ESCASA : Analytical estimation of atomic coordinates from coarse‐grained geometry for nuclear‐magnetic‐resonance ‐assisted protein structure modeling. I. Backbone and Hβ protons

Emilia Lubecka; Adam Liwo

doi:10.1002/jcc.26695

ESCASA : Analytical estimation of atomic coordinates from coarse‐grained geometry for nuclear‐magnetic‐resonance ‐assisted protein structure modeling. I. Backbone and Hβ protons

Abstract

A method for the estimation of coordinates of atoms in proteins from coarse-grained geometry by simple analytical formulas (ESCASA), for use in nuclear-magnetic-resonance (NMR) data-assisted coarse-grained simulations of proteins is proposed. In this paper, the formulas for the backbone Hα and amide (HN) protons, and the side-chain Hβ protons, given the Cα-trace, have been derived and parameterized, by using the interproton distances calculated from a set of 140 high-resolution non-homologous protein structures. The mean standard deviation over all types of proton pairs in the set was 0.44 Å after fitting. Validation against a set of 41 proteins with NMR-determined structures, which were not considered in parameterization, resulted in average standard deviation from average proton–proton distances of the NMR-determined structures of 0.25 Å, compared to 0.21 Å obtained with the PULCHRA all-atom-chain reconstruction algorithm and to the 0.12 Å standard deviation of the average-structure proton–proton distance of NMR-determined ensembles. The formulas provide analytical forces and can, therefore, be used in coarse-grained molecular dynamics.

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Emilia Lubecka dr inż.
Adam Liwo

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DOI:: Digital Object Identifier (open in new tab) 10.1002/JCC.26695
License: Copyright (2021 Wiley Periodicals LLC.)

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Keywords

COARSE GRAINING, DATA-ASSISTED MOLECULAR MODELING, NUCLEAR MAGNETIC RESONANCE, PROTEINS

Details

Category:: Articles
Type:: artykuły w czasopismach
Published in:: JOURNAL OF COMPUTATIONAL CHEMISTRY no. 42, pages 1579 - 1589,
ISSN: 0192-8651
Language:: English
Publication year:: 2021
Bibliographic description:: Lubecka E., Liwo A.: ESCASA : Analytical estimation of atomic coordinates from coarse‐grained geometry for nuclear‐magnetic‐resonance ‐assisted protein structure modeling. I. Backbone and Hβ protons// JOURNAL OF COMPUTATIONAL CHEMISTRY -Vol. 42,iss. 22 (2021), s.1579-1589
DOI:: Digital Object Identifier (open in new tab) 10.1002/jcc.26695
Verified by:: Gdańsk University of Technology