Literature DB >> 15306376

Water-protein interactions from high-resolution protein crystallography.

Masayoshi Nakasako1.   

Abstract

To understand the role of water in life at molecular and atomic levels, structures and interactions at the protein-water interface have been investigated by cryogenic X-ray crystallography. The method enabled a much clearer visualization of definite hydration sites on the protein surface than at ambient temperature. Using the structural models of proteins, including several hydration water molecules, the characteristics in hydration structures were systematically analysed for the amount, the interaction geometries between water molecules and proteins, and the local and global distribution of water molecules on the surface of proteins. The tetrahedral hydrogen-bond geometry of water molecules in bulk solvent was retained at the interface and enabled the extension of a three-dimensional chain connection of a hydrogen-bond network among hydration water molecules and polar protein atoms over the entire surface of proteins. Networks of hydrogen bonds were quite flexible to accommodate and/or to regulate the conformational changes of proteins such as domain motions. The present experimental results may have profound implications in the understanding of the physico-chemical principles governing the dynamics of proteins in an aqueous environment and a discussion of why water is essential to life at a molecular level.

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Year:  2004        PMID: 15306376      PMCID: PMC1693410          DOI: 10.1098/rstb.2004.1498

Source DB:  PubMed          Journal:  Philos Trans R Soc Lond B Biol Sci        ISSN: 0962-8436            Impact factor:   6.237


  47 in total

1.  Solvent density and long-range dipole field around a DNA-binding protein studied by molecular dynamics.

Authors:  J Higo; H Kono; H Nakamura; A Sarai
Journal:  Proteins       Date:  2000-08-01

2.  Is the first hydration shell of lysozyme of higher density than bulk water?

Authors:  Franci Merzel; Jeremy C Smith
Journal:  Proc Natl Acad Sci U S A       Date:  2002-04-16       Impact factor: 11.205

3.  Normal mode refinement: crystallographic refinement of protein dynamic structure. I. Theory and test by simulated diffraction data.

Authors:  A Kidera; N Go
Journal:  J Mol Biol       Date:  1992-05-20       Impact factor: 5.469

4.  Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons.

Authors:  A Nicholls; K A Sharp; B Honig
Journal:  Proteins       Date:  1991

5.  Hydration of proteins. A comparison of experimental residence times of water molecules solvating the bovine pancreatic trypsin inhibitor with theoretical model calculations.

Authors:  R M Brunne; E Liepinsh; G Otting; K Wüthrich; W F van Gunsteren
Journal:  J Mol Biol       Date:  1993-06-20       Impact factor: 5.469

6.  Critical exponents of protonic percolation in hydrated lysozyme powders.

Authors: 
Journal:  Phys Rev A Gen Phys       Date:  1988-04-01

7.  The structure of 2Zn pig insulin crystals at 1.5 A resolution.

Authors:  E N Baker; T L Blundell; J F Cutfield; S M Cutfield; E J Dodson; G G Dodson; D M Hodgkin; R E Hubbard; N W Isaacs; C D Reynolds
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  1988-07-06       Impact factor: 6.237

8.  Solvent-accessible surfaces of proteins and nucleic acids.

Authors:  M L Connolly
Journal:  Science       Date:  1983-08-19       Impact factor: 47.728

9.  Protein dynamics. Mössbauer spectroscopy on deoxymyoglobin crystals.

Authors:  F Parak; E W Knapp; D Kucheida
Journal:  J Mol Biol       Date:  1982-10-15       Impact factor: 5.469

10.  Water structure of a hydrophobic protein at atomic resolution: Pentagon rings of water molecules in crystals of crambin.

Authors:  M M Teeter
Journal:  Proc Natl Acad Sci U S A       Date:  1984-10       Impact factor: 11.205

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  35 in total

1.  Water Distribution, Dynamics, and Interactions with Alzheimer's β-Amyloid Fibrils Investigated by Solid-State NMR.

Authors:  Tuo Wang; Hyunil Jo; William F DeGrado; Mei Hong
Journal:  J Am Chem Soc       Date:  2017-04-21       Impact factor: 15.419

2.  Conserved water molecules stabilize the Omega-loop in class A beta-lactamases.

Authors:  Fabian Bös; Jürgen Pleiss
Journal:  Antimicrob Agents Chemother       Date:  2008-01-14       Impact factor: 5.191

3.  Incorporating dipolar solvents with variable density in Poisson-Boltzmann electrostatics.

Authors:  Cyril Azuara; Henri Orland; Michael Bon; Patrice Koehl; Marc Delarue
Journal:  Biophys J       Date:  2008-09-26       Impact factor: 4.033

4.  Structural biology: Finding the wet spots.

Authors:  Vincent J Hilser
Journal:  Nature       Date:  2011-01-13       Impact factor: 49.962

5.  Hydration shells of molecules in molecular association: A mechanism for biomolecular recognition.

Authors:  Valery I Lim; James F Curran; Maria B Garber
Journal:  J Theor Biol       Date:  2012-02-17       Impact factor: 2.691

6.  Effects of protein-crystal hydration and temperature on side-chain conformational heterogeneity in monoclinic lysozyme crystals.

Authors:  Hakan Atakisi; David W Moreau; Robert E Thorne
Journal:  Acta Crystallogr D Struct Biol       Date:  2018-04-03       Impact factor: 7.652

7.  Slow Dynamics of Tryptophan-Water Networks in Proteins.

Authors:  R Bryn Fenwick; David Oyen; H Jane Dyson; Peter E Wright
Journal:  J Am Chem Soc       Date:  2018-01-03       Impact factor: 15.419

8.  Blind prediction of interfacial water positions in CAPRI.

Authors:  Marc F Lensink; Iain H Moal; Paul A Bates; Panagiotis L Kastritis; Adrien S J Melquiond; Ezgi Karaca; Christophe Schmitz; Marc van Dijk; Alexandre M J J Bonvin; Miriam Eisenstein; Brian Jiménez-García; Solène Grosdidier; Albert Solernou; Laura Pérez-Cano; Chiara Pallara; Juan Fernández-Recio; Jianqing Xu; Pravin Muthu; Krishna Praneeth Kilambi; Jeffrey J Gray; Sergei Grudinin; Georgy Derevyanko; Julie C Mitchell; John Wieting; Eiji Kanamori; Yuko Tsuchiya; Yoichi Murakami; Joy Sarmiento; Daron M Standley; Matsuyuki Shirota; Kengo Kinoshita; Haruki Nakamura; Matthieu Chavent; David W Ritchie; Hahnbeom Park; Junsu Ko; Hasup Lee; Chaok Seok; Yang Shen; Dima Kozakov; Sandor Vajda; Petras J Kundrotas; Ilya A Vakser; Brian G Pierce; Howook Hwang; Thom Vreven; Zhiping Weng; Idit Buch; Efrat Farkash; Haim J Wolfson; Martin Zacharias; Sanbo Qin; Huan-Xiang Zhou; Shen-You Huang; Xiaoqin Zou; Justyna A Wojdyla; Colin Kleanthous; Shoshana J Wodak
Journal:  Proteins       Date:  2013-11-23

9.  Charge density-dependent modifications of hydration shell waters by Hofmeister ions.

Authors:  Feng Guo; Joel M Friedman
Journal:  J Am Chem Soc       Date:  2009-08-12       Impact factor: 15.419

10.  Hydration-state change of horse heart cytochrome c corresponding to trifluoroacetic-acid-induced unfolding.

Authors:  Yusuke Miyashita; Tetsuichi Wazawa; George Mogami; Satoshi Takahashi; Yoshihiro Sambongi; Makoto Suzuki
Journal:  Biophys J       Date:  2013-01-08       Impact factor: 4.033

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