Understanding the structural characteristics of compstatin by conformational space annealing.
The structural characteristics of the 13-residue compstatin molecule are investigated using the conformational space annealing (CSA) method with CHARMM force field and the GBSA continuum solvent model. In order to sample conformations in the energy range of the minimized NMR structures, we have used the stopping criterion to the CSA search when a conformation whose energy is less than -490 kcal/mol is found. With this stopping criterion, a great variety of conformations are generated around experimentally known structures. Twenty independent CSA runs starting from random states find 1000 representative conformations in the energy landscape of the compstatin, which are classified into thirty-one structural families. The majority of the conformations (94.4%) are in the coil state. Other conformers containing a 3(10)-helix, a pi-helix, a beta-hairpin, and an alpha-helix are also found.
Song
Mee Kyung
MK
School of Computational Sciences, Korea Institute for Advanced Study, 207-43 Cheongnyangni 2-dong, Dongdaemun-gu, Seoul 130-722, Korea.
Kim
Seung-Yeon
SY
Lee
Jooyoung
J
D008958:Models, Molecular; D019906:Nuclear Magnetic Resonance, Biomolecular; D010456:Peptides, Cyclic / Q000737:chemistry*; D017433:Protein Structure, Secondary
D010456:Peptides, Cyclic; C111828:compstatin