Literature DB >> 16968773

Protein surface hydration mapped by site-specific mutations.

Weihong Qiu1, Ya-Ting Kao, Luyuan Zhang, Yi Yang, Lijuan Wang, Wesley E Stites, Dongping Zhong, Ahmed H Zewail.   

Abstract

Water motion at protein surfaces is fundamental to protein structure, stability, dynamics, and function. By using intrinsic tryptophans as local optical probes, and with femtosecond resolution, it is possible to probe surface-water motions in the hydration layer. Here, we report our studies of local hydration dynamics at the surface of the enzyme Staphylococcus nuclease using site-specific mutations. From these studies of the WT and four related mutants, which change local charge distribution and structure, we are able to ascertain the contribution to solvation by protein side chains as relatively insignificant. We determined the time scales of hydration to be 3-5 ps and 100-150 ps. The former is the result of local librational/rotational motions of water near the surface; the latter is a direct measure of surface hydration assisted by fluctuations of the protein. Experimentally, these hydration dynamics of the WT and the four mutants are also consistent with results of the total dynamic Stokes shifts and fluorescence emission maxima and are correlated with their local charge distribution and structure. We discuss the role of protein fluctuation on the time scale of labile hydration and suggest reexamination of recent molecular dynamics simulations.

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Year:  2006        PMID: 16968773      PMCID: PMC1599899          DOI: 10.1073/pnas.0606235103

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


  33 in total

1.  Elucidation of information encoded in tryptophan 140 of staphylococcal nuclease.

Authors:  Satoshi Hirano; Hironari Kamikubo; Yoichi Yamazaki; Mikio Kataoka
Journal:  Proteins       Date:  2005-02-01

2.  Sensitivity of polar solvation dynamics to the secondary structures of aqueous proteins and the role of surface exposure of the probe.

Authors:  Sanjoy Bandyopadhyay; Sudip Chakraborty; Sundaram Balasubramanian; Biman Bagchi
Journal:  J Am Chem Soc       Date:  2005-03-23       Impact factor: 15.419

Review 3.  Water dynamics in the hydration layer around proteins and micelles.

Authors:  Biman Bagchi
Journal:  Chem Rev       Date:  2005-09       Impact factor: 60.622

4.  Molecular origin of time-dependent fluorescence shifts in proteins.

Authors:  Lennart Nilsson; Bertil Halle
Journal:  Proc Natl Acad Sci U S A       Date:  2005-09-14       Impact factor: 11.205

5.  Ultrafast fluorescence dynamics of tryptophan in the proteins monellin and IIAGlc.

Authors:  Jianhua Xu; Dmitri Toptygin; Karen J Graver; Rebecca A Albertini; Regina S Savtchenko; Norman D Meadow; Saul Roseman; Patrik R Callis; Ludwig Brand; Jay R Knutson
Journal:  J Am Chem Soc       Date:  2006-02-01       Impact factor: 15.419

6.  Toward understanding tryptophan fluorescence in proteins.

Authors:  Y Chen; M D Barkley
Journal:  Biochemistry       Date:  1998-07-14       Impact factor: 3.162

7.  Coupling between trans/cis proline isomerization and protein stability in staphylococcal nuclease.

Authors:  D M Truckses; J R Somoza; K E Prehoda; S C Miller; J L Markley
Journal:  Protein Sci       Date:  1996-09       Impact factor: 6.725

8.  Molecular dynamics study of water penetration in staphylococcal nuclease.

Authors:  Ana Damjanović; Bertrand García-Moreno; Eaton E Lattman; Angel E García
Journal:  Proteins       Date:  2005-08-15

9.  Human myoglobin recognition of oxygen: dynamics of the energy landscape.

Authors:  Yuhong Wang; J Spencer Baskin; Tianbing Xia; Ahmed H Zewail
Journal:  Proc Natl Acad Sci U S A       Date:  2004-12-15       Impact factor: 11.205

10.  Energetic contribution of side chain hydrogen bonding to the stability of staphylococcal nuclease.

Authors:  M P Byrne; R L Manuel; L G Lowe; W E Stites
Journal:  Biochemistry       Date:  1995-10-24       Impact factor: 3.162

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  36 in total

Review 1.  Dynamics and mechanisms of DNA repair by photolyase.

Authors:  Zheyun Liu; Lijuan Wang; Dongping Zhong
Journal:  Phys Chem Chem Phys       Date:  2015-05-14       Impact factor: 3.676

2.  Site-specific hydration dynamics of globular proteins and the role of constrained water in solvent exchange with amphiphilic cosolvents.

Authors:  John T King; Evan J Arthur; Charles L Brooks; Kevin J Kubarych
Journal:  J Phys Chem B       Date:  2012-05-07       Impact factor: 2.991

3.  Dissection of complex protein dynamics in human thioredoxin.

Authors:  Weihong Qiu; Lijuan Wang; Wenyun Lu; Amanda Boechler; David A R Sanders; Dongping Zhong
Journal:  Proc Natl Acad Sci U S A       Date:  2007-03-16       Impact factor: 11.205

4.  Mapping hydration dynamics around a protein surface.

Authors:  Luyuan Zhang; Lijuan Wang; Ya-Ting Kao; Weihong Qiu; Yi Yang; Oghaghare Okobiah; Dongping Zhong
Journal:  Proc Natl Acad Sci U S A       Date:  2007-11-14       Impact factor: 11.205

5.  Ultrafast solvation dynamics at binding and active sites of photolyases.

Authors:  Chih-Wei Chang; Lijun Guo; Ya-Ting Kao; Jiang Li; Chuang Tan; Tanping Li; Chaitanya Saxena; Zheyun Liu; Lijuan Wang; Aziz Sancar; Dongping Zhong
Journal:  Proc Natl Acad Sci U S A       Date:  2010-01-26       Impact factor: 11.205

6.  Implementing electrostatic polarization cannot fill the gap between experimental and theoretical measurements for the ultrafast fluorescence decay of myoglobin.

Authors:  Bingbing Lin; Ya Gao; Yongxiu Li; John Z H Zhang; Ye Mei
Journal:  J Mol Model       Date:  2014-03-27       Impact factor: 1.810

7.  A peptide's perspective of water dynamics.

Authors:  Ayanjeet Ghosh; Robin M Hochstrasser
Journal:  Chem Phys       Date:  2011-08-11       Impact factor: 2.348

Review 8.  The dark energy of proteins comes to light: conformational entropy and its role in protein function revealed by NMR relaxation.

Authors:  A Joshua Wand
Journal:  Curr Opin Struct Biol       Date:  2012-12-13       Impact factor: 6.809

9.  The effects of alpha-helical structure and cyanylated cysteine on each other.

Authors:  Lena Edelstein; Matthew A Stetz; Heather A McMahon; Casey H Londergan
Journal:  J Phys Chem B       Date:  2010-04-15       Impact factor: 2.991

10.  Validation of response function construction and probing heterogeneous protein hydration by intrinsic tryptophan.

Authors:  Yangzhong Qin; Chih-Wei Chang; Lijuan Wang; Dongping Zhong
Journal:  J Phys Chem B       Date:  2012-11-02       Impact factor: 2.991

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