Presence Of Water Molecules In Structure Research Articles

Water is a powerful dynamic allosteric modulator in rhodopsin activation.

Rhodopsin is an archetype for G protein-coupled receptors (GPCRs) which are membrane proteins involved in cellular signal transduction. Although GPCR X-ray structures show the presence of structural water molecules, their physiological role in the signaling process remains uncertain. Our previous work has shown that in lipid membranes rhodopsin activation is coupled to bulk water movements into the protein to stabilize the effector binding conformation [1,2]. Here we extend the experimental approach to explore modulation of the conformational energetics of rhodopsin activation in lipid membranes. We hypothesized that the thermodynamic stability of conformational substates of photoactivated rhodopsin is hydration mediated. Accordingly, we changed the osmotic stress on rhodopsin using different hydrophilic polymers including polyethylene glycols (PEGs), dextrans, polyvinylpyrrolidones, and their monomers. Reversible shifting of the metarhodopsin equilibrium due to the osmotic stress was probed using UV-visible spectroscopy. We observed that the rhodopsin activation is associated with a bulk influx of water due to the osmotic dehydration by large, excluded polymers which inhibit GPCR activation. By contrast small penetrable osmolytes and monomers have lower conformational entropy and showed a nonosmotic trend in rhodopsin activation. Small osmolytes penetrate the receptor core and stabilize the more expanded active state of rhodopsin until reaching a quantifiable saturation point. Both PEGs and dextrans with very high molar masses deviated in their trends from other large polymers due to a crowding effect, whereby extremely large osmolytes induce steric forces on rhodopsin and restrict their volume occupancy. Further studies of hydration effects on binding of the G-protein and receptor catalyzed exchange of GTP for GDP are expected to provide significant clues on the complete mechanism of G-protein binding and release

How the Environment Encourages the Natural Formation of Hydrated V2O5.

Herein, we report the microscopic and spectroscopic signatures of the hydrated V2O5 phase, prepared from the α-V2O5 powder, which was kept in deionized water inside an airtight glass container for approximately 2.5 years. The experimental results show an evolution of the V4+ component in V 2p3/2 core energy level spectra, and a peak corresponding to σ-OH– bond appeared in the valence band spectra in the hydrated V2O5 powder sample due to the water intercalation. Vanadium metal oxide particles were found to be self-nucleated into micro/nanorods after a long period of exposure to an extremely humid environment. The distinct features in the spectra obtained with high-resolution transmission electron microscopy, micro-Raman scattering, and X-ray photoelectron spectroscopy confirmed the presence of structural water molecules for the first time in the long-aged naturally hydrated V2O5 phase.

How osmotic stress and crowding affect G-protein-coupled receptor activation

G-protein-coupled receptors (GPCRs) are integral membrane proteins responsible for signal transduction across cellular membranes and constitute the largest class of medicinal targets. Although three-dimensional structures show the presence of structural water molecules within GPCRs, functional role of these water molecules has remained unknown. Our previous work has further shown a bulk influx of water stabilizing the active rhodopsin conformation [1]. Here we broadened the experimental approach to investigate how the conformational energetics of GPCR activation are modulated by water using a series of hydrophilic polymers including polyethylene glycols (PEGs), dextrans, polyvinylpyrrolidones, and their monomers.

From thorite to coffinite: A spectroscopic study of Th1−xUxSiO4 solid solutions

Coffinite (USiO4), along with Th1−xUxSiO4 uranothorite solid solutions, are frequently present in reduced economically exploitable uranium ores. They could also control the concentration of uranium in the environment in the case of accidental release from underground radwaste repository. This paper reports for the first time a thorough FTIR and Raman study relative to the Th1−xUxSiO4 system, including synthetic analogues of thorite and coffinite end-members. Both sets of spectra confirmed the formulation of the samples and allowed to rule out the presence of structural water molecules and/or hydroxyl groups in the coffinite. Also, no characteristic signal of UO22+ uranyl ion was recorded, ensuring that uranium was fully incorporated under its tetravalent oxidation state. The variation of the positions corresponding to SiO4 internal vibration modes was then followed versus the chemical composition of the samples. If the FTIR spectra did not revealed any significant shift in the bands position, several Raman modes followed a linear trend as a function of the uranium incorporation rate. On this basis, Raman spectroscopy could be considered as a promising tool for the semi-quantitative determination of chemical composition of uranothorite samples, particularly for those coming from mineral ores. Finally, the data collected for the coffinite end-member, as the first to be obtained on pure synthetic samples, allowed a review of the results previously reported in the literature for this compound.

Protein-Ligand Docking in the New Millennium – A Retrospective of 10 Years in the Field

Protein-ligand docking is currently an important tool in drug discovery efforts and an active area of research that has been the subject of important developments over the last decade. These are well portrayed in the rising number of available protein-ligand docking software programs, increasing level of sophistication of its most recent applications, and growing number of users. While starting by summarizing the key concepts in protein-ligand docking, this article presents an analysis of the evolution of this important field of research over the past decade. Particular attention is given to the massive range of alternatives, in terms of protein-ligand docking software programs currently available. The emerging trends in this field are the subject of special attention, while old established docking alternatives are critically revisited. Current challenges in the field of protein-ligand docking such as the treatment of protein flexibility, the presence of structural water molecules and its effect in docking, and the entropy of binding are dissected and discussed, trying to anticipate the next years in the field.

Analysis of structural water and CH···π interactions in HIV-1 protease and PTP1B complexes using a hydrogen bond prediction tool, HBPredicT

A hydrogen bond prediction tool HBPredicT is developed for detecting structural water molecules and CH···π interactions in PDB files of protein-ligand complexes. The program adds the missing hydrogen atoms to the protein, ligands, and oxygen atoms of water molecules and subsequently all the hydrogen bonds in the complex are located using specific geometrical criteria. Hydrogen bonds are classified into various types based on (i) donor and acceptor atoms, and interactions such as (ii) protein-protein, (iii) protein-ligand, (iv) protein-water, (v) ligand-water, (vi) water-water, and (vii) protein-water-ligand. Using the information in category (vii), the water molecules which form hydrogen bonds with the ligand and the protein simultaneously-the structural water-is identified and retrieved along with the associated ligand and protein residues. For CH···π interactions, the relevant portions of the corresponding structures are also extracted in the output. The application potential of this program is tested using 19 HIV-1 protease and 11 PTP1B inhibitor complexes. All the systems showed presence of structural water molecules and in several cases, the CH···π interaction between ligand and protein are detected. A rare occurrence of CH···π interactions emanating from both faces of a phenyl ring of the inhibitor is identified in HIV-1 protease 1D4L.

Electrostatic Lock-and-Key Model for the Study of Biological Isosterism: Role of Structural Water in the Binding of Basic Pancreatic Trypsin Inhibitor to ß-Trypsin

We propose the electrostatic lock-and-key model for the analysis of the interaction between beta-trypsin and basic pancreatic trypsin inhibitor (BPTI). Prerequisite for the proper recognition of the ligand by the protein is that, beside a steric complementarity, matching of electrostatic patterns is attained. It is found that the complementarity is imperfect in the vicinity of BPTI backbone carbonyl oxygen atoms and this imperfection is diminished by the presence of structural water molecules bound to the contact surface. Some novel types of biological isosteres are proposed. It is expected that the Gibbs free energy of binding increases upon changing the moieties greater than C = O ... H-OH and greater than C = O to greater than CHCH2 CH2OH and greater than CHOH groups, respectively.