Characterization of the residual structure in the unfolded state of the Delta 131 Delta fragment of staphylococcal nuclease

C. J. Francis, Kresten Lindorff-Larsen, R. B. Best, M. Bendruscolo

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38 Citationer (Scopus)

Abstract

The determination of the conformational preferences in unfolded states of proteins constitutes an important challenge in structural biology. We use inter-residue distances estimated from site-directed spin-labeling NMR experimental measurements as ensemble-averaged restraints in all-atom molecular dynamics simulations to characterise the residual structure of the 131 fragment of staphylococcal nuclease under physiological conditions. Our findings indicate that 131 under these conditions shows a tendency to form transiently hydrophobic clusters similar to those present in the native state of wild-type staphylococcal nuclease. Only rarely, however, all these interactions are simultaneously realized to generate conformations with an overall native topology. Proteins 2006. © 2006 Wiley-Liss, Inc.
OriginalsprogEngelsk
TidsskriftProteins - Structure Function and Bioinformatics
Vol/bind65
Udgave nummer1
Sider (fra-til)145-52
ISSN0887-3585
DOI
StatusUdgivet - 2006

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