Literature DB >> 10827960

On the temperature and pressure dependence of a range of properties of a type of water model commonly used in high-temperature protein unfolding simulations.

R Walser1, A E Mark, W F van Gunsteren.   

Abstract

Molecular dynamics simulations of protein folding and unfolding are often carried out at temperatures (400-600 K) that are much higher than physiological or room temperature to speed up the (un)folding process. Use of such high temperatures changes both the protein and solvent properties considerably, compared to physiological or room temperature. Water models designed for use in conjunction with biomolecules, such as the simple point charge (SPC) model, have generally been calibrated at room temperature and pressure. To determine the distortive effect of high simulation temperatures on the behavior of such "room temperature" water models, the structural, dynamic, and thermodynamic properties of the much-used SPC water model are investigated in the temperature range from 300 to 500 K. Both constant pressure and constant volume conditions, as used in protein simulations, were analyzed. We found that all properties analyzed change markedly with increasing temperature, but no phase transition in this temperature range was observed.

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Year:  2000        PMID: 10827960      PMCID: PMC1300865          DOI: 10.1016/S0006-3495(00)76820-2

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


  10 in total

1.  Simulation of the thermal denaturation of hen egg white lysozyme: trapping the molten globule state.

Authors:  A E Mark; W F van Gunsteren
Journal:  Biochemistry       Date:  1992-09-01       Impact factor: 3.162

2.  A model of the molten globule state from molecular dynamics simulations.

Authors:  V Daggett; M Levitt
Journal:  Proc Natl Acad Sci U S A       Date:  1992-06-01       Impact factor: 11.205

3.  Identification of functional and unfolding motions of cutinase as obtained from molecular dynamics computer simulations.

Authors:  L D Creveld; A Amadei; R C van Schaik; H A Pepermans; J de Vlieg; H J Berendsen
Journal:  Proteins       Date:  1998-11-01

4.  Molecular dynamics simulation of the unfolding of barnase: characterization of the major intermediate.

Authors:  A Li; V Daggett
Journal:  J Mol Biol       Date:  1998-01-30       Impact factor: 5.469

5.  Characterization of residual structure in the thermally denatured state of barnase by simulation and experiment: description of the folding pathway.

Authors:  C J Bond; K B Wong; J Clarke; A R Fersht; V Daggett
Journal:  Proc Natl Acad Sci U S A       Date:  1997-12-09       Impact factor: 11.205

6.  Differential stability of beta-sheets and alpha-helices in beta-lactamase: a high temperature molecular dynamics study of unfolding intermediates.

Authors:  S Vijayakumar; S Vishveshwara; G Ravishanker; D L Beveridge
Journal:  Biophys J       Date:  1993-12       Impact factor: 4.033

7.  Molecular dynamics simulation of protein denaturation: solvation of the hydrophobic cores and secondary structure of barnase.

Authors:  A Caflisch; M Karplus
Journal:  Proc Natl Acad Sci U S A       Date:  1994-03-01       Impact factor: 11.205

8.  Protein unfolding pathways explored through molecular dynamics simulations.

Authors:  V Daggett; M Levitt
Journal:  J Mol Biol       Date:  1993-07-20       Impact factor: 5.469

9.  Refolding of potato carboxypeptidase inhibitor by molecular dynamics simulations with disulfide bond constraints.

Authors:  M A Martí-Renom; R H Stote; E Querol; F X Avilés; M Karplus
Journal:  J Mol Biol       Date:  1998-11-20       Impact factor: 5.469

10.  Acid and thermal denaturation of barnase investigated by molecular dynamics simulations.

Authors:  A Caflisch; M Karplus
Journal:  J Mol Biol       Date:  1995-10-06       Impact factor: 5.469

  10 in total
  9 in total

1.  The free energy landscape for beta hairpin folding in explicit water.

Authors:  R Zhou; B J Berne; R Germain
Journal:  Proc Natl Acad Sci U S A       Date:  2001-12-18       Impact factor: 11.205

2.  Protein unfolding transitions in an intrinsically unstable annexin domain: molecular dynamics simulation and comparison with nuclear magnetic resonance data.

Authors:  Tru Huynh; Jeremy C Smith; Alain Sanson
Journal:  Biophys J       Date:  2002-08       Impact factor: 4.033

Review 3.  Structure, dynamics and reactions of protein hydration water.

Authors:  Jeremy C Smith; Franci Merzel; Ana-Nicoleta Bondar; Alexander Tournier; Stefan Fischer
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2004-08-29       Impact factor: 6.237

4.  Impact of the mutation A21G (Flemish variant) on Alzheimer's beta-amyloid dimers by molecular dynamics simulations.

Authors:  Alexis Huet; Philippe Derreumaux
Journal:  Biophys J       Date:  2006-08-04       Impact factor: 4.033

5.  Structural and hydration properties of the partially unfolded states of the prion protein.

Authors:  Alfonso De Simone; Adriana Zagari; Philippe Derreumaux
Journal:  Biophys J       Date:  2007-05-04       Impact factor: 4.033

6.  Translational hydration water dynamics drives the protein glass transition.

Authors:  Alexander L Tournier; Jiancong Xu; Jeremy C Smith
Journal:  Biophys J       Date:  2003-09       Impact factor: 4.033

7.  Remarkable patterns of surface water ordering around polarized buckminsterfullerene.

Authors:  Gaurav Chopra; Michael Levitt
Journal:  Proc Natl Acad Sci U S A       Date:  2011-08-15       Impact factor: 11.205

8.  Lipid Bilayer Interactions of Amyloidogenic N-Terminal Fragment of Apolipoprotein A-I Probed by Förster Resonance Energy Transfer and Molecular Dynamics Simulations.

Authors:  Galyna P Gorbenko; Valeriya Trusova; Chiharu Mizuguchi; Hiroyuki Saito
Journal:  J Fluoresc       Date:  2018-07-15       Impact factor: 2.217

9.  Interfacing CRYSTAL/AMBER to Optimize QM/MM Lennard⁻Jones Parameters for Water and to Study Solvation of TiO₂ Nanoparticles.

Authors:  Asmus Ougaard Dohn; Daniele Selli; Gianluca Fazio; Lorenzo Ferraro; Jens Jørgen Mortensen; Bartolomeo Civalleri; Cristiana Di Valentin
Journal:  Molecules       Date:  2018-11-13       Impact factor: 4.411

  9 in total

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