Computer simulations aimed at structure prediction of supersecondary motifs in proteins

Citation
F. Forcellino et P. Derreumaux, Computer simulations aimed at structure prediction of supersecondary motifs in proteins, PROTEINS, 45(2), 2001, pp. 159-166
Citations number
43
Language
INGLESE
art.tipo
Article
Categorie Soggetti
Biochemistry & Biophysics
Journal title
PROTEINS-STRUCTURE FUNCTION AND GENETICS
ISSN journal
0887-3585 → ACNP
Volume
45
Issue
2
Year of publication
2001
Pages
159 - 166
Database
ISI
SICI code
0887-3585(20011101)45:2<159:CSAASP>2.0.ZU;2-7
Abstract
It is well established that protein structures are more conserved than prot ein se. quences. One-third of all known protein structures can be classifie d into ten protein folds, which themselves are composed mainly of a-helical hairpin, beta hairpin, and Pap supersecondary structural elements. In this study, we explore the ability of a recent Monte Carlo-based procedure to g enerate the 3D structures of eight polypeptides that correspond to units of supersecondary structure and three-stranded antiparallel beta sheet. Start ing from extended or misfolded compact conformations, all Monte Carlo simul ations show significant success in predicting the native topology using a s implified chain representation and an energy model optimized on other struc tures. Preliminary results on model peptides from nucleotide binding protei ns suggest that this simple protein folding model can help clarify the rela tion between sequence and topology. (C) 2001 Wiley-Liss, Inc.