Protein folding rates estimated from contact predictions.

TitleProtein folding rates estimated from contact predictions.
Publication TypeJournal Article
Year of Publication2005
AuthorsPunta, M, Rost, B
JournalJ Mol Biol
Date Published2005 May 6
KeywordsAmino Acid Sequence, Animals, Protein Folding, Protein Structure, Secondary, Proteins, Statistics as Topic

Folding rates of small single-domain proteins that fold through simple two-state kinetics can be estimated from details of the three-dimensional protein structure. Previously, predictions of secondary structure had been exploited to predict folding rates from sequence. Here, we estimate two-state folding rates from predictions of internal residue-residue contacts in proteins of unknown structure. Our estimate is based on the correlation between the folding rate and the number of predicted long-range contacts normalized by the square of the protein length. It is well known that long-range order derived from known structures correlates with folding rates. The surprise was that estimates based on very noisy contact predictions were almost as accurate as the estimates based on known contacts. On average, our estimates were similar to those previously published from secondary structure predictions. The combination of these methods that exploit different sources of information improved performance. It appeared that the combined method reliably distinguished fast from slow two-state folders.

Alternate JournalJ. Mol. Biol.
PubMed ID15826649
Grant ListR01-GM64633-01 / GM / NIGMS NIH HHS / United States
R01-LM07329-01 / LM / NLM NIH HHS / United States