Literature DB >> 14990511

Hydration dynamics near a model protein surface.

Daniela Russo1, Greg Hura, Teresa Head-Gordon.   

Abstract

The evolution of water dynamics from dilute to very high concentration solutions of a prototypical hydrophobic amino acid with its polar backbone, N-acetyl-leucine-methylamide (NALMA), is studied by quasi-elastic neutron scattering (QENS) and molecular dynamics (MD) simulation for both the completely deuterated and completely hydrogenated leucine monomer. The NALMA-water system and the QENS data together provide a unique study for characterizing the dynamics of different hydration layers near a prototypical hydrophobic side chain and the backbone of which it is attached. We observe several unexpected features in the dynamics of these biological solutions under ambient conditions. The NALMA dynamics shows evidence of de Gennes narrowing, an indication of coherent long timescale structural relaxation dynamics. The translational and rotational water dynamics at the highest solute concentrations are found to be highly suppressed as characterized by long residential time and slow diffusion coefficients. The analysis of the more dilute concentration solutions models the first hydration shell with the 2.0 M spectra. We find that for outer layer hydration dynamics that the translational diffusion dynamics is still suppressed, although the rotational relaxation time and residential time are converged to bulk-water values. Molecular dynamics analysis of the first hydration shell water dynamics shows spatially heterogeneous water dynamics, with fast water motions near the hydrophobic side chain, and much slower water motions near the hydrophilic backbone. We discuss the hydration dynamics results of this model protein system in the context of protein function and protein-protein recognition.

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Year:  2004        PMID: 14990511      PMCID: PMC1304019          DOI: 10.1016/S0006-3495(04)74252-6

Source DB:  PubMed          Journal:  Biophys J        ISSN: 0006-3495            Impact factor:   4.033


  25 in total

1.  Molecular dynamics simulations of unfolding and refolding of a beta-hairpin fragment of protein G.

Authors:  V S Pande; D S Rokhsar
Journal:  Proc Natl Acad Sci U S A       Date:  1999-08-03       Impact factor: 11.205

2.  Hydration of denatured and molten globule proteins.

Authors:  V P Denisov; B H Jonsson; B Halle
Journal:  Nat Struct Biol       Date:  1999-03

3.  A view of dynamics changes in the molten globule-native folding step by quasielastic neutron scattering.

Authors:  Z Bu; D A Neumann; S H Lee; C M Brown; D M Engelman; C C Han
Journal:  J Mol Biol       Date:  2000-08-11       Impact factor: 5.469

Review 4.  An introduction to "Water in the cell": tamed Hydra?

Authors:  P Mentré
Journal:  Cell Mol Biol (Noisy-le-grand)       Date:  2001-07       Impact factor: 1.770

5.  Is the first hydration shell of lysozyme of higher density than bulk water?

Authors:  Franci Merzel; Jeremy C Smith
Journal:  Proc Natl Acad Sci U S A       Date:  2002-04-16       Impact factor: 11.205

6.  Biological water at the protein surface: dynamical solvation probed directly with femtosecond resolution.

Authors:  Samir Kumar Pal; Jorge Peon; Ahmed H Zewail
Journal:  Proc Natl Acad Sci U S A       Date:  2002-02-12       Impact factor: 11.205

7.  Probing the folding free energy landscape of the Src-SH3 protein domain.

Authors:  Joan-Emma Shea; Jose N Onuchic; Charles L Brooks
Journal:  Proc Natl Acad Sci U S A       Date:  2002-11-22       Impact factor: 11.205

8.  Molecular picture of folding of a small alpha/beta protein.

Authors:  F B Sheinerman; C L Brooks
Journal:  Proc Natl Acad Sci U S A       Date:  1998-02-17       Impact factor: 11.205

9.  Water-coupled low-frequency modes of myoglobin and lysozyme observed by inelastic neutron scattering.

Authors:  M Diehl; W Doster; W Petry; H Schober
Journal:  Biophys J       Date:  1997-11       Impact factor: 4.033

10.  Hydration-coupled dynamics in proteins studied by neutron scattering and NMR: the case of the typical EF-hand calcium-binding parvalbumin.

Authors:  J M Zanotti; M C Bellissent-Funel; J Parello
Journal:  Biophys J       Date:  1999-05       Impact factor: 4.033

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  30 in total

1.  A novel method reveals that solvent water favors polyproline II over beta-strand conformation in peptides and unfolded proteins: conditional hydrophobic accessible surface area (CHASA).

Authors:  Patrick J Fleming; Nicholas C Fitzkee; Mihaly Mezei; Rajgopal Srinivasan; George D Rose
Journal:  Protein Sci       Date:  2004-12-02       Impact factor: 6.725

2.  Decomposition of protein experimental compressibility into intrinsic and hydration shell contributions.

Authors:  Voichita M Dadarlat; Carol Beth Post
Journal:  Biophys J       Date:  2006-09-22       Impact factor: 4.033

3.  C-phycocyanin hydration water dynamics in the presence of trehalose: an incoherent elastic neutron scattering study at different energy resolutions.

Authors:  Frank Gabel; Marie-Claire Bellissent-Funel
Journal:  Biophys J       Date:  2007-03-09       Impact factor: 4.033

4.  Secondary structure bias in generalized Born solvent models: comparison of conformational ensembles and free energy of solvent polarization from explicit and implicit solvation.

Authors:  Daniel R Roe; Asim Okur; Lauren Wickstrom; Viktor Hornak; Carlos Simmerling
Journal:  J Phys Chem B       Date:  2007-01-27       Impact factor: 2.991

5.  The correlation of cold denaturation temperature with surface stability factor of proteins.

Authors:  Hamid Hadi-Alijanvand; Faizan Ahmad; A A Moosavi-Movahedi
Journal:  Protein J       Date:  2007-09       Impact factor: 2.371

6.  Accurate SAXS profile computation and its assessment by contrast variation experiments.

Authors:  Dina Schneidman-Duhovny; Michal Hammel; John A Tainer; Andrej Sali
Journal:  Biophys J       Date:  2013-08-20       Impact factor: 4.033

7.  Hydration dynamics as an intrinsic ruler for refining protein structure at lipid membrane interfaces.

Authors:  Chi-Yuan Cheng; Jobin Varkey; Mark R Ambroso; Ralf Langen; Songi Han
Journal:  Proc Natl Acad Sci U S A       Date:  2013-09-30       Impact factor: 11.205

8.  Cholesterol enhances surface water diffusion of phospholipid bilayers.

Authors:  Chi-Yuan Cheng; Luuk L C Olijve; Ravinath Kausik; Songi Han
Journal:  J Chem Phys       Date:  2014-12-14       Impact factor: 3.488

9.  Hydration water mobility is enhanced around tau amyloid fibers.

Authors:  Yann Fichou; Giorgio Schirò; François-Xavier Gallat; Cedric Laguri; Martine Moulin; Jérôme Combet; Michaela Zamponi; Michael Härtlein; Catherine Picart; Estelle Mossou; Hugues Lortat-Jacob; Jacques-Philippe Colletier; Douglas J Tobias; Martin Weik
Journal:  Proc Natl Acad Sci U S A       Date:  2015-04-27       Impact factor: 11.205

10.  Hierarchical organization of eglin c native state dynamics is shaped by competing direct and water-mediated interactions.

Authors:  Christopher Kroboth Materese; Christa Charisse Goldmon; Garegin A Papoian
Journal:  Proc Natl Acad Sci U S A       Date:  2008-07-29       Impact factor: 11.205

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