Identifying unfolding intermediates of FN-III(10) by steered molecular dynamics

TitleIdentifying unfolding intermediates of FN-III(10) by steered molecular dynamics
Publication TypeJournal Article
Year of Publication2002
AuthorsGao, M, Craig D, Vogel V, Schulten K
JournalJournal of molecular biology
Volume323
Pagination939-50
Date Published2002 Nov 8
Abstract

Experimental studies have indicated that FN-III modules undergo reversible unfolding as a mechanism of elasticity. The unfolding of FN-III modules, including the cell-binding FN-III(10) module, has further been suggested to be functionally relevant by exposing buried cryptic sites or modulating cell binding. While steered molecular dynamics (SMD) simulations have provided one tool to investigate this process, computational requirements so far have limited detailed analysis to the early stages of unfolding. Here, we use an extended periodic box to probe the unfolding of FN-III(10) for extensions longer than 60A. Up to three plateaus, corresponding to three metastable intermediates, were observed in the extension-time profile from SMD stretching of FN-III(10). The first and second plateaus correspond to a twisted and an aligned state prior to unraveling FN-III(10) beta-strands. The third plateau, at an extension of approximately 100A, follows unraveling of FN-III(10) A and B-strands and precedes breaking of inter-strand hydrogen bonds between F and G-strands. The simulations revealed three forced unfolding pathways of FN-III(10), one of which is preferentially selected under physiological conditions. Implications for fibronectin fibrillogenesis are discussed.

Pub Med Link

http://www.ncbi.nlm.nih.gov/pubmed/12417205?dopt=Abstract

Alternate JournalJ. Mol. Biol.
Citekey12417205