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Abstract

We have captured the binding of a peptide to a PDZ domain by unbiased molecular dynamics simulations. Analysis of the trajectories reveals on-pathway encounter complex formation, which is driven by electrostatic interactions between negatively charged carboxylate groups in the peptide and positively charged side chains surrounding the binding site. In contrast, the final stereospecific complex, which matches the crystal structure, features completely different interactions, namely the burial of the hydrophobic side chain of the peptide C-terminal residue and backbone hydrogen bonds. The simulations show that nonnative salt bridges stabilize kinetically the encounter complex during binding. Unbinding follows the inverse sequence of events with the same nonnative salt bridges in the encounter complex. Thus, in contrast to protein folding, which is driven by native interactions, the binding of charged peptides can be steered by nonnative interactions, which might be a general mechanism, e.g., in the recognition of histone tails by bromodomains.

Year of Publication
2015
Journal
Biophysical Journal
Volume
108
Issue
9
Number of Pages
2362-2370
Date Published
2015 May 5
Type of Article
Research Article
ISSN Number
1542-0086
DOI
10.1016/j.bpj.2015.03.038
Alternate Journal
Biophys. J.
PMCID
PMC4423040
PMID
25954893
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