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Characterization of the residual structure in the unfolded state of the Δ131Δ fragment of staphylococcal nuclease
Author(s) -
Francis Christopher J.,
LindorffLarsen Kresten,
Best Robert B.,
Vendruscolo Michele
Publication year - 2006
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.21077
Subject(s) - nuclease , residual , chemistry , protein structure , molecular dynamics , crystallography , biophysics , computational biology , chemical physics , dna , computational chemistry , biology , biochemistry , computer science , algorithm
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 Δ131Δ fragment of staphylococcal nuclease under physiological conditions. Our findings indicate that Δ131Δ 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.