On the calculation of binding free energies using continuum methods: application to MHC class I protein-peptide interactions

Protein Science : a Publication of the Protein Society
N FroloffB Honig

Abstract

This paper describes a methodology to calculate the binding free energy (delta G) of a protein-ligand complex using a continuum model of the solvent. A formal thermodynamic cycle is used to decompose the binding free energy into electrostatic and non-electrostatic contributions. In this cycle, the reactants are discharged in water, associated as purely nonpolar entities, and the final complex is then recharged. The total electrostatic free energies of the protein, the ligand, and the complex in water are calculated with the finite difference Poisson-Boltzmann (FDPB) method. The nonpolar (hydrophobic) binding free energy is calculated using a free energy-surface area relationship, with a single alkane/water surface tension coefficient (gamma aw). The loss in backbone and side-chain configurational entropy upon binding is estimated and added to the electrostatic and the nonpolar components of delta G. The methodology is applied to the binding of the murine MHC class I protein H-2Kb with three distinct peptides, and to the human MHC class I protein HLA-A2 in complex with five different peptides. Despite significant differences in the amino acid sequences of the different peptides, the experimental binding free energy differences (...Continue Reading

References

Jan 1, 1977·Annual Review of Biophysics and Bioengineering·F M Richards
May 25, 1977·Journal of Molecular Biology·F C BernsteinM Tasumi
Dec 1, 1992·The Journal of Experimental Medicine·B CatipovićJ P Schneck
Jan 1, 1991·Methods in Enzymology·T P Straatsma, J A McCammon
Jan 1, 1990·Annual Review of Biophysics and Biophysical Chemistry·K A Sharp, B Honig
Oct 5, 1990·Journal of Molecular Biology·J A IppolitoD W Christianson
Jan 1, 1989·Annual Review of Biophysics and Biophysical Chemistry·D L Beveridge, F M DiCapua
Oct 1, 1989·Protein Engineering·A V Finkelstein, J Janin
Oct 23, 1987·Science·J A McCammon
Aug 1, 1971·Proceedings of the National Academy of Sciences of the United States of America·M I Page, W P Jencks
Feb 14, 1971·Journal of Molecular Biology·B Lee, F M Richards
Dec 1, 1984·Journal of Medicinal Chemistry·P R AndrewsJ L Martin
Jun 5, 1982·Journal of Molecular Biology·J Warwicker, H C Watson
Jun 2, 1995·Journal of Molecular Biology·Y AltuviaH Margalit
Jul 7, 1995·Journal of Molecular Biology·R M Jackson, M J Sternberg
Sep 22, 1995·Journal of Molecular Biology·A S Yang, B Honig
Sep 22, 1995·Journal of Molecular Biology·A S Yang, B Honig
Mar 28, 1995·Proceedings of the National Academy of Sciences of the United States of America·D H FremontI A Wilson
Jan 1, 1995·Proteins·J Janin
Jan 1, 1995·Advances in Protein Chemistry·B Honig, A S Yang
Feb 1, 1995·Current Opinion in Structural Biology·R L Stanfield, I A Wilson
Mar 1, 1995·Protein Science : a Publication of the Protein Society·J Shen, J Wendoloski
Nov 1, 1993·Pharmacology & Therapeutics·J J WendoloskiP C Weber
Aug 1, 1993·Proceedings of the National Academy of Sciences of the United States of America·L A ShermanJ A Bluestone
Feb 15, 1993·Proceedings of the National Academy of Sciences of the United States of America·D H WilliamsR A Maplestone
Jun 5, 1993·Journal of Molecular Biology·S D Pickett, M J Sternberg
Oct 1, 1995·Biophysical Journal·R A Friedman, B Honig
Dec 22, 1995·Journal of Medicinal Chemistry· Ajay, M A Murcko
Nov 1, 1995·Protein Science : a Publication of the Protein Society·A J Doig, M J Sternberg
Feb 1, 1996·Protein Science : a Publication of the Protein Society·T Zhang, D E Koshland
Oct 1, 1996·Biophysical Journal·J K Myers, C N Pace

❮ Previous
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Citations

Oct 15, 1998·Journal of Molecular Recognition : JMR·M A Olson, L Cuff
Jul 9, 1999·Journal of Molecular Recognition : JMR·M SchapiraR Abagyan
Oct 3, 2006·Journal of Molecular Modeling·Gregor MlinsekTom Solmajer
Oct 12, 2010·Journal of Computer-aided Molecular Design·Constanza CárdenasF Javier Luque
Dec 1, 2005·Journal of Biological Physics·Ran FriedmanMenachem Gutman
Nov 26, 2003·Journal of Molecular Biology·Felix B SheinermanBarry Honig
Jun 11, 2002·Journal of Molecular Biology·Felix B Sheinerman, Barry Honig
Jun 27, 2002·Journal of Molecular Biology·Vasso ApostolopoulosMagdalena Plebanski
Apr 23, 2003·Journal of Molecular Biology·Karthikeyan DiraviyamDiana Murray
Dec 22, 1999·Pharmacology & Therapeutics·D Joseph-McCarthy
Oct 10, 2006·Biophysical Chemistry·M A Olson
Apr 8, 2000·Current Opinion in Structural Biology·F B SheinermanB Honig
Jun 19, 1998·Current Opinion in Structural Biology·A Warshel, A Papazyan
Jun 19, 1998·Current Opinion in Structural Biology·J A McCammon
Apr 5, 2003·Journal of Molecular Graphics & Modelling·Lilee CuffMark A Olson
Jul 17, 1998·Current Opinion in Chemical Biology·M L Lamb, W L Jorgensen
Sep 28, 2006·Journal of the American Chemical Society·Nathalie BasdevantMarco Ceruso
Oct 18, 2000·Proceedings of the National Academy of Sciences of the United States of America·H PanV J Hilser
May 8, 2000·Journal of Biomolecular Structure & Dynamics·S LiangL Lai
Sep 6, 2003·Journal of Biomolecular Structure & Dynamics·L N Drozdov-TikhomirovV Y Potapov
Jul 1, 2004·The Journal of Experimental Medicine·Danielle ZernichJames McCluskey
Jan 11, 2013·Open Biology·Atanas Patronov, Irini Doytchinova
Mar 3, 2006·Acta Crystallographica. Section F, Structural Biology and Crystallization Communications·Shojiro KadonoToshiro Kozono
Oct 18, 2001·Protein Science : a Publication of the Protein Society·R NorelB Honig
Mar 27, 2001·Protein Science : a Publication of the Protein Society·L P Lee, B Tidor
Jan 13, 2000·Protein Science : a Publication of the Protein Society·F PolticelliB Honig
Aug 13, 1998·Immunological Reviews·Z Weng, C DeLisi
Aug 2, 2008·PLoS Computational Biology·Jihua HaoJames P Basilion
Oct 5, 2013·The Journal of Chemical Physics·Changbong Hyeon, D Thirumalai
Aug 7, 2013·Journal of Structural Biology·Christian ReichenAndreas Plückthun
Nov 3, 2004·Proceedings of the National Academy of Sciences of the United States of America·Osamu MiyashitaMelvin Y Okamura
Apr 5, 2002·Proteins·Themis LazaridisFrancois Gandolfo
Oct 25, 2011·FEBS Letters·Cláudio M Soares, António M Baptista
Jan 27, 2009·Journal of Molecular Graphics & Modelling·Madhurima Das, Gautam Basu
Dec 6, 2008·Biophysical Chemistry·Oliwia SzklarczykJan M Antosiewicz
Mar 14, 2008·Journal of Molecular Biology·John EargleZaida Luthey-Schulten

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