Characterization of the residual structure in the unfolded state of the Delta 131 Delta fragment of staphylococcal nuclease
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| 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. |
| Original language | English |
|---|---|
| Journal | Proteins - Structure Function and Bioinformatics |
| Volume | 65 |
| Issue number | 1 |
| Pages (from-to) | 145-52 |
| ISSN | 0887-3585 |
| DOIs | |
| Publication status | Published - 2006 |
ID: 1099761