Role of water mediated interactions in protein-protein recognition landscapes

Journal of the American Chemical Society
Garegin A PapoianPeter G Wolynes

Abstract

The energy landscape picture of protein folding and binding is employed to optimize a number of pair potentials for direct and water-mediated interactions in protein complex interfaces. We find that water-mediated interactions greatly complement direct interactions in discriminating against various types of trap interactions that model those present in the cell. We highlight the context dependent nature of knowledge-based binding potentials, as contrasted with the situation for autonomous folding. By performing a Principal Component Analysis (PCA) of the corresponding interaction matrixes, we rationalize the strength of the recognition signal for each combination of the contact type and reference trap states using the differential in the idealized "canonical" amino acid compositions of native and trap layers. The comparison of direct and water-mediated contact potential matrixes emphasizes the importance of partial solvation in stabilizing charged groups in the protein interfaces. Specific water-mediated interresidue interactions are expected to influence significantly the kinetics as well as thermodynamics of protein association.

References

Nov 1, 1987·Proceedings of the National Academy of Sciences of the United States of America·J D Bryngelson, P G Wolynes
Jan 1, 1997·Annual Review of Physical Chemistry·J N OnuchicP G Wolynes
Aug 1, 1994·Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics·S Ramanathan, E Shakhnovich
Nov 5, 1999·Journal of Molecular Biology·P E Wright, H J Dyson
Nov 28, 2000·Proteins·P RomeroA K Dunker
Jun 8, 2001·Annual Review of Biochemistry·J Frydman
Aug 9, 2001·Journal of Molecular Biology·M GottschalkB Halle
Oct 18, 2001·Journal of Chemical Information and Computer Sciences·L F Pacios
Jan 24, 2002·Proceedings of the National Academy of Sciences of the United States of America·Margaret S CheungJosé N Onuchic
Feb 13, 2002·Current Opinion in Structural Biology·H Jane Dyson, Peter E Wright
Jun 19, 2002·Accounts of Chemical Research·Vladimir MakarovMichael Feig
Feb 26, 2003·Biopolymers·Garegin A Papoian, Peter G Wolynes
Apr 17, 2003·Proceedings of the National Academy of Sciences of the United States of America·Gennady M VerkhivkerPeter W Rose

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Citations

Jun 10, 2011·Journal of Biosciences·R SabarinathanK Sekar
Apr 20, 2005·Current Opinion in Structural Biology·Cyril Deremble, Richard Lavery
Sep 8, 2010·Quarterly Reviews of Biophysics·Pavel I Zhuravlev, Garegin A Papoian
Jan 26, 2010·Journal of the American Chemical Society·Mariano Andrea ScorciapinoMatteo Ceccarelli
Jan 21, 2011·The Journal of Physical Chemistry. a·Soohaeng Yoo, Sotiris S Xantheas
Mar 31, 2011·Nature Communications·Mazen AhmadVolkhard Helms
Sep 29, 2011·Nature Communications·Changbong Hyeon, D Thirumalai
Mar 23, 2011·Physical Chemistry Chemical Physics : PCCP·Ravinath Kausik, Songi Han
Jul 31, 2008·Proceedings of the National Academy of Sciences of the United States of America·Christopher Kroboth MatereseGaregin A Papoian
Oct 27, 2010·Proceedings of the National Academy of Sciences of the United States of America·Jingyuan LiB J Berne
Jan 29, 2011·Proceedings of the National Academy of Sciences of the United States of America·Diego U FerreiroPeter G Wolynes
Apr 6, 2011·Proceedings of the National Academy of Sciences of the United States of America·Xin ZhangShu-ou Shan
Nov 7, 2012·Proceedings of the National Academy of Sciences of the United States of America·Weihua ZhengPeter G Wolynes
May 13, 2006·Annual Review of Biophysics and Biomolecular Structure·Yaakov Levy, José N Onuchic
Jan 12, 2007·BMC Structural Biology·Francesca SpyrakisAndrea Mozzarelli
Jul 23, 2005·The Journal of Chemical Physics·Patricia SchaeferQiang Cui
Mar 6, 2014·The Journal of Physical Chemistry Letters·Chad W LawrenceScott A Showalter
Mar 13, 2014·The Journal of Physical Chemistry. a·Vanesa VaqueroJosé L Alonso
Apr 17, 2012·The Journal of Chemical Physics·Ricky B NellasTongye Shen
Oct 5, 2013·The Journal of Chemical Physics·Ha H TruongPeter G Wolynes
Feb 11, 2014·Journal of Structural and Functional Genomics·Samuel H Light, Wayne F Anderson
Nov 5, 2003·Proceedings of the National Academy of Sciences of the United States of America·Julia M Shifman, Stephen L Mayo
Mar 3, 2004·Proceedings of the National Academy of Sciences of the United States of America·Yaakov Levy, José N Onuchic
Feb 28, 2004·Proceedings of the National Academy of Sciences of the United States of America·Garegin A PapoianPeter G Wolynes
May 20, 2014·Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy·Halina AbramczykAlina Morawiec-Sztandera
Sep 14, 2004·Proceedings of the National Academy of Sciences of the United States of America·Sichun YangJosé N Onuchic
Dec 14, 2007·Proceedings of the National Academy of Sciences of the United States of America·Diego U FerreiroPeter G Wolynes
Jul 18, 2014·Proceedings of the National Academy of Sciences of the United States of America·Bobby L KimPeter G Wolynes
Jan 8, 2016·Chemical Reviews·Andre A S T Ribeiro, Vanessa Ortiz
Feb 10, 2016·Proceedings of the National Academy of Sciences of the United States of America·Nicholas P SchaferPeter G Wolynes
Jul 18, 2015·Protein Science : a Publication of the Protein Society·Min-Yeh TsaiPeter G Wolynes
May 16, 2014·The Journal of Physical Chemistry. B·Evan J ArthurCharles L Brooks
Nov 18, 2014·Journal of Chemical Theory and Computation·Robert B BestJeetain Mittal
Apr 28, 2005·Proteins·Francis RodierJoël Janin
Nov 20, 2012·Proteins·Panagiotis L KastritisAlexandre M J J Bonvin
Aug 15, 2013·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Anna Jean Wirth, Martin Gruebele
Feb 27, 2016·Journal of Biomolecular Structure & Dynamics·Nikolay A AlemasovVladimir A Ivanisenko

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