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Study of correlations between protein peptide plane dynamics and side chain dynamics
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Number of Authors: 52019 (English)In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 14, no 4, article id e0215141Article in journal (Refereed) Published
Abstract [en]

Protein dynamics is pivotal to biological processes. However, experiments are very demanding and difficult to perform, and all-atom molecular dynamics simulations can still not provide all the answers. This motivates us to analyze protein dynamics in terms of different reduced coordinate representations. We then need to resolve how to reconstruct the full all-atom dynamics from its coarse grained approximation. Accordingly we scrutinize all-atom molecular dynamics trajectories in terms of crystallographic Protein Data Bank (PDB) structures, and inquire to what extent is it possible to predict the dynamics of side chain C beta atoms in terms of the static properties of backbone Ca and O atoms. Here we find that simulated C beta dynamics at near physiological conditions can be reconstructed with very high precision, using the knowledge of the crystallographic backbone Ca and O positions. The precision we can reach with our PDB-based Statistical Method reconstruction exceeds that of popular all-atom reconstruction methods such as Remo and Pulchra, and is fully comparable with the precision of the highly elaborate Scwrl4 all-atom reconstruction method that we have enhanced with the knowledge of the backbone Ca and O atom positions. We then conclude that in a dynamical protein that moves around at physiological conditions, the relative positions of its C beta atoms with respect to the backbone Ca and O atoms, deviate very little from their relative positions in static crystallographic PDB structures. This proposes that the dynamics of a biologically active protein could remain subject to very similar, stringent stereochemical constraints that dictate the structure of a folded crystallographic protein. Thus, our results provide a strong impetus to the development of coarse grained techniques that are based on reduced coordinate representations.

Place, publisher, year, edition, pages
2019. Vol. 14, no 4, article id e0215141
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Biological Sciences
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URN: urn:nbn:se:su:diva-168334DOI: 10.1371/journal.pone.0215141ISI: 000464349000038PubMedID: 30978222OAI: oai:DiVA.org:su-168334DiVA, id: diva2:1315403
Available from: 2019-05-13 Created: 2019-05-13 Last updated: 2019-05-13Bibliographically approved

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Niemi, Antti J.
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Nordic Institute for Theoretical Physics (Nordita)
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