TITLE

Conformational landscape of the HIV-V3 hairpin loop from all-atom free-energy simulations

AUTHOR(S)
Verma, Abhinav; Wenzel, Wolfgang
PUB. DATE
March 2008
SOURCE
Journal of Chemical Physics;3/14/2008, Vol. 128 Issue 10, p105103
SOURCE TYPE
Academic Journal
DOC. TYPE
Article
ABSTRACT
Small beta hairpins have many distinct biological functions, including their involvement in chemokine and viral receptor recognition. The relevance of structural similarities between different hairpin loops with near homologous sequences is not yet understood, calling for the development of methods for de novo hairpin structure prediction and simulation. De novo folding of beta strands is more difficult than that of helical proteins because of nonlocal hydrogen bonding patterns that connect amino acids that are distant in the amino acid sequence and there is a large variety of possible hydrogen bond patterns. Here we use a greedy version of the basin hopping technique with our free-energy forcefield PFF02 to reproducibly and predictively fold the hairpin structure of a HIV-V3 loop. We performed 20 independent basin hopping runs for 500 cycles corresponding to 7.4×107 energy evaluations each. The lowest energy structure found in the simulation has a backbone root mean square deviation (bRMSD) of only 2.04 Å to the native conformation. The lowest 9 out of the 20 simulations converged to conformations deviating less than 2.5 Å bRMSD from native.
ACCESSION #
31335080

 

Share

Read the Article

Courtesy of

Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics