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Published in

American Chemical Society, Journal of Physical Chemistry B (Soft Condensed Matter and Biophysical Chemistry), 24(118), p. 6561-6569, 2014

DOI: 10.1021/jp500958r

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Evaluating the Strength of Salt Bridges: A Comparison of Current Biomolecular Force Fields

Journal article published in 2014 by Karl T. Debiec, Angela M. Gronenborn ORCID, Lillian T. Chong
This paper is made freely available by the publisher.
This paper is made freely available by the publisher.

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Abstract

Recent advances in computer hardware and software have made rigorous evaluation of current biomolecular force fields using μs-scale simulations possible. Force fields differ, importantly in their treatment of electrostatic interactions, including the formation of salt bridges in proteins. Here we conducted an extensive evaluation of salt bridge interactions in the latest AMBER, CHARMM, and OPLS force fields using μs-scale molecular dynamics simulations of amino acid analogs in explicit solvent. We focused on salt bridges between three different pairs of oppositely charged amino acids: Arg/Asp, Lys/Asp, and His(+)/Asp. Our results revealed considerable variability in the predicted KA values of the salt bridges for these force fields as well as differences from experimental data: almost all of the force fields overestimate the strengths of the salt bridges. When amino acids are represented by side-chain analogs, the AMBER ff03 force field overestimates the KA values the least, while for complete amino acids, the AMBER ff13α force field yields the lowest KA value, most likely caused by an altered balance of side-chain/side-chain and side-chain/backbone contacts. These findings confirm the notion that the implicit incorporation of solvent polarization improves the accuracy of modeling salt bridge interactions.