Literature DB >> 17766342

A water-explicit lattice model of heat-, cold-, and pressure-induced protein unfolding.

Bryan A Patel1, Pablo G Debenedetti, Frank H Stillinger, Peter J Rossky.   

Abstract

We investigate the effect of temperature and pressure on polypeptide conformational stability using a two-dimensional square lattice model in which water is represented explicitly. The model captures many aspects of water thermodynamics, including the existence of density anomalies, and we consider here the simplest representation of a protein: a hydrophobic homopolymer. We show that an explicit treatment of hydrophobic hydration is sufficient to produce cold, pressure, and thermal denaturation. We investigate the effects of the enthalpic and entropic components of the water-protein interactions on the overall folding phase diagram, and show that even a schematic model such as the one we consider yields reasonable values for the temperature and pressure ranges within which highly compact homopolymer configurations are thermodynamically stable.

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Year:  2007        PMID: 17766342      PMCID: PMC2098741          DOI: 10.1529/biophysj.107.108530

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


  37 in total

1.  Putting proteins back into water

Authors: 
Journal:  Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics       Date:  2000-12

2.  Determining the density of states for classical statistical models: a random walk algorithm to produce a flat histogram.

Authors:  F Wang; D P Landau
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2001-10-17

3.  Beta-hairpin folding mechanism of a nine-residue peptide revealed from molecular dynamics simulations in explicit water.

Authors:  Xiongwu Wu; Bernard R Brooks
Journal:  Biophys J       Date:  2004-04       Impact factor: 4.033

4.  An all-atom force field for tertiary structure prediction of helical proteins.

Authors:  T Herges; W Wenzel
Journal:  Biophys J       Date:  2004-11       Impact factor: 4.033

5.  Singularity-free interpretation of the thermodynamics of supercooled water.

Authors: 
Journal:  Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics       Date:  1996-06

6.  Effects of lengthscales and attractions on the collapse of hydrophobic polymers in water.

Authors:  Manoj V Athawale; Gaurav Goel; Tuhin Ghosh; Thomas M Truskett; Shekhar Garde
Journal:  Proc Natl Acad Sci U S A       Date:  2007-01-10       Impact factor: 11.205

7.  Hydrophobicity of amino acid residues in globular proteins.

Authors:  G D Rose; A R Geselowitz; G J Lesser; R H Lee; M H Zehfus
Journal:  Science       Date:  1985-08-30       Impact factor: 47.728

8.  Folding and misfolding of the papillomavirus E6 interacting peptide E6ap.

Authors:  Bianxiao Cui; Min-Yi Shen; Karl F Freed
Journal:  Proc Natl Acad Sci U S A       Date:  2003-05-27       Impact factor: 11.205

9.  Hydrophobic collapse in multidomain protein folding.

Authors:  Ruhong Zhou; Xuhui Huang; Claudio J Margulis; Bruce J Berne
Journal:  Science       Date:  2004-09-10       Impact factor: 47.728

10.  Temperature-dependent conformational transitions and hydrogen-bond dynamics of the elastin-like octapeptide GVG(VPGVG): a molecular-dynamics study.

Authors:  Roger Rousseau; Eduard Schreiner; Axel Kohlmeyer; Dominik Marx
Journal:  Biophys J       Date:  2004-03       Impact factor: 4.033

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  3 in total

1.  Understanding the role of hydrogen bonds in water dynamics and protein stability.

Authors:  Valentino Bianco; Svilen Iskrov; Giancarlo Franzese
Journal:  J Biol Phys       Date:  2011-10-01       Impact factor: 1.365

2.  Computational investigation of cold denaturation in the Trp-cage miniprotein.

Authors:  Sang Beom Kim; Jeremy C Palmer; Pablo G Debenedetti
Journal:  Proc Natl Acad Sci U S A       Date:  2016-07-25       Impact factor: 11.205

3.  A coarse-grained protein model in a water-like solvent.

Authors:  Sumit Sharma; Sanat K Kumar; Sergey V Buldyrev; Pablo G Debenedetti; Peter J Rossky; H Eugene Stanley
Journal:  Sci Rep       Date:  2013       Impact factor: 4.379

  3 in total

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