Literature DB >> 18816066

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

Nozomi Ando1, Buz Barstow, Walter A Baase, Andrew Fields, Brian W Matthews, Sol M Gruner.   

Abstract

Using small-angle X-ray scattering (SAXS) and tryptophan fluorescence spectroscopy, we have identified multiple compact denatured states of a series of T4 lysozyme mutants that are stabilized by high pressures. Recent studies imply that the mechanism of pressure denaturation is the penetration of water into the protein rather than the transfer of hydrophobic residues into water. To investigate water penetration and the volume change associated with pressure denaturation, we studied the solution behavior of four T4 lysozyme mutants having different cavity volumes at low and neutral pH up to a pressure of 400 MPa (0.1 MPa = 0.9869 atm). At low pH, L99A T4 lysozyme expanded from a compact folded state to a partially unfolded state with a corresponding change in radius of gyration from 17 to 32 A. The volume change upon denaturation correlated well with the total cavity volume, indicating that all of the molecule's major cavities are hydrated with pressure. As a direct comparison to high-pressure crystal structures of L99A T4 lysozyme solved at neutral pH [Collins, M. D., Hummer, G., Quillin, M. L., Matthews, B. W., and Gruner, S. M. (2005) Proc. Natl. Acad. Sci. U.S.A. 102, 16668-16671], pressure denaturation of L99A and the structurally similar L99G/E108V mutant was studied at neutral pH. The pressure-denatured state at neutral pH is even more compact than at low pH, and the small volume changes associated with denaturation suggest that the preferential filling of large cavities is responsible for the compactness of the pressure-denatured state. These results confirm that pressure denaturation is characteristically distinct from thermal or chemical denaturation.

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Year:  2008        PMID: 18816066      PMCID: PMC2664309          DOI: 10.1021/bi801287m

Source DB:  PubMed          Journal:  Biochemistry        ISSN: 0006-2960            Impact factor:   3.162


  51 in total

1.  Volume, expansivity and isothermal compressibility changes associated with temperature and pressure unfolding of Staphylococcal nuclease.

Authors:  H Seemann; R Winter; C A Royer
Journal:  J Mol Biol       Date:  2001-04-06       Impact factor: 5.469

Review 2.  Compressibility of protein transitions.

Authors:  Nicolas Taulier; Tigran V Chalikian
Journal:  Biochim Biophys Acta       Date:  2002-03-25

Review 3.  Pressure-temperature phase diagrams of biomolecules.

Authors:  László Smeller
Journal:  Biochim Biophys Acta       Date:  2002-03-25

4.  Time resolved collapse of a folding protein observed with small angle x-ray scattering.

Authors:  L Pollack; M W Tate; A C Finnefrock; C Kalidas; S Trotter; N C Darnton; L Lurio; R H Austin; C A Batt; S M Gruner; S G Mochrie
Journal:  Phys Rev Lett       Date:  2001-05-21       Impact factor: 9.161

5.  Structural and thermodynamic analysis of the binding of solvent at internal sites in T4 lysozyme.

Authors:  J Xu; W A Baase; M L Quillin; E P Baldwin; B W Matthews
Journal:  Protein Sci       Date:  2001-05       Impact factor: 6.725

6.  Mechanisms of tryptophan fluorescence shifts in proteins.

Authors:  J T Vivian; P R Callis
Journal:  Biophys J       Date:  2001-05       Impact factor: 4.033

7.  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

8.  The introduction of strain and its effects on the structure and stability of T4 lysozyme.

Authors:  R Liu; W A Baase; B W Matthews
Journal:  J Mol Biol       Date:  2000-01-07       Impact factor: 5.469

9.  Pressure versus heat-induced unfolding of ribonuclease A: the case of hydrophobic interactions within a chain-folding initiation site.

Authors:  J Torrent; J P Connelly; M G Coll; M Ribó; R Lange; M Vilanova
Journal:  Biochemistry       Date:  1999-11-30       Impact factor: 3.162

10.  Pressure dissociation and conformational drift of the beta dimer of tryptophan synthase.

Authors:  J L Silva; E W Miles; G Weber
Journal:  Biochemistry       Date:  1986-09-23       Impact factor: 3.162

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  22 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.  Single-crystal CVD diamonds as small-angle X-ray scattering windows for high-pressure research.

Authors:  Suntao Wang; Yu-Fei Meng; Nozomi Ando; Mark Tate; Szczesny Krasnicki; Chih-Shiue Yan; Qi Liang; Joseph Lai; Ho-Kwang Mao; Sol M Gruner; Russell J Hemley
Journal:  J Appl Crystallogr       Date:  2012-04-25       Impact factor: 3.304

3.  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

4.  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

5.  High-pressure SAXS study of folded and unfolded ensembles of proteins.

Authors:  Martin A Schroer; Michael Paulus; Christoph Jeworrek; Christina Krywka; Saskia Schmacke; Yong Zhai; D C Florian Wieland; Christoph J Sahle; Michael Chimenti; Catherine A Royer; Bertrand Garcia-Moreno; Metin Tolan; Roland Winter
Journal:  Biophys J       Date:  2010-11-17       Impact factor: 4.033

6.  Coupling of pressure-induced structural shifts to spectral changes in a yellow fluorescent protein.

Authors:  Buz Barstow; Nozomi Ando; Chae Un Kim; Sol M Gruner
Journal:  Biophys J       Date:  2009-09-16       Impact factor: 4.033

7.  Small-angle solution scattering using the mixed-mode pixel array detector.

Authors:  Lucas J Koerner; Richard E Gillilan; Katherine S Green; Suntao Wang; Sol M Gruner
Journal:  J Synchrotron Radiat       Date:  2010-12-08       Impact factor: 2.616

8.  Structure-relaxation mechanism for the response of T4 lysozyme cavity mutants to hydrostatic pressure.

Authors:  Michael T Lerch; Carlos J López; Zhongyu Yang; Margaux J Kreitman; Joseph Horwitz; Wayne L Hubbell
Journal:  Proc Natl Acad Sci U S A       Date:  2015-04-27       Impact factor: 11.205

9.  Cavity as a source of conformational fluctuation and high-energy state: high-pressure NMR study of a cavity-enlarged mutant of T4 lysozyme.

Authors:  Akihiro Maeno; Daniel Sindhikara; Fumio Hirata; Renee Otten; Frederick W Dahlquist; Shigeyuki Yokoyama; Kazuyuki Akasaka; Frans A A Mulder; Ryo Kitahara
Journal:  Biophys J       Date:  2015-01-06       Impact factor: 4.033

10.  Reply to Kitahara and Mulder: An ensemble view of protein stability best explains pressure effects in a T4 lysozyme cavity mutant.

Authors:  A Joshua Wand; Nathaniel V Nucci
Journal:  Proc Natl Acad Sci U S A       Date:  2015-01-28       Impact factor: 11.205

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