Hydrophobicity regained

Protein Science : a Publication of the Protein Society
P A Karplus

Abstract

A widespread practice is to use free energies of transfer between organic solvents and water (delta G0transfer to define hydrophobicity scales for the amino acid side chains. A comparison of four delta G0transfer scales reveals that the values for hydrogen-bonding side chains are highly dependent on the non-aqueous environment. This property of polar side chains violates the assumptions underlying the paradigm of equating delta G0transfer with hydrophobicity or even with a generic solvation energy that is directly relevant to protein stability and ligand binding energetics. This simple regaining of the original concept of hydrophobicity reveals a flaw in approaches that use delta G0transfer values to derive generic estimates of the energetics of the burial of polar groups, and allows the introduction of a "pure" hydrophobicity scale for the amino acid residues.

References

Jan 1, 1992·Protein Science : a Publication of the Protein Society·N Horton, M Lewis
Aug 7, 1990·Biochemistry·K A Dill
Jan 1, 1990·Proteins·G J Lesser, G D Rose
Oct 12, 1990·Science·K A Dill
Jan 16, 1986·Nature·D Eisenberg, A D McLachlan
Jan 1, 1995·Proteins·J Janin
Jan 1, 1995·Advances in Protein Chemistry·B Honig, A S Yang
Jan 1, 1993·Annual Review of Biophysics and Biomolecular Structure·G D Rose, R Wolfenden
Jan 1, 1993·Progress in Biophysics and Molecular Biology·P K Ponnuswamy
Oct 1, 1995·Protein Science : a Publication of the Protein Society·M D CummingsR J Read
Jan 1, 1995·Methods in Enzymology·B Lee
Jan 1, 1995·Advances in Protein Chemistry·G I Makhatadze, P L Privalov
Dec 1, 1995·Protein Science : a Publication of the Protein Society·A H JufferP Argos
Jan 10, 1997·The Journal of Biological Chemistry·K A Dill
Jan 1, 1997·Annual Review of Biophysics and Biomolecular Structure·H S Chan, K A Dill
Jan 1, 1959·Advances in Protein Chemistry·W KAUZMANN
Aug 1, 1974·Proceedings of the National Academy of Sciences of the United States of America·J A ReynoldsC Tanford

❮ Previous
Next ❯

Citations

Dec 24, 2002·Journal of Computational Chemistry·J L Klepeis, C A Floudas
Apr 16, 1998·Protein Science : a Publication of the Protein Society·S PalmeC Slingsby
Mar 12, 2008·European Biophysics Journal : EBJ·Sylvia E McLainAnthony Watts
Feb 5, 2005·Bulletin of Mathematical Biology·Robersy SánchezRicardo Grau
Sep 8, 2009·Journal of the American Society for Mass Spectrometry·D Keith WilliamsDavid C Muddiman
Jul 25, 2003·Journal of Chromatography. a·Kallol M BiswasJohn G Dorsey
May 19, 2000·Microbes and Infection·R J Doyle
Jul 13, 2005·Biochemistry·Maneesh K YadavM Reza Ghadiri
Oct 24, 2012·Biochemistry·Eric S DayAdrian Whitty
Feb 10, 2009·Biochemistry·James L HouglandCarol A Fierke
Mar 29, 2011·Journal of Chemical Information and Modeling·Andrei L LomizeHenry I Mosberg
Jul 24, 2008·Journal of the American Chemical Society·Alexei ValiaevStefan Zauscher
Dec 23, 2008·The Journal of Physical Chemistry. B·Kristopher G UrieJay R Winkler
Jan 11, 2007·Nature Biotechnology·Alan C ChengEnoch S Huang
Feb 14, 1998·Nature Structural Biology·T N PhamS Koide
Feb 28, 2003·European Journal of Biochemistry·Patrick MassonOksana Lockridge
May 25, 2011·Proceedings of the National Academy of Sciences of the United States of America·Karin ÖjemalmGunnar von Heijne
May 29, 2012·The Journal of Biological Chemistry·Anshu P GounderJason G Smith
Jul 21, 1998·Journal of Biomolecular Structure & Dynamics·D Pal, P Chakrabarti
Sep 22, 2001·Journal of Biomolecular Structure & Dynamics·D Pal, P Chakrabarti
Aug 15, 2012·Journal of Biomolecular Structure & Dynamics·Ejaz AhmadRizwan Hasan Khan
Apr 27, 2005·BMC Bioinformatics·Kshitiz GuptaS Ramakumar
Nov 16, 2001·Biochemical and Biophysical Research Communications·K AdachiM J McDonald
Jan 10, 2002·Journal of Molecular Biology·Michael A WeissPanayotis G Katsoyannis
May 27, 2009·The Journal of Chemical Physics·Marcos R Betancourt, Sheyore J Omovie
Oct 8, 2003·Proceedings of the National Academy of Sciences of the United States of America·Oscar MilletLewis E Kay
Feb 28, 2002·Molecular Biology and Evolution·Chen SuMasatoshi Nei
Oct 1, 2010·Physical Chemistry Chemical Physics : PCCP·Giuseppe Graziano
Aug 24, 2012·Chemical Communications : Chem Comm·Jessica A LehrmanSamuel I Stupp
Nov 4, 2011·Physical Chemistry Chemical Physics : PCCP·J J SeguraJ Fraxedas
May 6, 2015·Journal of Chemical Theory and Computation·Zuojun GuoJianwei Che
Mar 8, 2011·Journal of Molecular Biology·C Nick PaceGerald R Grimsley
Oct 19, 2010·Journal of Molecular Biology·Stefano M Marino, Vadim N Gladyshev
Jun 1, 2004·Protein Science : a Publication of the Protein Society·Gian Gaetano TartagliaAmedeo Caflisch
Apr 30, 2003·Protein Science : a Publication of the Protein Society·Guangshun WangAlan Peterkofsky
Jul 15, 2009·APMIS : Acta Pathologica, Microbiologica, Et Immunologica Scandinavica·Emilios Andrew PapanastasiouBarney Michael Bishop
Jun 26, 2003·Protein Science : a Publication of the Protein Society·Satoshi Ohnishi, David Shortle
Oct 27, 2007·Protein Science : a Publication of the Protein Society·Manoj CheriyanCarol A Fierke
May 5, 2006·Protein Science : a Publication of the Protein Society·Teaster T BairdCharles S Craik

❮ Previous
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