PMID: 11604044Oct 18, 2001Paper

Distinct molecular surfaces and hydrophobicity of amino acid residues in proteins

Journal of Chemical Information and Computer Sciences
L F Pacios

Abstract

Hydrophobicity is a useful concept to rationalize the role played by amino acid residues in terms of buried or exposed conformation with regard to the aqueous environment in proteins. The relationship of this concept with distinct approaches to represent the molecular surface is analyzed by computing reliable surface areas for three definitions namely the van der Waals, solvent-accessible, and solvent-excluded molecular surfaces. The surface areas are obtained for all of the naturally occurring amino acids by first setting a proper reference standard state and then calculating their values for a database of proteins containing a total of 4297 residues. Despite the great differences in these molecular surfaces, proper indexes are here defined for handling the information of interest to study the hydrophobic behavior of amino acids provided by such surfaces.

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Citations

Oct 3, 2008·Proceedings of the National Academy of Sciences of the United States of America·Yana K ReshetnyakDonald M Engelman
Dec 25, 2003·Proceedings of the National Academy of Sciences of the United States of America·Yaakov LevyJosé N Onuchic
Apr 3, 2007·The Journal of Allergy and Clinical Immunology·Gema López-TorrejónLuis F Pacios
May 24, 2015·Amino Acids·Aneta PanuszkoJanusz Stangret
Jun 9, 2004·Journal of Molecular Biology·Yaakov LevyPeter G Wolynes
Aug 19, 2008·Biophysical Journal·Ronald D Hills, Charles L Brooks
Nov 24, 2004·Journal of Chemical Information and Computer Sciences·Yizong ChengXiaoyang Qi
Jul 26, 2013·The Journal of Physical Chemistry. B·Stefano PianaDavid E Shaw
Dec 3, 2013·The Journal of Physical Chemistry. B·Marco A BlancoChristopher J Roberts
May 5, 2011·Journal of Chemical Information and Modeling·Luis F PaciosAraceli Díaz-Perales
Mar 11, 2004·Journal of Computational Chemistry·Matthias KeilJürgen Brickmann
Feb 26, 2003·Biopolymers·Garegin A Papoian, Peter G Wolynes
Apr 8, 2017·The Journal of Chemical Physics·Nirnay SamantaRajib Kumar Mitra
Apr 7, 2021·The Journal of Physical Chemistry. B·Hassan ShahfarChristopher J Roberts
Oct 14, 2008·Journal of Chemical Theory and Computation·Peter L WarburtonPaul G Mezey
Sep 17, 2004·Journal of the American Chemical Society·Garegin A PapoianPeter G Wolynes
Feb 18, 2005·Journal of Medicinal Chemistry·Matthew D Kelly, Ricardo L Mancera

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