Computer simulations aimed at structure prediction of supersecondary motifs in proteins

Forcellino, F Derreumaux, P

F. Forcellino et P. Derreumaux, Computer simulations aimed at structure prediction of supersecondary motifs in proteins, PROTEINS, 45(2), 2001, pp. 159-166

43

INGLESE

Article

Biochemistry & Biophysics

PROTEINS-STRUCTURE FUNCTION AND GENETICS

0887-3585 → ACNP

45

2

2001

159 - 166

ISI

0887-3585(20011101)45:2<159:CSAASP>2.0.ZU;2-7

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.