J. Phys.: Cond. Matt. 17
, S1515-S1522 (2005)
ISSN: 0953-8984, SCI
What determines the structures of native folds of proteins?
A. Trovato, T. X. Hoang, J. R. Banavar, A. Maritan and F. Seno
We review a simple physical model (Hoang et al 2004 Proc. Natl Acad. Sci.
USA 101 7960, Banavar et al 2004 Phys. Rev. E at press) which captures the
essential physico-chemical ingredients that determine protein structure, such
as the inherent anisotropy of a chain molecule, the geometrical and energetic
constraints placed by hydrogen bonds, sterics, and hydrophobicity. Within this
framework, marginally compact conformations resembling the native state folds
of proteins emerge as competing minima in the free energy landscape. Here
we demonstrate that a hydrophobic-polar (HP) sequence composed of regularly
repeated patterns has as its ground state a β-helical structure remarkably similar
to a known architecture in the Protein Data Bank.