Prediction of protein-protein complexes using replica exchange with repulsive scaling.

Journal of Computational Chemistry
Till SiebenmorgenMartin Zacharias

Abstract

The realistic prediction of protein-protein complex structures is import to ultimately model the interaction of all proteins in a cell and for the design of new protein-protein interactions. In principle, molecular dynamics (MD) simulations allow one to follow the association process under realistic conditions including full partner flexibility and surrounding solvent. However, due to the many local binding energy minima at the surface of protein partners, MD simulations are frequently trapped for long times in transient association states. We have designed a replica-exchange based scheme employing different levels of a repulsive biasing between partners in each replica simulation. The bias acts only on intermolecular interactions based on an increase in effective pairwise van der Waals radii (repulsive scaling (RS)-REMD) without affecting interactions within each protein or with the solvent. For a set of five protein test cases (out of six) the RS-REMD technique allowed the sampling of near-native complex structures even when starting from the opposide site with respect to the native binding site for one partner. Using the same start structures and same computational demand regular MD simulations sampled near native complex st...Continue Reading

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Citations

Jan 31, 2021·Physical Chemistry Chemical Physics : PCCP·Małgorzata M KogutSergey A Samsonov
Dec 29, 2020·Current Opinion in Structural Biology·Ameya Harmalkar, Jeffrey J Gray
Mar 27, 2021·Journal of Computational Chemistry·Martyna Maszota-ZieleniakSergey A Samsonov
Jul 25, 2021·International Journal of Molecular Sciences·Mateusz KurcinskiAndrzej Kolinski
May 8, 2020·The Journal of Physical Chemistry. B·Alfredo Jost LopezJuergen Koefinger
Aug 18, 2021·Matrix Biology Plus·Martyna Maszota-ZieleniakSergey A Samsonov
Oct 20, 2020·Journal of Chemical Information and Modeling·Till Siebenmorgen, Martin Zacharias
Sep 9, 2021·Journal of Chemical Information and Modeling·Mateusz MarciszSergey A Samsonov

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