Biophysics
Packing helices in proteins by global optimization of a potential energy
function
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and
* 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