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J Chem Phys. 2009 Jun 7;130(21):215106. doi: 10.1063/1.3148186.

Application of the Wang-Landau algorithm to the dimerization of glycophorin A.

Author information

1
Department of Biochemistry and Molecular Biology, Computational Systems Biology Laboratory and Institute of Bioinformatics, The University of Georgia, Athens, Georgia 30602, USA. clairegervais@csbl.bmb.uga.edu

Abstract

A two-step Monte Carlo procedure is developed to investigate the dimerization process of the homodimer glycophorin A. In the first step, the energy density of states of the system is estimated by the Wang-Landau algorithm. In the second step, a production run is performed during which various energetical and structural observables are sampled to provide insight into the thermodynamics of the system. All seven residues LIxxGVxxGVxxT constituting the contact interface play a dominating role in the dimerization, however at different stages of the process. The leucine motif and to some extent the GxxxG motif are involved at the very beginning of the dimerization when the two helices come into contact, ensuring an interface already similar to the native one. At a lower temperature, the threonine motif stabilizes by hydrogen bonding the dimer, which finally converges toward its native state at around 300 K. The power and flexibility of the procedure employed here makes it an interesting alternative to other Monte Carlo methods for the study of similar protein systems.

PMID:
19508105
PMCID:
PMC2719476
DOI:
10.1063/1.3148186
[Indexed for MEDLINE]
Free PMC Article

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