Literature DB >> 16269539

Cooperative water filling of a nonpolar protein cavity observed by high-pressure crystallography and simulation.

Marcus D Collins1, Gerhard Hummer, Michael L Quillin, Brian W Matthews, Sol M Gruner.   

Abstract

Formation of a water-expelling nonpolar core is the paradigm of protein folding and stability. Although experiment largely confirms this picture, water buried in "hydrophobic" cavities is required for the function of some proteins. Hydration of the protein core has also been suggested as the mechanism of pressure-induced unfolding. We therefore are led to ask whether even the most nonpolar protein core is truly hydrophobic (i.e., water-repelling). To answer this question we probed the hydration of an approximately 160-A(3), highly hydrophobic cavity created by mutation in T4 lysozyme by using high-pressure crystallography and molecular dynamics simulation. We show that application of modest pressure causes approximately four water molecules to enter the cavity while the protein itself remains essentially unchanged. The highly cooperative filling is primarily due to a small change in bulk water activity, which implies that changing solvent conditions or, equivalently, cavity polarity can dramatically affect interior hydration of proteins and thereby influence both protein activity and folding.

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Year:  2005        PMID: 16269539      PMCID: PMC1283839          DOI: 10.1073/pnas.0508224102

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


  27 in total

1.  Detection, delineation, measurement and display of cavities in macromolecular structures.

Authors:  G J Kleywegt; T A Jones
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  1994-03-01

2.  The pressure dependence of hydrophobic interactions is consistent with the observed pressure denaturation of proteins.

Authors:  G Hummer; S Garde; A E García; M E Paulaitis; L R Pratt
Journal:  Proc Natl Acad Sci U S A       Date:  1998-02-17       Impact factor: 11.205

3.  Energetic origins of specificity of ligand binding in an interior nonpolar cavity of T4 lysozyme.

Authors:  A Morton; W A Baase; B W Matthews
Journal:  Biochemistry       Date:  1995-07-11       Impact factor: 3.162

4.  Structural and energetic responses to cavity-creating mutations in hydrophobic cores: observation of a buried water molecule and the hydrophilic nature of such hydrophobic cavities.

Authors:  A M Buckle; P Cramer; A R Fersht
Journal:  Biochemistry       Date:  1996-04-09       Impact factor: 3.162

5.  Response of a protein structure to cavity-creating mutations and its relation to the hydrophobic effect.

Authors:  A E Eriksson; W A Baase; X J Zhang; D W Heinz; M Blaber; E P Baldwin; B W Matthews
Journal:  Science       Date:  1992-01-10       Impact factor: 47.728

6.  Hydrophilicity of cavities in proteins.

Authors:  L Zhang; J Hermans
Journal:  Proteins       Date:  1996-04

7.  The catalytic pathway of cytochrome p450cam at atomic resolution.

Authors:  I Schlichting; J Berendzen; K Chu; A M Stock; S A Maves; D E Benson; R M Sweet; D Ringe; G A Petsko; S G Sligar
Journal:  Science       Date:  2000-03-03       Impact factor: 47.728

8.  Water clusters in nonpolar cavities.

Authors:  Subramanian Vaitheeswaran; Hao Yin; Jayendran C Rasaiah; Gerhard Hummer
Journal:  Proc Natl Acad Sci U S A       Date:  2004-11-30       Impact factor: 11.205

9.  Crystallographic structures of the M and N intermediates of bacteriorhodopsin: assembly of a hydrogen-bonded chain of water molecules between Asp-96 and the retinal Schiff base.

Authors:  Brigitte Schobert; Leonid S Brown; Janos K Lanyi
Journal:  J Mol Biol       Date:  2003-07-11       Impact factor: 5.469

10.  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

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  65 in total

1.  Cavities determine the pressure unfolding of proteins.

Authors:  Julien Roche; Jose A Caro; Douglas R Norberto; Philippe Barthe; Christian Roumestand; Jamie L Schlessman; Angel E Garcia; Bertrand E García-Moreno; Catherine A Royer
Journal:  Proc Natl Acad Sci U S A       Date:  2012-04-10       Impact factor: 11.205

2.  Structure-function perturbation and dissociation of tetrameric urate oxidase by high hydrostatic pressure.

Authors:  Eric Girard; Stéphane Marchal; Javier Perez; Stéphanie Finet; Richard Kahn; Roger Fourme; Guillaume Marassio; Anne-Claire Dhaussy; Thierry Prangé; Marion Giffard; Fabienne Dulin; Françoise Bonneté; Reinhard Lange; Jacques H Abraini; Mohamed Mezouar; Nathalie Colloc'h
Journal:  Biophys J       Date:  2010-05-19       Impact factor: 4.033

3.  Molecular dynamics free energy calculations to assess the possibility of water existence in protein nonpolar cavities.

Authors:  Masataka Oikawa; Yoshiteru Yonetani
Journal:  Biophys J       Date:  2010-06-16       Impact factor: 4.033

4.  A self-consistent phase-field approach to implicit solvation of charged molecules with Poisson-Boltzmann electrostatics.

Authors:  Hui Sun; Jiayi Wen; Yanxiang Zhao; Bo Li; J Andrew McCammon
Journal:  J Chem Phys       Date:  2015-12-28       Impact factor: 3.488

5.  Motifs for molecular recognition exploiting hydrophobic enclosure in protein-ligand binding.

Authors:  Tom Young; Robert Abel; Byungchan Kim; Bruce J Berne; Richard A Friesner
Journal:  Proc Natl Acad Sci U S A       Date:  2007-01-04       Impact factor: 11.205

6.  An extended dynamical hydration shell around proteins.

Authors:  Simon Ebbinghaus; Seung Joong Kim; Matthias Heyden; Xin Yu; Udo Heugen; Martin Gruebele; David M Leitner; Martina Havenith
Journal:  Proc Natl Acad Sci U S A       Date:  2007-12-19       Impact factor: 11.205

7.  Theoretical study of the partial molar volume change associated with the pressure-induced structural transition of ubiquitin.

Authors:  Takashi Imai; Shusaku Ohyama; Andriy Kovalenko; Fumio Hirata
Journal:  Protein Sci       Date:  2007-07-27       Impact factor: 6.725

8.  Hydrophobicity of protein surfaces: Separating geometry from chemistry.

Authors:  Nicolas Giovambattista; Carlos F Lopez; Peter J Rossky; Pablo G Debenedetti
Journal:  Proc Natl Acad Sci U S A       Date:  2008-02-11       Impact factor: 11.205

Review 9.  Computations of standard binding free energies with molecular dynamics simulations.

Authors:  Yuqing Deng; Benoît Roux
Journal:  J Phys Chem B       Date:  2009-02-26       Impact factor: 2.991

10.  Structural and thermodynamic characterization of T4 lysozyme mutants and the contribution of internal cavities to pressure denaturation.

Authors:  Nozomi Ando; Buz Barstow; Walter A Baase; Andrew Fields; Brian W Matthews; Sol M Gruner
Journal:  Biochemistry       Date:  2008-09-25       Impact factor: 3.162

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