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Starting structure dependence of NMR order parameters derived from MD simulations: implications for judging force-field quality |
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| Authors: | Koller Alrun N Schwalbe Harald Gohlke Holger |
| Affiliation: | * Department of Biological Sciences, Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Goethe-University, Frankfurt am Main, Germany † Department of Biochemistry, Chemistry, and Pharmacy, Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Goethe-University, Frankfurt am Main, Germany |
| Abstract: | Comparing experimental generalized N-H S2 order parameters to those calculated from molecular dynamics trajectories is increasingly used to judge force-field quality and completeness of sampling. Herein we demonstrate for the well-investigated system hen egg white lysozyme that different experimental starting structures can lead to significant differences in molecular-dynamics-derived S2 parameters that can be even larger than S2 parameter deviations due to different force fields. Caution should thus be taken in general when simulated S2 parameters are compared to experimental data with the aim of judging force-field quality. We show that adequately sampling flexible regions (∼100 ns) and only calculating S2 parameters averaged over short time windows proved necessary to obtain consistent results irrespective of the starting structure. |
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