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Can the geometry of all-atom protein trajectories be reconstructed from the knowledge of C time evolution? A study of peptide plane O and side chain C atoms
Stockholm University, Nordic Institute for Theoretical Physics (Nordita).
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Number of Authors: 52019 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 150, no 22, article id 225103Article in journal (Refereed) Published
Abstract [en]

We inquire to what extent can the geometry of protein peptide plane and side chain atoms be reconstructed from the knowledge of C time evolution. Due to the lack of experimental data, we analyze all atom molecular dynamics trajectories from the Anton supercomputer, and for clarity, we limit our attention to the peptide plane O atoms and side chain C atoms. We reconstruct their positions using four different approaches. Three of these are the publicly available reconstruction programs Pulchra, Remo, and Scwrl4. The fourth, Statistical Method, builds entirely on the statistical analysis of Protein Data Bank structures. All four methods place the O and C atoms accurately along the Anton trajectories; the Statistical Method gives results that are closest to the Anton data. The results suggest that when a protein moves under physiological conditions, its all atom structures can be reconstructed with high accuracy from the knowledge of the C atom positions. This can help to better understand and improve all atom force fields, and advance reconstruction and refinement methods for reduced protein structures. The results provide impetus for the development of effective coarse grained force fields in terms of reduced coordinates.

Place, publisher, year, edition, pages
2019. Vol. 150, no 22, article id 225103
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Chemical Sciences Biological Sciences
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URN: urn:nbn:se:su:diva-171132DOI: 10.1063/1.5082627ISI: 000471692400006PubMedID: 31202245OAI: oai:DiVA.org:su-171132DiVA, id: diva2:1351407
Available from: 2019-09-16 Created: 2019-09-16 Last updated: 2019-09-16Bibliographically approved

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Dai, JinNiemi, Antti J.
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