Packing helices in proteins by global optimization of a potential energy function.
An efficient method has been developed for packing alpha-helices in proteins. It treats alpha-helices as rigid bodies and uses a simplified Lennard-Jones potential with Miyazawa-Jernigan contact-energy parameters to describe the interactions between the alpha-helical elements in this coarse-grained system. Global conformational searches to generate packing arrangements rapidly are carried out with a Monte Carlo-with-minimization type of approach. The results for 42 proteins show that the approach reproduces native-like folds of alpha-helical proteins as low-energy local minima of this highly simplified potential function.
Nanias
Marian
M
Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301, USA.
Chinchio
Maurizio
M
Pillardy
Jarosław
J
Ripoll
Daniel R
DR
Scheraga
Harold A
HA
D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*
D011506:Proteins