دورية أكاديمية
أعرض في EDS

Energy landscapes for proteins described by the UNRES coarse-grained potential.

التفاصيل البيبلوغرافية
العنوان: Energy landscapes for proteins described by the UNRES coarse-grained potential.
المؤلفون: Wesołowski PA; Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK. Electronic address: paw61@cam.ac.uk., Sieradzan AK; Faculty of Chemistry, Gdansk University, Wita Stwosza 63, 80-308 Gdańsk, Poland., Winnicki MJ; Faculty of Chemistry, Gdansk University, Wita Stwosza 63, 80-308 Gdańsk, Poland; Oklahoma Medical Research Foundation, 825 NE 13th St., Oklahoma City, OK 73104, USA; Intercollegiate Faculty of Biotechnology, University of Gdańsk and the Medical University of Gdańsk, Abrahama 58, 80-307 Gdańsk, Poland., Morgan JWR; Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK; Downing College, University of Cambridge, Regent St., Cambridge CB2 1DQ, UK., Wales DJ; Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK. Electronic address: dw34@cam.ac.uk.
المصدر: Biophysical chemistry [Biophys Chem] 2023 Dec; Vol. 303, pp. 107107. Date of Electronic Publication: 2023 Sep 12.
نوع المنشور: Journal Article; Research Support, Non-U.S. Gov't
اللغة: English
بيانات الدورية: Publisher: Elsevier Science B.V Country of Publication: Netherlands NLM ID: 0403171 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1873-4200 (Electronic) Linking ISSN: 03014622 NLM ISO Abbreviation: Biophys Chem Subsets: MEDLINE
أسماء مطبوعة: Publication: Amsterdam : Elsevier Science B.V
Original Publication: Amsterdam, North-Holland Pub. Co.
مواضيع طبية MeSH: Proteins*/chemistry , Software*, Protein Conformation ; Protein Structure, Secondary ; Thermodynamics ; Molecular Dynamics Simulation
مستخلص: The self-assembly of proteins is encoded in the underlying potential energy surface (PES), from which we can predict structure, dynamics, and thermodynamic properties. However, the corresponding analysis becomes increasingly challenging with larger protein sizes, due to the computational time required, which grows significantly with the number of atoms. Coarse-grained models offer an attractive approach to reduce the computational cost. In this Feature Article, we describe our implementation of the UNited RESidue (UNRES) coarse-grained potential in the Cambridge energy landscapes software. We have applied this framework to explore the energy landscapes of four proteins that exhibit native states involving different secondary structures. Here we have tested the ability of the UNRES potential to represent the global energy landscape of proteins containing up to 100 amino acid residues. The resulting potential energy landscapes exhibit good agreement with experiment, with low-lying minima close to the PDB geometries and to results obtained using the all-atom AMBER force field. The new program interfaces will allow us to investigate larger biomolecules in future work, using the UNRES potential in combination with all the methodology available in the computational energy landscapes framework.
Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.
(Copyright © 2023 The Authors. Published by Elsevier B.V. All rights reserved.)
فهرسة مساهمة: Keywords: Energy landscape; Potential energy surface; Proteins; UNRES coarse-grained model
المشرفين على المادة: 0 (Proteins)
تواريخ الأحداث: Date Created: 20231020 Date Completed: 20231110 Latest Revision: 20240105
رمز التحديث: 20240105
DOI: 10.1016/j.bpc.2023.107107
PMID: 37862761
قاعدة البيانات: MEDLINE
الوصف
تدمد:1873-4200
DOI:10.1016/j.bpc.2023.107107