Literature DB >> 12488010

Molecular recognition--viewed through the eyes of the solvent.

A Ben-Naim1.   

Abstract

The binding of a ligand L to a specific site on an adsorbent molecule P is usually studied within the lock-and-key model. In this article we argue that the presence of an aqueous solvent may change dramatically the means by which a ligand recognizes its binding site. The main factor, originating from the specific property of water, is the ability of a water molecule to form a hydrogen-bond-bridge between a functional group on L and a functional group on P. This factor will change the criterion for selecting the best binding site. Copyright 2002 Elsevier Science B.V.

Entities:  

Mesh:

Substances:

Year:  2002        PMID: 12488010     DOI: 10.1016/s0301-4622(02)00165-5

Source DB:  PubMed          Journal:  Biophys Chem        ISSN: 0301-4622            Impact factor:   2.352


  7 in total

1.  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

2.  Increase in the Intracellular Bulk Water Content in the Early Phase of Cell Death of Keratinocytes, Corneoptosis, as Revealed by 65 GHz Near-Field CMOS Dielectric Sensor.

Authors:  Keiichiro Shiraga; Yuichi Ogawa; Shojiro Kikuchi; Masayuki Amagai; Takeshi Matsui
Journal:  Molecules       Date:  2022-04-30       Impact factor: 4.927

3.  Lone pair ... pi interactions between water oxygens and aromatic residues: quantum chemical studies based on high-resolution protein structures and model compounds.

Authors:  Alok Jain; Venkatnarayan Ramanathan; Ramasubbu Sankararamakrishnan
Journal:  Protein Sci       Date:  2009-03       Impact factor: 6.725

Review 4.  Molecular docking as a popular tool in drug design, an in silico travel.

Authors:  Jerome de Ruyck; Guillaume Brysbaert; Ralf Blossey; Marc F Lensink
Journal:  Adv Appl Bioinform Chem       Date:  2016-06-28

5.  On the ability of molecular dynamics simulation and continuum electrostatics to treat interfacial water molecules in protein-protein complexes.

Authors:  Guillaume Copie; Fabrizio Cleri; Ralf Blossey; Marc F Lensink
Journal:  Sci Rep       Date:  2016-12-01       Impact factor: 4.379

6.  Hydration of AMP and ATP molecules in aqueous solution and solid films.

Authors:  Dzhigangir Faizullin; Nataliya Zakharchenko; Yuriy Zuev; Alexander Puzenko; Evgeniya Levy; Yuri Feldman
Journal:  Int J Mol Sci       Date:  2013-11-20       Impact factor: 5.923

7.  The Inclusion of Water Molecules in Residue Interaction Networks Identifies Additional Central Residues.

Authors:  Guillaume Brysbaert; Ralf Blossey; Marc F Lensink
Journal:  Front Mol Biosci       Date:  2018-10-11
  7 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.