Published online before print
February 5, 2003, 10.1073/pnas.252760199;
Proc. Natl. Acad. Sci. USA, Vol. 100, Issue 4, 1706-1710,
February 18, 2003
* Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301; and Computational Biology Service Unit, Cornell Theory Center, Ithaca, NY 14853-3801
Contributed by Harold A. Scheraga, December 13, 2002
An efficient method has been developed for packing -helices in proteins. It treats -helices as rigid bodies and uses a simplified Lennard-Jones potential with Miyazawa-Jernigan contact-energy parameters to describe the interactions between the -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 -helical proteins as low-energy local minima of this highly simplified potential function.
To whom correspondence should be addressed. E-mail: has5@cornell.edu.
www.pnas.org/cgi/doi/10.1073/pnas.252760199