Supplementary data for paper on PsaA metal ion force-field comparison.
MacDermott-Opeskin, H., A McDevitt, C., & L O’Mara, M. (2020). Comparing Non-Bonded Metal Ion Models in the Divalent Cation Binding Protein PsaA. Journal of Chemical Theory and Computation, 16(3), 1913–1923. https://doi.org/10.1021/acs.jctc.9b01180
@article{MacDermott-Opeskin2020,
abstract = {Divalent metal cations are essential for many biological processes, however accurately modeling divalent metal ions has proved a significant challenge for molecular dynamics forcefields. Here we show that the choice of ion model influences the observed dynamics in PsaA, a metal binding protein from Streptococcus pneumoniae. We conduct extensive unbiased simulations and free energy calculations of PsaA bound to its cognate ligand Mn2+ and inhibitory ligand Zn2+ using three nonbonded ion models: a 12-6 model, a 12-6-4 model and a multisite model. The observed coordination geometries and metal binding dynamics are sensitive to the choice of ion model, with the most dramatic differences observed in free energy calculations of ion release. We show that the conformational ensemble of Mn-bound PsaA is more similar to the crystallographic metal bound open state. This work extends current models of PsaA metal binding and provides a framework for the rationalization of experimentally determined metal binding behavior.},
author = {MacDermott-Opeskin, Hugo and {A McDevitt}, Christopher and {L O'Mara}, Megan},
doi = {10.1021/acs.jctc.9b01180},
issn = {1549-9618},
journal = {Journal of Chemical Theory and Computation},
number = {3},
pages = {1913--1923},
title = {{Comparing Non-Bonded Metal Ion Models in the Divalent Cation Binding Protein PsaA}},
url = {https://pubs.acs.org/doi/10.1021/acs.jctc.9b01180},
volume = {16},
year = {2020}
}