Separable cooperative and localized translational motions of water confined by a chemically heterogeneous environment

Malardier-Jugroot, Cécile; Head‐Gordon, Teresa

doi:10.1039/b616997j

Cited by 24 publications

(62 citation statements)

References 28 publications

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“…S11), indicating a similar relaxation (22,26). However, the barriers for the inner-layer coupled motions are smaller than those obtained by experiments in several other proteins (27)(28)(29). (iv) The prefactors for the hydration water motions are always greater than those of the driven tryptophan relaxations.…”

Section: Significancementioning

confidence: 75%

Dynamics and mechanism of ultrafast water–protein interactions

Qin

Wang

Zhong

2016

Proc. Natl. Acad. Sci. U.S.A.

129

157

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Protein hydration is essential to its structure, dynamics, and function, but water-protein interactions have not been directly observed in real time at physiological temperature to our awareness. By using a tryptophan scan with femtosecond spectroscopy, we simultaneously measured the hydration water dynamics and protein side-chain motions with temperature dependence. We observed the heterogeneous hydration dynamics around the global protein surface with two types of coupled motions, collective water/side-chain reorientation in a few picoseconds and cooperative water/sidechain restructuring in tens of picoseconds. The ultrafast dynamics in hundreds of femtoseconds is from the outer-layer, bulk-type mobile water molecules in the hydration shell. We also found that the hydration water dynamics are always faster than protein sidechain relaxations but with the same energy barriers, indicating hydration shell fluctuations driving protein side-chain motions on the picosecond time scales and thus elucidating their ultimate relationship.hydration shell dynamics | protein side-chain motion | water-driven relaxation | coupled fluctuation | tryptophan scan W ater-protein interactions are critical to protein structural stability and flexibility, functional dynamics, and biological activities (1, 2). Various methods such as neutron scattering (3), NMR (4), laser spectroscopy (5, 6), and molecular dynamics (MD) simulations (7) have been used to reveal protein surface hydration and coupled water-protein dynamics on different time and length scales. Hydration water molecules often participate in various protein functions and their motions even directly "control" protein fluctuations (2, 8). Frauenfelder et al. recently proposed a unified model for protein dynamics (8): large-scale protein motions are slaved to the fluctuations of bulk solvent and controlled by solvent viscosity while internal protein motions are slaved to the fluctuations of the hydration shell and controlled by hydration water. However, direct measurements of such coupled fluctuations at physiological temperature are challenging as a result of the ultrafast nature of water motions, and therefore most studies are indirect or at low temperature (3, 4). Here, we used a tryptophan (W) scan to probe global surface hydration (9) and used femtosecond spectroscopy to follow hydration water motions and local side-chain fluctuations in real time. With temperature dependence, we systematically measured their dynamics and thus finally elucidate their ultimate relationship. Results and DiscussionTryptophan Scan and Femtosecond Fluorescence Spectroscopy. We used DNA polymerase IV (Dpo4) (10), a hyperthermal enzyme without a single tryptophan residue, as a model protein, and designed 10 tryptophan mutants, one at a time, to probe four different domains (Fig. 1A). We performed systematic measurements of tryptophan fluorescence intensity changes with wavelength and time and thereby constructed 3D fluorescence profiles (SI Appendix, SI Note 1). One example of an R176W mutant is ...

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Section: Significancementioning

confidence: 75%

Dynamics and mechanism of ultrafast water–protein interactions

Qin

Wang

Zhong

2016

Proc. Natl. Acad. Sci. U.S.A.

129

157

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“…It should be noted that suppression of translational water dynamics via ''chemical confinement" in the molecular solutions has been commonly observed in chemical mixtures [22,23] and concentrated solutions of biomolecules [24][25][26][27]. One interesting example was a study of a dimethyl-sulfoxide/water mixture [22] where self-diffusion coefficient and the residence time between jumps for water molecules became Arrhenius, in contrast to nonArrhenius behavior in pure water.…”

Section: Effects Of Ion Hydration and Confinement On Dynamicsmentioning

confidence: 95%

Dynamics of water in LiCl and CaCl2 aqueous solutions confined in silica matrices: A backscattering neutron spectroscopy study

et al. 2008

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“…Given the qualitative improvement in solution structure using the AMOEBA model, we also compared the changes in water dynamics as a function of temperature against our experimental data. Based on quasi-elastic neutron scattering (QENS) experiments, the amphiphilic NALMA peptide solution exhibits two translational relaxations at low temperatures, while the hydrophilic peptide shows only a single translational process, with transport properties of water near both peptide chemistries being very suppressed with respect to bulk dynamics 75,76. This is a real stress test for any force field given the range of dynamical trends that depend on amino acid chemistry and temperature.…”

Section: Condensed Phase Structure and Dynamicsmentioning

confidence: 99%

Current Status of the AMOEBA Polarizable Force Field

Ponder¹,

Wu²,

et al. 2010

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Molecular force fields have been approaching a generational transition over the past several years, moving away from well-established and well-tuned, but intrinsically limited, fixed point charge models towards more intricate and expensive polarizable models that should allow more accurate description of molecular properties. The recently introduced AMOEBA force field is a leading publicly available example of this next generation of theoretical model, but to date has only received relatively limited validation, which we address here. We show that the AMOEBA force field is in fact a significant improvement over fixed charge models for small molecule structural and thermodynamic observables in particular, although further fine-tuning is necessary to describe solvation free energies of drug-like small molecules, dynamical properties away from ambient conditions, and possible improvements in aromatic interactions. State of the art electronic structure calculations reveal generally very good agreement with AMOEBA for demanding problems such as relative conformational energies of the alanine tetrapeptide and isomers of water sulfate complexes. AMOEBA is shown to be especially successful on protein-ligand binding and computational X-ray crystallography where polarization and accurate electrostatics are critical.

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Separable cooperative and localized translational motions of water confined by a chemically heterogeneous environment

Cited by 24 publications

References 28 publications

Dynamics and mechanism of ultrafast water–protein interactions

Dynamics and mechanism of ultrafast water–protein interactions

Dynamics of water in LiCl and CaCl2 aqueous solutions confined in silica matrices: A backscattering neutron spectroscopy study

Current Status of the AMOEBA Polarizable Force Field

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