Document type: Article | Language: English | Cited References: 63 |
Abstract:
We propose an alternative
stochastic strategy to search secondary structures based on the generalized
simulated annealing (GSA) algorithm, by using conformational preferences
based on the Ramachandran map. We optimize the search for polypeptide conformational
space and apply to peptides considered to be good alpha-helix promoters
above a critical number of residues. Our strategy to obtain conformational
energies consist in coupling a classical force field (THOR package) with
the GSA procedure, biasing the Phi x Psi backbone angles to the allowed
regions in the Ramachandran map. For polyalanines we obtained stable alpha-helix
structures when the number of residues were equal or exceeded 13 amino
acids residues. We also observed that the energy gap between the global
minimum and the first local minimum tends to increase with the polypeptide
size. These conformations were generated by performing 2880 stochastic
molecular optimizations with a continuum medium approach. When compared
with molecular dynamics or Monte Carlo methods, GSA can be considered the
fastest.
KeyWords Plus:
MOLECULAR-DYNAMICS SIMULATION, ALANINE-BASED PEPTIDES, COIL TRANSITION,
ALPHA-HELICES, OPTIMIZATION, STABILITY, KINETICS, PATHWAYS, MODEL, WATER
Addresses:
Bisch PM, Univ Fed Rio de Janeiro, Inst Biofis, CCS, Bloco G Ilha Fundao,
BR-21919900 Rio De Janeiro, Brazil
Univ Fed Rio de Janeiro, Inst Biofis Carlos Chagas Filho, BR-21919900
Rio De Janeiro, Brazil
Univ Estadual Feira de Santana, Dept Fis, Feira De Santana, Brazil
Univ Brasilia, Inst Quim, Brasilia, DF, Brazil
Publisher: BIOPHYSICAL SOCIETY, BETHESDA
ISSN: 0006-3495