Hydration Sites Research Articles

Role of Explicit Solvation in the Simulation of Resonance Raman Spectra within Short-Time Dynamics Approximation.

In short-time dynamics approximation, relative resonance Raman (RR) intensity of a vibrational mode primarily depends on the magnitude of square of the excited-state gradient along the corresponding normal coordinate, ground-state normal mode eigenvector, and harmonic vibrational wavenumbers. In this study, through simulation of RR spectra of guanosine-5'-monophosphate (GMP) in two ππ* singlet excited states, we analyze how the explicitly hydrogen-bonded local solvation structure of the chromophore dictates intensities of the RR active modes in an unprecedented manner. We show that the accuracy of the structural model of solvated chromophore plays a decisive role in determining an optimal theoretical method for prediction of the Franck-Condon region of the ππ* excited states. 9-Methylguanine (9-meG) in complex with six water molecules (9-meG·6H2O) is found out to be the most accurate one for describing GMP in two different bright electronic states. We find that explicit hydrogen-bonded water molecules strongly influence computed RR intensities of GMP by modulating both the ground-state normal mode vectors and the excited-state energy gradients. We find that simultaneous inclusion of six explicit waters to describe the solute-solvent interaction near all hydration sites is essential for reliable prediction of the features of RR spectra in Lb and Bb electronic states of GMP.

Tritium Retention in Hexavalent Chromate-Conversion–Coated Aluminum Alloy

In this work, Aluminum 6061-T6 samples were subjected to MIL-DTL-5541F type-I, class-3 anodic coatings, where a yellow irradiate finish was achieved. Both chromate-conversion coatings (CCCs) and unmodified samples were exposed to deuterium-tritium (PT = 0.51 atm) gas for 24 h at room temperature. Following loading, the samples were subjected to one of two desorption techniques: temperature-programmed desorption or a surface stripping technique. The results show that chromic-acid anodizing of aluminum dramatically increases the total quantity of tritium retained by the treated surface as compared to unmodified aluminum. X-ray photoelectron spectroscopy and scanning electron microscopy studies of both treated aluminum and unmodified samples indicate that the CCCs contain significant quantities of hydrated chromium. Using transmission electron microscopy, the surface is shown to have significant cracking and fracturing of the film and leads to a highly grained and porous surface. Such surface defects coupled with the vast quantity of hydration sites are likely reasons for the increased retained tritium inventory observed for CCC samples. Because of the physical and chemical properties of unmodified CCC samples, they are not suitable for use in tritium environments.

Large-Scale Study of Hydration Environments through Hydration Sites.

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

Hybrid QM/MM vs Pure MM Molecular Dynamics for Evaluating Water Distribution within p21N-ras and the Resulting GTP Electronic Density.

p21ras protein activity, regulated by GTP hydrolysis, constitutes an active field of research for the development of cancer targeted therapies that would concern ∼30% of human tumors to which specific mutations have been associated. Indeed, the catalyzing mechanisms provided by the protein environment during GTP hydrolysis and how they are impaired by specific mutations remain to be fully elucidated. In this article, we present results from molecular mechanics (MM) molecular dynamics (MD) simulations and density functional theory (DFT) calculations carried out for wild-type p21 N-ras and six Gln 61 mutants. In the first part, we present the water distribution within the active site of the wild-type protein according to MM MD. Significant differences are observed when comparing the results to the previous distribution assessed through quantum mechanics/molecular mechanics (QM/MM) MD. Such method-dependent results highlight the importance of accounting for the electrostatic coupling between the protein complex and the solvent molecules in identifying hydration sites. In the second part, we present the results from DFT calculations performed to determine the electronic distribution of the GTP ligand, considering the wild-type active site arrangement according to both classical and hybrid approaches. Only in the QM/MM-based configuration is the ligand electronic density similar to that of a GDP-like state observed experimentally. For this reason, in the last set of calculations carried out for p21 N-ras Gln 61 mutants, only the active site structural conformations obtained through hybrid MD are considered. Through the analysis of the GTP electronic density, we conclude that the wild-type active site arrangement according to QM/MM MD is closer to a catalytically efficient conformation of the protein than the arrangement according to MM MD. Hence, water distribution according to the hybrid approach must correspond to the optimal placement of solvent in the active site. Within all of the studied Gln 61 substituted proteins, p21ras major catalyzing effect, which consists of stabilizing a more GDP-like state, is lost.

Discovery of 7H-pyrrolo[2,3-d]pyrimidine derivatives as selective covalent irreversible inhibitors of interleukin-2-inducible T-cell kinase (Itk)

Interleukin-2-inducible T-cell kinase (Itk) plays an important role in multiple signal transduction pathways in T and mast cells, and is a potential drug target for treating inflammatory diseases, autoimmune diseases, and T cell leukemia/lymphoma. Herein, we describe the discovery of a series of covalent Itk inhibitors based on the 7H-pyrrolo[2,3-d]pyrimidine scaffold. Placing an appropriate substitution group at a hydration site of the ATP binding pocket of Itk and using a saturated heterocyclic ring as a linker to the reactive group were crucial for selectivity. The optimized compound 9 showed potent activity against Itk, excellent selectivity for Itk over Btk and other structurally related kinases, inhibition of phospholipase C-γ1 (PLC-γ1) phosphorylation in cells, and anti-proliferative effects against multiple T leukemia/lymphoma cell lines. Compound 9 can serve as a valuable compound for further determination of functions of Itk.

Molecular dynamics simulation of the hydration of adenosine phosphates

The hydration behavior of adenosine triphosphate (ATP), adenosine diphosphate (ADP), and adenosine monophosphate (AMP) has been investigated with molecular dynamics simulations. The spatial distribution of water molecules around different hydration sites of the adenosine phosphates and the average times that water molecules spend in the vicinity of the hydration sites of the phosphate, ribose, and adenine groups have been examined in order to characterize the hydration extent of different regions of the ATP, ADP, and AMP molecules. The water molecules strongly hydrate the negatively-charged phosphate groups of the adenosine phosphates and the interaction between the oxygen and nitrogen atoms of the ribose and adenine rings with water molecules lead to the full hydration of these groups by the water molecules as well. The adenosine phosphates ATP, ADP, and AMP were found to be fully hydrated by the water molecules regardless of the magnitude of their negative charges. Results of this work provide atomic-level information about the hydration of ATP, ADP, and AMP were and are expected to help better understand the behavior of these molecules in biological systems.

Predicting Skin Permeability by Means of Computational Approaches: Reliability and Caveats in Pharmaceutical Studies.

The skin is the main barrier between the internal body environment and the external one. The characteristics of this barrier and its properties are able to modify and affect drug delivery and chemical toxicity parameters. Therefore, it is not surprising that permeability of many different compounds has been measured through several in vitro and in vivo techniques. Moreover, many different in silico approaches have been used to identify the correlation between the structure of the permeants and their permeability, to reproduce the skin behavior, and to predict the ability of specific chemicals to permeate this barrier. A significant number of issues, like interlaboratory variability, experimental conditions, data set building rationales, and skin site of origin and hydration, still prevent us from obtaining a definitive predictive skin permeability model. This review wants to show the main advances and the principal approaches in computational methods used to predict this property, to enlighten the main issues that have arisen, and to address the challenges to develop in future research.

Assessing the Predictive Power of Relative Binding Free Energy Calculations for Test Cases Involving Displacement of Binding Site Water Molecules.

Improved sampling methodologies, more accurate force fields, and access to longer simulation time scales have led to an increased application of Relative Binding Free Energy (RBFE) calculations in drug discovery projects. In order to assess the strengths and limitations of such tools, adequate benchmark sets are required that challenge the methodology in certain well-defined aspects. We applied Free Energy Perturbation (FEP) calculations to six congeneric ligand pairs taken from the literature, in which addition of a functional group resulted in the displacement of buried binding site water molecules and compared the calculated relative binding free energies with the experimental ones. We started the perturbations from different initial solvation states and registered large inconsistencies (large hysteresis) between the calculated values. We furthermore applied a Grand Canonical Monte Carlo (GCMC) solvent sampling step prior to the FEP calculation that led to a smaller hysteresis for the simulations. By applying a hydration site analysis to the trajectories of the end-states of the perturbation, we could point out that the low accuracy of the predictions as well as the high dependence of the prediction on the chosen initial state is likely caused by the trapping of binding site water molecules and/or insufficient solvation of buried cavities that are formed upon completion of the perturbation. This work highlights that RBFE calculations can suffer from slow solvent exchange of buried parts of the binding sites with the bulk.

Prediction of GABARAP interaction with the GABA type A receptor.

We have performed docking simulations on GABARAP interacting with the GABA type A receptor using SwarmDock. We have also used a novel method to study hydration sites on the surface of these two proteins; this method identifies regions around proteins where desolvation is relatively easy, and these are possible locations where proteins can bind each other. There is a high degree of consistency between the predictions of these two methods. Moreover, we have also identified binding sites on GABARAP for other proteins, and listed possible binding sites for as yet unknown proteins on both GABARAP and the GABA type A receptor intracellular domain.

Efficient and Accurate Hydration Site Profiling for Enclosed Binding Sites.

Molecular dynamics (MD) simulations allow for accurate prediction of the thermodynamic profile of binding-site water molecules critical for protein-ligand association. Whereas this hydration-site profiling converges rapidly for solvent-exposed sites independent of the initial water placement, an accurate and reliable placement is required for water molecules in occluded binding sites. Here, we present an accurate and efficient hydration-site prediction method for occluded binding sites combining water placement based on 3D-RISM and MD simulations using WATsite.

Water Distribution within Wild-Type NRas Protein and Q61 Mutants during Unrestrained QM/MM Dynamics

Point mutations in p21ras are associated with ∼30% of human tumors by disrupting its GTP hydrolysis cycle, which is critical to its molecular switch function in cellular signaling pathways. In this work, we investigate the impact of Gln 61 substitutions in the structure of the p21N-ras active site and particularly focus on water reorganization around GTP, which appears to be crucial to evaluate favorable and unfavorable hydration sites for hydrolysis. The NRas-GTP complex is analyzed using a hybrid quantum mechanics/molecular mechanics approach, treating for the first time to our knowledge transient water molecules at the ab initio level and leading to results that account for the electrostatic coupling between the protein complex and the solvent. We show that for the wild-type protein, water molecules are found around the GTP γ-phosphate group, forming an arch extended from residues 12 to 35. Two density peaks are observed, supporting previous results that suggest the presence of two water molecules in the active site, one in the vicinity of residue 35 and a second one stabilized by hydrogen bonds formed with nitrogen backbone atoms of residues 12 and 60. The structural changes observed in NRas Gln 61 mutants result in the drastic delocalization of water molecules that we discuss. In mutants Q61H and Q61K, for which water distribution is overlocalized next to residue 60, the second density peak supports the hypothesis of a second water molecule. We also conclude that Gly 60 indirectly participates in GTP hydrolysis by correctly positioning transient water molecules in the protein complex and that Gln 61 has an indirect steric effect in stabilizing the preorganized catalytic site.

Wet Sunscreens in the Gas Phase: Structures of Isolated and Microsolvated Oxybenzone.

New insights into the structural intricacies of solvated sunscreen compounds are presented. Using high-resolution rotational spectroscopy with supersonic jets and quantum-chemistry calculations, we navigate the conformational space of oxybenzone and oxybenzone-water clusters. We unambiguously assign the global minimum structure, resolving any prevailing ambiguities, and locate the primary hydration sites of the ground-state enol conformer. Two microsolvated molecular models of oxybenzone are validated by rotational spectroscopy of isotopically enriched species. Theoretical predictions based on these models suggest that water influences the ground-state enol-keto energetic constraints and that its effect is biased depending on which water docking-site is at play.

Effect of colloidal nanosilica on early-age compressive strength of oil well cement stone at low temperature

The compressive strength of cement stone rises slowly when cementing marine shallow section at low temperature, resulting in increased drilling cost and risk. This paper presents results of experimental study that was conducted to investigate the effect of low temperature on early-age compressive strength of cement stone admixed with colloidal nanosilica. The compressive strength of cement stones was measured after aging at 4 °C for 1, 3, and 7 days respectively. The hydration products of different aging cement stone were analyzed by X-ray diffraction and Fourier Transform infrared spectroscopy, and the microstructures were observed by scanning electron microscopy. In addition, the hydration exotherm of colloidal nanosilica modified cement slurry during hydration process was tested at 20 °C. The results indicated that the compressive strength of cement stone significantly improved by colloidal nanosilica. Interestingly, colloidal nanosilica retarded the initial hydration, and then promote the hydration process afterward. The mechanism of colloidal nanosilica to improve the compressive strength of cement stone was that colloidal nanosilica consumed calcium hydroxide to produce additional calcium silicate hydrate, filling large pores and cracks inside cement stone. More importantly, nanosilica particles provided nucleation sites of cement hydration and modified the internal structure of the hardened stone. The improvement of early-age compressive strength of oil well cement stone is beneficial to saving costs and reducing risk.

Dissecting water binding sites at protein–protein interfaces: a lesson from the atomic structures in the Protein Data Bank

We dissect the protein–protein interfaces into water preservation (WP), water hydration (WH) and water dehydration (WD) sites by comparing the water-mediated hydrogen bonds (H-bond) in the bound and unbound states of the interacting subunits. Upon subunit complexation, if a H-bond between an interface water and a protein polar group is retained, we assign it as WP site; if it is lost, we assign it as WD site and if a new H-bond is created, we assign it as WH site. We find that the density of WD sites is highest followed by WH and WP sites except in antigen and (or) antibody complexes, where the density of WH sites is highest followed by WD and WP sites. Furthermore, we find that WP sites are the most conserved followed by WD and WH sites in all class of complexes except in antigen and (or) antibody complexes, where WD sites are the most conserved followed by WH and WP sites. A significant number of WP and WH sites are involved in water bridges that stabilize the subunit interactions. At WH sites, the residues involved in water bridges are significantly better conserved than the other residues. However, no such difference is observed at WP sites. Interestingly, WD sites are generally replaced with direct H-bonds upon subunit complexation. Significantly, we observe many water-mediated H-bonds remain preserved in spite of large conformational changes upon subunit complexation. These findings have implications in predicting and engineering water binding sites at protein–protein interfaces.

Water-mediated conformational preselection mechanism in substrate binding cooperativity to protein kinase A

Substrate binding cooperativity in protein kinase A (PKA) seems to involve allosteric coupling between the two binding sites. It received significant attention, but its molecular basis still remains not entirely clear. Based on long molecular dynamics of PKA and its complexes, we characterized an allosteric pathway that links ATP binding to the redistribution of states adopted by a protein substrate positioning segment in favor of those that warrant correct binding. We demonstrate that the cooperativity mechanism critically depends on the presence of water in two distinct, buried hydration sites. One holds just a single water molecule, which acts as a switchable hydrogen bond bridge along the allosteric pathway. The second, filled with partially disordered solvent, is essential for providing a smooth free energy landscape underlying conformational transitions of the peptide binding region. Our findings remain in agreement with experimental data, also concerning the cooperativity abolishing effect of the Y204A mutation, and indicate a plausible molecular mechanism contributing to experimentally observed binding cooperativity of the two substrates.

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.

Effect of brine salinity and guar gum on the transport of barium through dolomite rocks: Implications for unconventional oil and gas wastewater disposal

This research aimed to elucidate the effect of brine salinity and guar gum on the sorption and transport of Ba in dolomite rocks collected from the Arbuckle formation in Oklahoma, USA. Guar gum represents the most important organic additive used in viscosified fracturing fluids, and Ba constitutes the most common and abundant heavy metal found in unconventional oil and gas (UOG) wastewater. Batch experiments conducted using powdered dolomite rocks (500–600 μm particle size) revealed that at brine salinities of UOG wastewater, chloro-complexation reactions between Ba and Cl ions and pH changes that results from dolomite dissolution are the controlling factors of Ba sorption on dolomite. Competition of Ba with common cations (Ca and Mg) for hydration sites of dolomite, plays a secondary role. Core-flooding experiments conducted to analyze the transport of Ba through natural and synthetic dolomite core plugs are in agreement with the batch sorption experimental results. The transport of Ba through dolomite rocks, increases with increasing brine salinity (0–180,000 mg-NaCl/L). The presence guar gum (50–500 mg/L) does not affect the transport of Ba through dolomite rocks of high flow properties (25–29.6% porosity, 9.6–13.7 mD permeability). However, core-flooding experiments conducted using tight dolomite rocks (6.5–8.6% porosity, 0.06–0.3 mD permeability), revealed that guar gum can retard the transport of Ba by clogging high permeability/porosity regions of tight dolomite rocks. The mechanism of Ba sorption on dolomite can be represented by a sorption model that accounts for both surface complexation reactions on three distinct hydration sites (>CaOHo, >MgOHo, and >CO3Ho), and the kinetic dissolution of dolomite. These results are important in understanding and predicting the fate of Ba present in UOG wastewater disposed into deep dolomite saline aquifers.

Protein Hydraulics: Water Mediated Cooperativity of Substrate Binding in PKA

Catalytic subunits of protein kinases share a common fold centered around several precisely arranged key motifs. Multiple amino acids mutations within such conserved regions have been identified to either abrogate kinase catalytic function or switch it to permanently active state, in any case leading to severe disorders. The analysis of crystallographic structures representing diverse kinases reveals the presence of at least several water molecules whose positions within the protein core are equally well preserved as amino acid types in many functionally important locations. It remains unknown whether those water molecules play any important role, and whether their removal - disturbing local interaction patterns to no smaller degree than amino acid mutations - can affect kinase stability and function. We present the results of long computer simulations of PKA catalytic subunit targeted at the analysis of water structure, kinetics and affinity to buried hydration sites. In addition to already available structural information our simulations give insights into hydration pockets filled by disordered, highly mobile water molecules, not fully resolved in X-ray structures. We show that such regions are vital for the existence of flexible or partially disordered protein segments such as the activation and peptide binding loops in kinases. We further demonstrate that communication between the ATP and protein binding sites involves an isolated water molecule embedded between the DFG and YRD regions. Modification of its hydrogen bonding pattern induced by ATP binding affects the configuration of the DFG+1 residue. This in turn shifts the conformational equilibrium of the P+1 peptide positioning loop, promoting more frequent occurrence of peptide binding conformation. The above findings complement well NMR-based data on changes in local kinase mobility upon substrate binding, and provide mechanistic explanation for experimentally observed binding cooperativity of the two substrates.

AquaMMapS: An Alternative Tool to Monitor the Role of Water Molecules During Protein-Ligand Association.

Unquestionably, water appears to be an active player in the noncovalent protein-ligand binding process, as it can either bridge interactions between protein and ligand or can be replaced by the bound ligand. Accordingly, in the last decade, alternative computational methodologies have been sought with the aim of predicting the position and thermodynamic profile of water molecules (i.e., hydration sites) in the binding site using either the ligand-bound or ligand-free protein conformation. Herein, we present an alternative approach, named AquaMMapS, that provides a three-dimensional sampling of putative hydration sites. Interestingly, AquaMMapS can post-inspect molecular dynamics (MD) trajectories obtained from different MD engines using indifferently crystallographic or docking-driven structures as a starting point. Moreover, AquaMMapS is naturally integrated into supervised molecular dynamics (SuMD) simulations, presenting the possibility to inspect hydration sites during the ligand-protein association process. Finally, a penalty scoring method, named AquaMMapScoring(AMS), was developed to evaluate the number and nature of the water molecules displaced by a ligand approaching its binding site during the binding event, guiding a medicinal chemist to explore the most suitable regions of a ligand that can be decorated either with or without interfering with the interaction networks mediated by water molecules with specific recognition regions of the protein.

Prediction of Ordered Water Molecules in Protein Binding Sites from Molecular Dynamics Simulations: The Impact of Ligand Binding on Hydration Networks.

Water plays a major role in ligand binding and is attracting increasing attention in structure-based drug design. Water molecules can make large contributions to binding affinity by bridging protein–ligand interactions or by being displaced upon complex formation, but these phenomena are challenging to model at the molecular level. Herein, networks of ordered water molecules in protein binding sites were analyzed by clustering of molecular dynamics (MD) simulation trajectories. Locations of ordered waters (hydration sites) were first identified from simulations of high resolution crystal structures of 13 protein–ligand complexes. The MD-derived hydration sites reproduced 73% of the binding site water molecules observed in the crystal structures. If the simulations were repeated without the cocrystallized ligands, a majority (58%) of the crystal waters in the binding sites were still predicted. In addition, comparison of the hydration sites obtained from simulations carried out in the absence of ligands to those identified for the complexes revealed that the networks of ordered water molecules were preserved to a large extent, suggesting that the locations of waters in a protein–ligand interface are mainly dictated by the protein. Analysis of >1000 crystal structures showed that hydration sites bridged protein–ligand interactions in complexes with different ligands, and those with high MD-derived occupancies were more likely to correspond to experimentally observed ordered water molecules. The results demonstrate that ordered water molecules relevant for modeling of protein–ligand complexes can be identified from MD simulations. Our findings could contribute to development of improved methods for structure-based virtual screening and lead optimization.