Improved interaction potentials for charged residues in proteins

The Journal of Physical Chemistry. B
Kasper P Jensen

Abstract

Electrostatic interactions dominate the structure and free energy of biomolecules. To obtain accurate free energies involving charged groups from molecular simulations, OPLS-AA parameters have been reoptimized using Monte Carlo free energy perturbation. New parameters fit a self-consistent, experimental set of hydration free energies for acetate (Asp), propionate (Glu), 4-methylimidazolium (Hip), n-butylammonium (Lys), and n-propylguanidinium (Arg), all resembling charged residue side chains, including beta-carbons. It is shown that OPLS-AA free energies depend critically on the type of water model, TIP4P or TIP3P; i.e., each water model requires specific water-charged molecule interaction potentials. New models (models 1 and 3) are thus described for both water models. Uncertainties in relative free energies of charged residues are approximately 2 kcal/mol with the new parameters, due to variations in system setup (MAEs of ca. 1 kcal/mol) and noise from simulations (ca. 1 kcal/mol). The latter error of approximately 1 kcal/mol contrasts MAEs from standard OPLS-AA of up to 13 kcal/mol for the entire series of charged residues or up to 5 kcal/mol for the cationic series Lys, Arg, and Hip. The new parameters can be used directly ...Continue Reading

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Citations

Jul 3, 2008·The Journal of Physical Chemistry. B·In Suk Joung, Thomas E Cheatham
May 6, 2009·Angewandte Chemie·Hans-Jörg Schneider
Aug 11, 2015·Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry·Arun Kumar Somavarapu, Kasper P Kepp
Feb 17, 2019·The Journal of Chemical Physics·Jeffry Setiadi, Serdar Kuyucak
Sep 1, 2019·The Journal of Chemical Physics·Rukmankesh Mehra, Kasper P Kepp
Jun 19, 2018·PeerJ·Mustapha Carab AhmedKresten Lindorff-Larsen
Jul 8, 2009·The Journal of Physical Chemistry. B·Jens Carlsson, Johan Aqvist
Aug 30, 2018·The Journal of Physical Chemistry. a·Kasper P Kepp
Jul 9, 2013·Journal of Chemical Theory and Computation·Niels J Christensen, Kasper P Kepp
Jan 12, 2019·Journal of Chemical Theory and Computation·Viet Hoang ManJunmei Wang
Aug 26, 2017·ACS Chemical Neuroscience·Arun Kumar Somavarapu, Kasper P Kepp
Jul 27, 2018·Journal of Chemical Information and Modeling·Haiyang ZhangChunhua Yin
May 19, 2020·The Journal of Physical Chemistry. B·Rukmankesh Mehra, Kasper P Kepp
Feb 24, 2018·The Journal of Physical Chemistry. B·Brian DohertyOrlando Acevedo
Jul 5, 2019·The Journal of Physical Chemistry. a·Kasper P Kepp

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