eprintid: 1304861
rev_number: 54
eprint_status: archive
userid: 608
dir: disk0/01/30/48/61
datestamp: 2011-04-27 20:51:12
lastmod: 2021-09-19 23:12:56
status_changed: 2012-06-15 15:51:27
type: article
metadata_visibility: show
item_issues_count: 0
creators_name: Streeter, I
creators_name: de Leeuw, NH
title: A molecular dynamics study of the interprotein interactions in collagen fibrils
ispublished: pub
divisions: UCL
divisions: B04
divisions: C06
keywords: I COLLAGEN, TRIPLE-HELIX, SALT BRIDGES, PROTEIN, STABILITY, WATER, BACKBONE, PACKING, DRIVEN, FORCES
abstract: Molecular dynamics simulations of collagen are used to investigate at the atomistic level the nature of the interprotein interactions that are present within a collagen fibril, and which are responsible for the fibril's thermodynamic stability. Simulations both of a collagen fibril and of a fully solvated tropocollagen are compared in order to study the interactions that arise between the proteins upon the process of fibrillogenesis. The interactions studied include direct interprotein hydrogen bonds, water-mediated interprotein hydrogen bonds, and hydrophobic interactions. The simulations are used to quantify the number of interprotein interactions; to study which functional groups contribute most towards the interactions; and to investigate the spatial distribution of interprotein interactions throughout the fibril's D period. The processes of collagen fibrillogenesis and protein folding are then compared with each other, because these two physical processes share many similarities in concept, but the latter has been studied more widely. Molecular dynamics simulations of a bacteriophage T4 lysozyme protein, both in its native state and in an unfolded state, are used as an illustrative example of a typical protein folding process, for direct comparison with the collagen simulations.
date: 2011-04-07
publisher: ROYAL SOC CHEMISTRY
official_url: http://dx.doi.org/10.1039/c0sm01192d
vfaculties: VGHCSCI
vfaculties: VMPS
oa_status: green
language: eng
primo: open
primo_central: open_green
article_type_text: Article
verified: verified_manual
elements_source: Web of Science
elements_id: 306274
doi: 10.1039/c0sm01192d
language_elements: EN
lyricists_name: De Leeuw, Nora
lyricists_name: STREETER, IAN
lyricists_id: NHDEL32
lyricists_id: ISTRE17
full_text_status: public
publication: Soft Matter
volume: 7
number: 7
pagerange: 3373 - 3382
issn: 1744-683X
citation:        Streeter, I;    de Leeuw, NH;      (2011)    A molecular dynamics study of the interprotein interactions in collagen fibrils.                   Soft Matter , 7  (7)   3373 - 3382.    10.1039/c0sm01192d <https://doi.org/10.1039/c0sm01192d>.       Green open access   
 
document_url: https://discovery.ucl.ac.uk/id/eprint/1304861/1/1304861_draft%20v1.pdf