The electrostatic embedding contribution to DFT calculations of ligand-amino acid residues interaction

Journal of Molecular Modeling
Tamires C da Silva RibeiroVinícius Manzoni

Abstract

In this work, we demonstrate that the inclusion of long-range interactions has a significant impact on the estimation of ligand-protein binding energies. Within the scope of the electrostatically embedded adaptation of the molecular fragmentation with conjugated caps (EE-AMFCC) scheme, we unveil the role played by long-range contributions in distinct levels of quantum mechanical calculations. As a prototypical system, we consider ibuprofen coupled to the human serum albumin. In particular, we show that some relevant ligand-residue interaction energies can only be accurately captured in density functional theory (DFT) approaches when the electrostatic background is properly represented by an explicit point charge distribution. Graphical Abstract (left) The binding site FA3/FA4 of HSA containing the attached IBU. (right) Absolute value of difference between the biding energies calculated including the electrostatic embedding and the energies calculated without the electrostatic embedding using the HF, B3LYP, CAM-B3LYP, and MP2 methodologies.

References

Jan 1, 1985·Advances in Protein Chemistry·T Peters
Jul 2, 1999·Protein Engineering·S SugioK Kobayashi
Aug 29, 2002·Nature Structural Biology·Martin Karplus, J Andrew McCammon
Sep 30, 2003·Journal of Computational Chemistry·D W ZhangJ Z H Zhang
Feb 21, 2004·Journal of the American College of Cardiology·Patricia A Howard, Patrice Delafontaine
Jun 11, 2005·The Journal of Chemical Physics·Vitali Deev, Michael A Collins
Sep 20, 2005·Journal of Molecular Biology·Jamie GhumanStephen Curry
Jan 6, 2006·IUBMB Life·Mauro FasanoPaolo Ascenzi
Jul 14, 2006·The Journal of Physical Chemistry. a·Ryan P A Bettens, Adrian M Lee
Oct 26, 2007·The Journal of Physical Chemistry. B·Klefah A K Musa, Leif A Eriksson
Nov 26, 2009·Current Topics in Medicinal Chemistry·Ting ZhouAmedeo Caflisch
Feb 2, 2010·Biophysical Chemistry·Luciano GalantiniNicolae V Pavel
May 26, 2010·Arquivos brasileiros de cardiologia·Michel Batlouni
Jun 17, 2011·Diabetology & Metabolic Syndrome·Eva Frei
May 10, 2012·Journal of Computational Chemistry·Jens Antony, Stefan Grimme
Apr 7, 2015·Chemical Reviews·Michael A Collins, Ryan P A Bettens
Apr 29, 2015·Physical Chemistry Chemical Physics : PCCP·José X Lima NetoValder N Freire

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