Role of native topology investigated by multiple unfolding simulations of four SH3 domains

TitleRole of native topology investigated by multiple unfolding simulations of four SH3 domains
Publication TypeJournal Article
Year of Publication2001
AuthorsGsponer J., Caflisch A.
JournalJournal of Molecular Biology
Volume309
Issue1
Pagination285-298
Date Published2001 May 25
Type of ArticleResearch Article
ISSN0022-2836
KeywordsAmino Acid Sequence, Animals, Binding Sites, Chickens, Computer Simulation, Crystallography, X-Ray, Hydrogen Bonding, Kinetics, Models, Molecular, Molecular Sequence Data, Mutation, Protein Denaturation, Protein Engineering, Protein Folding, Protein Structure, Secondary, Proto-Oncogene Proteins pp60(c-src), Spectrin, src Homology Domains, Temperature
Abstract

The relative importance of amino acid sequence and native topology in the unfolding process of two SH3 domains and two circular permutants was investigated by 120 molecular dynamics runs at 375 K for a total simulation time of 0.72 μs. The α-spectrin (aSH3) and src SH3 (sSH3) domains, which have the same topology and a sequence identity of only 34%, show similar unfolding pathways. The disappearance of the three-stranded antiparallel β-sheet is the last unfolding event, in agreement with a large repertoire of kinetic data derived from point mutations as well as glycine insertions and disulfide crosslinks. Two alternative routes of β-sheet unfolding have emerged from the analysis of the trajectories. One is statistically preferred in aSH3 (n-src loop breaks before distal hair-pin) and the inverse in sSH3. An elongation of the β2-β3 hairpin was observed during the unfolding of sSH3 at 375 K and in 300 K simulations started from the putative transition state of sSH3 in accord with unusual kinetic data for point mutations at the n-src loop. The change of connectivity in the permutants influenced the sequence of unfolding events mainly at the permutation site. Regions where the connectivity remained unaffected showed the same chronology of contact disappearance. Taken together with previous folding simulations of two designed three-stranded antiparallel β-sheet peptides, these results indicate that, at least for small β-sheet proteins, the folding mechanism is primarily defined by the native state topology, whilst specific interactions determine the statistically predominant folding route.

DOI10.1006/jmbi.2001.4552
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Alternate JournalJ. Mol. Biol.
PubMed ID11491296
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