Literature DB >> 15448207

Bulk-solvent and hydration-shell fluctuations, similar to alpha- and beta-fluctuations in glasses, control protein motions and functions.

P W Fenimore1, Hans Frauenfelder, B H McMahon, R D Young.   

Abstract

The concept that proteins exist in numerous different conformations or conformational substates, described by an energy landscape, is now accepted, but the dynamics is incompletely explored. We have previously shown that large-scale protein motions, such as the exit of a ligand from the protein interior, follow the dielectric fluctuations in the bulk solvent. Here, we demonstrate, by using mean-square displacements (msd) from Mossbauer and neutron-scattering experiments, that fluctuations in the hydration shell control fast fluctuations in the protein. We call the first type solvent-slaved or alpha-fluctuations and the second type hydration-shell-coupled or beta-fluctuations. Solvent-slaved motions are similar to the alpha-fluctuations in glasses. Their temperature dependence can be approximated by a Vogel-Tammann-Fulcher relation and they are absent in a solid environment. Hydration-shell-coupled fluctuations are similar to the beta-relaxation in glasses. They can be approximated by a Ferry or an Arrhenius relation, are much reduced or absent in dehydrated proteins, and occur in hydrated proteins even if embedded in a solid. They can be responsible for internal processes such as the migration of ligands within myoglobin. The existence of two functionally important fluctuations in proteins, one slaved to bulk motions and the other coupled to hydration-shell fluctuations, implies that the environment can control protein functions through different avenues and that no real protein transition occurs at approximately 200 K. The large number of conformational substates is essential; proteins cannot function without this reservoir of entropy, which resides mainly in the hydration shell.

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Year:  2004        PMID: 15448207      PMCID: PMC521939          DOI: 10.1073/pnas.0405573101

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  39 in total

1.  Geminate rebinding in trehalose-glass embedded myoglobins reveals residue-specific control of intramolecular trajectories.

Authors:  David Dantsker; Uri Samuni; Adam J Friedman; Ming Yang; Anandhi Ray; Joel M Friedman
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2.  Direct observation of tiers in the energy landscape of a chromoprotein: a single-molecule study.

Authors:  Clemens Hofmann; Thijs J Aartsma; Hartmut Michel; Jürgen Köhler
Journal:  Proc Natl Acad Sci U S A       Date:  2003-12-11       Impact factor: 11.205

3.  Slaving: solvent fluctuations dominate protein dynamics and functions.

Authors:  P W Fenimore; H Frauenfelder; B H McMahon; F G Parak
Journal:  Proc Natl Acad Sci U S A       Date:  2002-11-20       Impact factor: 11.205

4.  Effect of the environment on the protein dynamical transition: a neutron scattering study.

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Journal:  Biophys J       Date:  2002-08       Impact factor: 4.033

5.  Classification of secondary relaxation in glass-formers based on dynamic properties.

Authors:  K L Ngai; M Paluch
Journal:  J Chem Phys       Date:  2004-01-08       Impact factor: 3.488

6.  The energy landscapes and motions of proteins.

Authors:  H Frauenfelder; S G Sligar; P G Wolynes
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Review 7.  Cooperative charge fluctuations by migrating protons in globular proteins.

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Authors:  A Ansari; J Berendzen; S F Bowne; H Frauenfelder; I E Iben; T B Sauke; E Shyamsunder; R D Young
Journal:  Proc Natl Acad Sci U S A       Date:  1985-08       Impact factor: 11.205

9.  Protein dynamics. Mössbauer spectroscopy on deoxymyoglobin crystals.

Authors:  F Parak; E W Knapp; D Kucheida
Journal:  J Mol Biol       Date:  1982-10-15       Impact factor: 5.469

10.  Hydrogen and deuterium in myoglobin as seen by a neutron structure determination at 1.5 A resolution.

Authors:  Andreas Ostermann; Ichiro Tanaka; Niklas Engler; Nobuo Niimura; Fritz G Parak
Journal:  Biophys Chem       Date:  2002-03-28       Impact factor: 2.352

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  113 in total

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Journal:  Proc Natl Acad Sci U S A       Date:  2011-12-13       Impact factor: 11.205

2.  Dynamics of biological macromolecules: not a simple slaving by hydration water.

Authors:  S Khodadadi; J H Roh; A Kisliuk; E Mamontov; M Tyagi; S A Woodson; R M Briber; A P Sokolov
Journal:  Biophys J       Date:  2010-04-07       Impact factor: 4.033

3.  Joint X-ray and neutron refinement with phenix.refine.

Authors:  Pavel V Afonine; Marat Mustyakimov; Ralf W Grosse-Kunstleve; Nigel W Moriarty; Paul Langan; Paul D Adams
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2010-10-20

4.  Solvent effect on librational dynamics of spin-labelled haemoglobin by ED- and CW-EPR.

Authors:  Francesco Scarpelli; Rosa Bartucci; Luigi Sportelli; Rita Guzzi
Journal:  Eur Biophys J       Date:  2010-11-25       Impact factor: 1.733

Review 5.  Coupled motions in enzyme catalysis.

Authors:  Vishal C Nashine; Sharon Hammes-Schiffer; Stephen J Benkovic
Journal:  Curr Opin Chem Biol       Date:  2010-08-20       Impact factor: 8.822

6.  Resolution and Characterization of Chemical Steps in Enzyme Catalytic Sequences by Using Low-Temperature and Time-Resolved, Full-Spectrum EPR Spectroscopy in Fluid Cryosolvent and Frozen Solution Systems.

Authors:  Miao Wang; Chen Zhu; Meghan Kohne; Kurt Warncke
Journal:  Methods Enzymol       Date:  2015-09-14       Impact factor: 1.600

7.  A Biophysical Perspective on Enzyme Catalysis.

Authors:  Pratul K Agarwal
Journal:  Biochemistry       Date:  2018-12-18       Impact factor: 3.162

8.  Solution properties of γ-crystallins: hydration of fish and mammal γ-crystallins.

Authors:  Huaying Zhao; Yingwei Chen; Lenka Rezabkova; Zhengrong Wu; Graeme Wistow; Peter Schuck
Journal:  Protein Sci       Date:  2013-11-27       Impact factor: 6.725

9.  Coupling of protein and hydration-water dynamics in biological membranes.

Authors:  K Wood; M Plazanet; F Gabel; B Kessler; D Oesterhelt; D J Tobias; G Zaccai; M Weik
Journal:  Proc Natl Acad Sci U S A       Date:  2007-11-06       Impact factor: 11.205

Review 10.  Effects of glycosylation on the stability of protein pharmaceuticals.

Authors:  Ricardo J Solá; Kai Griebenow
Journal:  J Pharm Sci       Date:  2009-04       Impact factor: 3.534

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