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Effect of solvent model when probing protein dynamics with molecular dynamics

Artikel i vetenskaplig tidskrift
Författare Samuel Genheden
Publicerad i Journal of Molecular Graphics and Modelling
Volym 71
Sidor 80-87
ISSN 1093-3263
Publiceringsår 2017
Publicerad vid Institutionen för kemi och molekylärbiologi
Sidor 80-87
Språk en
Länkar doi.org/10.1016/j.jmgm.2016.11.002
Ämnesord Coarse-graining, Implicit solvent, Molecular dynamics, Order parameters, Protein dynamics
Ämneskategorier Statistisk mekanik

Sammanfattning

We probe the dynamics of the Bpti and Galectin-3 proteins using molecular dynamics simulations employing three water models at different levels of resolution, viz. the atomistic TIP4P-Ewald, the coarse-grained Elba and an implicit generalised Born model. The dynamics are quantified indirectly by model-free order parameters, S2 of the backbone N-H and selected side-chain bond vectors, which also have been determined experimentally through NMR relaxation measurements. For the backbone, the order parameters produced with the three solvent models agree to a large extent with experiments, giving average unsigned deviations between 0.03 and 0.06. For the side-chains, for which the experimental data is incomplete, the deviations are considerably larger with mean deviations between 0.13 and 0.17. However, for both backbone and side-chains, it is difficult to pick a winner, as all models perform equally well overall. For a more complete set of side-chain vectors, we resort to analysing the variation among the estimates from different solvent models. Unfortunately, the variations are found to be sizeable with mean deviations between 0.11 and 0.15. Implications for computational assessment of protein dynamics are discussed.

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