Immobilized water in hydrophobic hydration (original) (raw)
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Journal of the American Chemical Society, 2019
Although perfluorination is known to enhance hydrophobicity and change protein activity, its influence on hydration-shell structure and thermodynamics remains an open question. Here we address that question by combining experimental Raman multivariate curve resolution spectroscopy with theoretical classical simulations and quantum mechanical calculations. Perfluorination of the terminal methyl group of ethanol is found to enhance the disruption of its hydration-shell hydrogen bond network. Our results reveal that this disruption is not due to the associated volume change but rather to the electrostatic stabilization of the water dangling OH•••F interaction. Thus, the hydration shell structure of fluorinated methyl groups results from a delicate balance of solute−water interactions that is intrinsically different from that associated with a methyl group.
2014
Water-protein interactions dictate many processes crucial to protein function including folding, dynamics, interactions with other biomolecules, and enzymatic catalysis. Here we examine the effect of surface fluorination on water-protein interactions. Modification of designed coiled-coil proteins by incorporation of 5,5,5-trifluoroleucine or (4S)-2-amino-4-methylhexanoic acid enables systematic examination of the effects of sidechain volume and fluorination on solvation dynamics. Using ultrafast fluorescence spectroscopy, we find that fluorinated side chains exert electrostatic drag on neighboring water molecules, slowing water motion at the protein surface.
The journal of physical chemistry. B, 2018
The aqueous mixture of 2,2,2-Trifluoroethanol (TFE) is one of the important alcoholic solvents which has been extensively used for understanding the stability of proteins as well as several chemical reactions. In this paper, the deconvolution of the IR lines in the OH stretching region has been applied to understand the local structure of water-water, alcohol-water and alcohol-alcohol interactions in the water mixture of TFE and ethanol (ETH). Further, MD simulation, quantum chemical and atoms in molecules calculations have been performed to encode the local structure information obtained from the experimental data. Addition of small amount of alcohol in the pure aqueous medium enhances the aggregation of water molecules for the case of ETH whereas, the hydrogen bond between TFE and water is dominant contributor for TFE. The -CF3 substitution changes the orientation and hydrogen bonding site of water molecules from the hydrophilic OH terminal to the hydrophobic -CF3 terminal of TFE ...
Collective properties of hydration: long range and specificity of hydrophobic interactions
Biophysical Journal, 1997
We report results of molecular dynamics (MD) simulations of composite model solutes in explicit molecular water solvent, eliciting novel aspects of the recently demonstrated, strong many-body character of hydration. Our solutes consist of identical apolar (hydrophobic) elements in fixed configurations. Results show that the many-body character of PMF is sufficiently strong to cause 1) a remarkable extension of the range of hydrophobic interactions between pairs of solute elements, up to distances large enough to rule out pairwise interactions of any type, and 2) a SIF that drives one of the hydrophobic solute elements toward the solvent rather than away from it. These findings complement recent data concerning SIFs on a protein at single-residue resolution and on model systems. They illustrate new important consequences of the collective character of hydration and of PMF and reveal new aspects of hydrophobic interactions and, in general, of SIFs. Their relevance to protein recognition, conformation, function, and folding and to the observed slight yet significant nonadditivity of functional effects of distant point mutations in proteins is discussed. These results point out the functional role of the configurational and dynamical states (and related statistical weights) corresponding to the complex configurational energy landscape of the two interacting systems: biomolecule + water.
Long-Time Correlations and Hydrophobe-Modified Hydrogen- Bonding Dynamics in Hydrophobic Hydration
The physical mechanisms behind hydrophobic hydration have been debated for over 65 years. Spectroscopic techniques have the ability to probe the dynamics of water in increasing detail, but many fundamental issues remain controversial. We have performed systematic first-principles ab initio Car−Parrinello molecular dynamics simulations over a broad temperature range and provide a detailed microscopic view on the dynamics of hydration water around a hydrophobic molecule, tetramethylurea. Our simulations provide a unifying view and resolve some of the controversies concerning femtosecond-infrared, THz−GHz dielectric relaxation, and nuclear magnetic resonance experiments and classical molecular dynamics simulations. Our computational results are in good quantitative agreement with experiments, and we provide a physical picture of the long-debated "iceberg" model; we show that the slow, long-time component is present within the hydration shell and that molecular jumps and over-coordination play important roles. We show that the structure and dynamics of hydration water around an organic molecule are non-uniform.
2017_Intech_FTIR for hydrated macromolecules.pdf
The interaction between biological macromolecules (proteins, nucleic acids, lipids and other biomolecules in the cell) and environmental water is an important determining factor in their conformational properties, stability and function. The hydration processes of biopolymers have been extensively studied in the past 20 years with reference to a considerable variety of models and concepts. In all recent works, a distinction is made between intracellular water that maintains the ordinary liquid state (bulk water) and water ordered in extended hydrogen‐bonded lattices at the surface and structured in the internal grooves of macromolecules (hydration water) in dependence on the chemical properties of the macromolecule surface. FTIR spectroscopy has been implemented in this field both for the sensitivity in the conformational analysis of biological macromol‐ ecules and the reliability in the investigation of the water network. A perturbation tech‐ nique such as dehydration‐rehydration treatment modifies the macromolecule structure and water distribution. It was applied to two structurally different proteins: lysozyme, a globular (α + β) protein and collagen, a fibrous protein characterized by the triple helix structure. Submitted to the treatment both of them display irreversible conformational changes.
Hydration Structure in Dilute Hydrofluoric Acid
2011
We have performed the multistate empirical valence bond (MS-EVB) molecular dynamics simulations of a dilute hydrofluoric acid solution at ambient temperature to study the hydration structure associated with its weak acidity. The developed MS-EVB model showed reasonable agreement with experiment and previous ab initio molecular dynamics and reference interaction site model self-consistent field simulations for the free energy and structural properties. The local tetrahedral and translational order parameters around the fluorine atom significantly increase in the transition and product states of the HF dissociation reaction. This indicates that the angular and translational rearrangements of the hydrogen-bond topology are necessary especially around the fluorine atom. At the transition state of the proton transfer, the tetrahedral order parameters are very large, whereas the translational order parameters are not. This suggests that for the proton transfer to occur the large angular rearrangements of the hydrogen-bond topology are more necessary than the translational ones.
Langmuir, 2013
The microscopic dynamic properties of water molecules present in the vicinity of a protein are expected to be sensitive to its local conformational motions and the presence of polar and charged groups at the surface capable of anchoring water molecules through hydrogen bonds. In this work, we attempt to understand such sensitivity by performing detailed molecular dynamics simulations of the globular protein barstar solvated in aqueous medium. Our calculations demonstrate that enhanced confinement at the protein surface on freezing its local motions leads to increasingly restricted water mobility with long residence times around the secondary structures. It is found that the inability of the surface water molecules to bind with the protein residues by hydrogen bonds in the absence of protein−water (PW) electrostatic interactions is compensated by enhanced water−water hydrogen bonds around the protein with uniform bulklike behaviors. Importantly, it is further noticed that in contrast to the PW hydrogen bond relaxation time scale, the kinetics of the breaking and formation of such bonds are not affected on freezing the protein's conformational motions.