Literature DB >> 21448160

Adhesive water networks facilitate binding of protein interfaces.

Mazen Ahmad1, Wei Gu, Tihamér Geyer, Volkhard Helms.   

Abstract

Water structure has an essential role in biological assembly. Hydrophobic dewetting has been documented as a general mechanism for the assembly of hydrophobic surfaces; however, the association mechanism of hydrophilic interfaces remains mysterious and cannot be explained by simple continuum water models that ignore the solvent structure. Here we study the association of two hydrophilic proteins using unbiased extensive molecular dynamics simulations that reproducibly recovered the native bound complex. The water in the interfacial gap forms an adhesive hydrogen-bond network between the interfaces stabilizing early intermediates before native contacts are formed. Furthermore, the interfacial gap solvent showed a reduced dielectric shielding up to distances of few nanometres during the diffusive phase. The interfacial gap solvent generates an anisotropic dielectric shielding with a strongly preferred directionality for the electrostatic interactions along the association direction.

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Year:  2011        PMID: 21448160     DOI: 10.1038/ncomms1258

Source DB:  PubMed          Journal:  Nat Commun        ISSN: 2041-1723            Impact factor:   14.919


  34 in total

1.  The Xplor-NIH NMR molecular structure determination package.

Authors:  Charles D Schwieters; John J Kuszewski; Nico Tjandra; G Marius Clore
Journal:  J Magn Reson       Date:  2003-01       Impact factor: 2.229

2.  Charge-based interactions between peptides observed as the dominant force for association in aqueous solution.

Authors:  Sylvia E McLain; Alan K Soper; Isabella Daidone; Jeremy C Smith; Anthony Watts
Journal:  Angew Chem Int Ed Engl       Date:  2008       Impact factor: 15.336

Review 3.  Water as a biomolecule.

Authors:  Philip Ball
Journal:  Chemphyschem       Date:  2008-12-22       Impact factor: 3.102

4.  Quantifying water density fluctuations and compressibility of hydration shells of hydrophobic solutes and proteins.

Authors:  Sapna Sarupria; Shekhar Garde
Journal:  Phys Rev Lett       Date:  2009-07-17       Impact factor: 9.161

5.  The role of water in sequence-independent ligand binding by an oligopeptide transporter protein.

Authors:  J R Tame; S H Sleigh; A J Wilkinson; J E Ladbury
Journal:  Nat Struct Biol       Date:  1996-12

6.  Energetics of protein-protein interactions: analysis of the barnase-barstar interface by single mutations and double mutant cycles.

Authors:  G Schreiber; A R Fersht
Journal:  J Mol Biol       Date:  1995-04-28       Impact factor: 5.469

7.  Rapid, electrostatically assisted association of proteins.

Authors:  G Schreiber; A R Fersht
Journal:  Nat Struct Biol       Date:  1996-05

8.  Hydration of protein-protein interfaces.

Authors:  Francis Rodier; Ranjit Prasad Bahadur; Pinak Chakrabarti; Joël Janin
Journal:  Proteins       Date:  2005-07-01

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

Review 10.  Fundamental aspects of protein-protein association kinetics.

Authors:  G Schreiber; G Haran; H-X Zhou
Journal:  Chem Rev       Date:  2009-03-11       Impact factor: 60.622

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  36 in total

1.  Crowding induces differences in the diffusion of thermophilic and mesophilic proteins: a new look at neutron scattering results.

Authors:  Enrique Marcos; Pau Mestres; Ramon Crehuet
Journal:  Biophys J       Date:  2011-12-07       Impact factor: 4.033

2.  Enzymatic turnover of macromolecules generates long-lasting protein-water-coupled motions beyond reaction steady state.

Authors:  Jessica Dielmann-Gessner; Moran Grossman; Valeria Conti Nibali; Benjamin Born; Inna Solomonov; Gregg B Fields; Martina Havenith; Irit Sagi
Journal:  Proc Natl Acad Sci U S A       Date:  2014-11-25       Impact factor: 11.205

3.  Solvated protein-DNA docking using HADDOCK.

Authors:  Marc van Dijk; Koen M Visscher; Panagiotis L Kastritis; Alexandre M J J Bonvin
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4.  Mechanism of the Association Pathways for a Pair of Fast and Slow Binding Ligands of HIV-1 Protease.

Authors:  Yu-Ming M Huang; Mark Anthony V Raymundo; Wei Chen; Chia-En A Chang
Journal:  Biochemistry       Date:  2017-02-21       Impact factor: 3.162

5.  Shape complementarity and hydrogen bond preferences in protein-protein interfaces: implications for antibody modeling and protein-protein docking.

Authors:  Daisuke Kuroda; Jeffrey J Gray
Journal:  Bioinformatics       Date:  2016-04-19       Impact factor: 6.937

6.  Dissociation of a Dynamic Protein Complex Studied by All-Atom Molecular Simulations.

Authors:  Liqun Zhang; Susmita Borthakur; Matthias Buck
Journal:  Biophys J       Date:  2016-02-23       Impact factor: 4.033

7.  Exploring the Free-Energy Landscape and Thermodynamics of Protein-Protein Association.

Authors:  Celine Tse; Lauren Wickstrom; Mamuka Kvaratskhelia; Emilio Gallicchio; Ronald Levy; Nanjie Deng
Journal:  Biophys J       Date:  2020-08-12       Impact factor: 4.033

8.  Complete protein-protein association kinetics in atomic detail revealed by molecular dynamics simulations and Markov modelling.

Authors:  Nuria Plattner; Stefan Doerr; Gianni De Fabritiis; Frank Noé
Journal:  Nat Chem       Date:  2017-06-05       Impact factor: 24.427

9.  Stretching Single Collagen Fibrils Reveals Nonlinear Mechanical Behavior.

Authors:  Emilie Gachon; Patrick Mesquida
Journal:  Biophys J       Date:  2020-02-04       Impact factor: 4.033

10.  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
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