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Atomistic Modeling of Collagen Proteins in Their Fibrillar Environment

Streeter, I; de Leeuw, NH; (2010) Atomistic Modeling of Collagen Proteins in Their Fibrillar Environment. Journal of Physical Chemistry B , 114 (41) 13263 - 13270. 10.1021/jp1059984. Green open access

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Abstract

Molecular dynamics simulations can aid studies of the structural and physicochemical properties of proteins, by predicting their dynamics,-energetics, and interactions with their local environment at the atomistic level. We argue that nonstandard protocols are needed to realistically model collagen proteins, which in their biological state aggregate to form collagen fibrils, and so should not be treated as fully solvated molecules. A new modeling approach is presented that can account for the local environment of collagen molecules within a fibril and which therefore simulates aspects of their behavior that would not otherwise be distinguished. This modeling approach exploits periodic boundaries to replicate the supermolecular arrangement of collagen proteins within the fibril, in an approach. that is more commonly associated with modeling crystalline solids rather than mesoscopic protein aggregates. Initial simulations show agreement with experimental observations and corroborate. theories of the fibril's structure.

Type:Article
Title:Atomistic Modeling of Collagen Proteins in Their Fibrillar Environment
Open access status:An open access version is available from UCL Discovery
DOI:10.1021/jp1059984
Publisher version:http://dx.doi.org/10.1021/jp1059984
Language:English
Additional information:This document is the Accepted Manuscript version of a Published Work that appeared in final form in Journal of Physical Chemistry B copyright 2010 American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see http://dx.doi.org/10.1021/jp1059984
Keywords:MOLECULAR-DYNAMICS, SWELLING PRESSURE, TRIPLE-HELIX, WATER, SIMULATION, STABILITY, HYDRATION, FLUID
UCL classification:UCL > School of Life and Medical Sciences > Faculty of Medical Sciences > Surgery and Interventional Science (Division of) > Institute of Orthopaedics and Musculoskeletal Science
UCL > School of BEAMS > Faculty of Maths and Physical Sciences > Chemistry

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