protein concentrations. Hydration structure was analyzed in terms of radial distribution functions, three-dimensional hydration sites, and preservation of tetrahedral coordination. Analysis of hydration dynamics focused on self-diffusion rates and dielectric constants as a function of crowding. The results show significant changes in both structure and dynamics of water under highly crowded conditions. The structure of water is altered mostly beyond the first solvation shell. Diffusion rates and dielectric constants are significantly reduced following linear trends as a function of crowding reflecting highly constrained water in crowded environments. The reduced dynamics of diffusion is expected to be strongly related to hydrodynamic properties of crowded cellular environments while the reduced dielectric constant under crowded conditions has implications for the stability of biomolecules in crowded environments. The results from this study suggest a prescription for modeling solvation in simulations of cellular environments.

The role of conserved waters in conformational transitions of Q61H K-ras

To investigate the stability and functional role of long-residence water molecules in the Q61H variant of the signaling protein K-ras, we analyzed all available Ras crystal structures and conformers derived from a series of independent explicit solvent molecular dynamics (MD) simulations totaling 1.76 µs. We show that the protein samples a different region of phase space in the presence and absence of several crystallographically conserved and buried water molecules. The dynamics of these waters is coupled with the local as well as the global motions of the protein, in contrast to less buried waters whose exchange with bulk is only loosely coupled with the motion of loops in their vicinity. Aided by two novel reaction coordinates involving the distance (d) between the C_α atoms of G60 at switch 2 and G10 at the P-loop and the N-C_α-C-O dihedral (ξ) of G60, we further show that three water molecules located in lobe1, at the interface between the lobes and at lobe2, are involved in the relative motion of residues at the two lobes of Q61H K-ras. Moreover, a d/ξ plot classifies the available Ras x-ray structures and MD-derived K-ras conformers into active GTP-, intermediate GTP-, inactive GDP-bound, and nucleotide-free conformational states. The population of these states and the transition between them is modulated by water-mediated correlated motions involving the functionally critical switch 2, P-loop and helix 3. These results suggest that water molecules act as allosteric ligands to induce a population shift among distinct switch 2 conformations that differ in effector recognition.

K-ras belongs to the Ras family of G-proteins that regulate cell proliferation and development. To execute its function, K-ras adopts different conformational states when it is active and inactive. In addition to these two states, it samples many transient intermediate conformations as it makes the transition from one state to the other. Mutations that affect the population of these states can cause cancer or developmental disorder. Using simulation approaches, here we show that a number of water molecules buried within the structure of an oncogenic K-ras protein modulate the distribution of its conformational states. Moreover, a detailed analysis based on two novel structural parameters revealed the existence of long-range water-mediated interactions that facilitate a dynamic coupling between the two lobes of the protein. These findings pave the way for a dynamics-guided strategy to inhibit abnormal Ras signaling.

Variable interactions between protein crowders and biomolecular solutes are important in understanding cellular crowding

The effect of cellular crowding was examined from molecular dynamics simulations of chymotrypsin inhibitor 2 (CI2) in the presence of either lysozyme or bovine serum albumin (BSA) crowder molecules as a complement to recent experimental studies of the same systems (Miklos, A. C.; Sarkar, M.; Wang, Y.; Pielak, G. J. J. Am. Chem. Soc.2011, 133, 7116). The simulations confirm a destabilization and significantly slowed diffusion of CI2 in the presence of lysozyme and indicate that this observation is a result of extensive, nonspecific protein-protein interactions between CI2 and lysozyme. CI2 interacts much less with BSA crowders corresponding to a weak effect of crowding. Energetic analysis suggests an overall favorable crowding free energy in the presence of lysozyme, while weaker interactions with BSA appear to be unfavorable.

Structure of hydration water in proteins: a comparison of molecular dynamics simulations and database analysis

Hydration layer water molecules play important structural and functional roles in proteins. Despite being a critical component in biomolecular systems, characterizing the properties of hydration water poses a challenge for both experiments and simulations. In this context we investigate the local structure of hydration water molecules as a function of the distance from the protein and water molecules respectively in 188 high resolution protein structures and compare it with those obtained from molecular dynamics simulations. Tetrahedral order parameter of water in proteins calculated from previous and present simulation studies show that the potential of bulk water overestimates the average tetrahedral order parameter compared to those calculated from crystal structures. Hydration waters are found to be more ordered at a distance between the first and second solvation shell from the protein surface. The values of the order parameter decrease sharply when the water molecules are located very near or far away from the protein surface. At small water-water distance, the values of order parameter of water are very low. The average order parameter records a maximum value at a distance equivalent to the first solvation layer with respect to the water-water radial distribution and asymptotically approaches a constant value at large distances. Results from present analysis will help to get a better insight into structure of hydration water around proteins. The analysis will also help to improve the accuracy of water models on the protein surface.

Long-range hydration effect of lipid membrane studied by terahertz time-domain spectroscopy

The hydration state of biomolecules is believed to affect their self-assembly. The hydration state of phospholipid bilayers is studied precisely by terahertz spectroscopy, by which water perturbed by a lipid membrane is detected sensitively from the observation of the relaxation dynamics of water molecules in the subpicosecond time scale. Combined with x-ray observation of the lamellar structure of the lipid, a long-range hydration effect on up to 4-5 layers of water is confirmed. Most water molecules in the lamellae fall into the hydration water, and condensation of them is also indicated.