On the theory of noncovalent binding

Biophysical Journal
Mihail Mihailescu, Michael K Gilson

Abstract

It is widely accepted that the binding constant of a receptor and ligand can be written as a two-body integral involving the interaction energy of the receptor and the ligand. Interestingly, however, three different theories of binding in the literature dictate three distinct integrals. The present study uses theory, as well as simulations of binding experiments, to test the validity of the three integrals. When binding is measured by a signal that detects the ligand in the binding site, the most accurate results are obtained by an integral of the Boltzmann factor, where the bound complex is defined in terms of an exclusive binding region. A novel prediction of this approach, that expanding a ligand can increase its binding constant, is borne out by the simulations. The simulations also show that abnormal binding isotherms can be obtained when the region over which the signal is detected deviates markedly from the exclusion zone. Interestingly, the binding constant measured by equilibrium dialysis, rather than by monitoring a localized signal, can yield a binding constant that differs from that obtained from a signal measurement, and that is matched best by the integral of the Mayer factor.

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Citations

Mar 1, 2012·Journal of Computer-aided Molecular Design·Hari S MuddanaMichael K Gilson
Jul 11, 2009·Chemical Reviews·Huan-Xiang Zhou, Michael K Gilson
Jan 17, 2009·The Journal of Physical Chemistry. B·Yuqing Deng, Benoît Roux
May 21, 2010·The European Physical Journal. E, Soft Matter·F Thalmann
Jan 5, 2007·Annual Review of Biophysics and Biomolecular Structure·Michael K Gilson, Huan-Xiang Zhou
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Feb 23, 2007·Chemical Biology & Drug Design·Chia-En A ChangJ Andrew McCammon
May 26, 2020·Journal of Computational Chemistry·Yoshiaki Tanida, Azuma Matsuura
Nov 15, 2017·Journal of Computer-aided Molecular Design·Oleksandr Yakovenko, Steven J M Jones
May 28, 2016·Journal of Computational Chemistry·Piero Procacci
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Sep 1, 2006·Journal of Chemical Theory and Computation·Yuqing Deng, Benoît Roux
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Jul 10, 2021·The Journal of Chemical Physics·E Duboué-Dijon, J Hénin
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Oct 8, 2004·Journal of the American Chemical Society·Chia-En Chang, Michael K Gilson
Sep 1, 2005·Journal of Chemical Theory and Computation·Chia-En ChangMichael K Gilson

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