Determination of pair-wise inter-residue interaction forces from folding pathways and their implementation in coarse-grained folding prediction

Sefer Baday, Burak Erman, Yaman Arkun*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

Abstract

Interaction forces among residue pairs are determined from optimum folding pathways along which a protein represented as a coarse-grained chain of α-carbons goes from different initial configurations to a known native state. A dynamic optimization approach is employed that uses the coarse-grained model to compute the optimal folding pathways. The pair-wise interaction forces obtained in this manner are incorporated into the coarse-grained model which is then simulated to fold the protein from a new set of initial configurations in a predictive way. We show that the folding pathways predicted in this manner are near-optimal. We applied the technique to the secondary structures: helix and β-sheet.

Original languageEnglish
Pages (from-to)1949-1961
Number of pages13
JournalPhysical Chemistry Chemical Physics
Volume11
Issue number12
DOIs
Publication statusPublished - 2009
Externally publishedYes

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