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

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.

SUBMITTER: Gervais C

PROVIDER: S-EPMC2719476 | biostudies-literature | 2009 Jun

REPOSITORIES: biostudies-literature

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

Gervais Claire C Wüst Thomas T Landau D P DP Xu Ying Y

The Journal of chemical physics 20090601 21

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 ...[more]

PMID: 19508105

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Project description:MotivationThermodynamics-based dynamic programming RNA secondary structure algorithms have been of immense importance in molecular biology, where applications range from the detection of novel selenoproteins using expressed sequence tag (EST) data, to the determination of microRNA genes and their targets. Dynamic programming algorithms have been developed to compute the minimum free energy secondary structure and partition function of a given RNA sequence, the minimum free-energy and partition function for the hybridization of two RNA molecules, etc. However, the applicability of dynamic programming methods depends on disallowing certain types of interactions (pseudoknots, zig-zags, etc.), as their inclusion renders structure prediction an nondeterministic polynomial time (NP)-complete problem. Nevertheless, such interactions have been observed in X-ray structures.ResultsA non-Boltzmannian Monte Carlo algorithm was designed by Wang and Landau to estimate the density of states for complex systems, such as the Ising model, that exhibit a phase transition. In this article, we apply the Wang-Landau (WL) method to compute the density of states for secondary structures of a given RNA sequence, and for hybridizations of two RNA sequences. Our method is shown to be much faster than existent software, such as RNAsubopt. From density of states, we compute the partition function over all secondary structures and over all pseudoknot-free hybridizations. The advantage of the WL method is that by adding a function to evaluate the free energy of arbitrary pseudoknotted structures and of arbitrary hybridizations, we can estimate thermodynamic parameters for situations known to be NP-complete. This extension to pseudoknots will be made in the sequel to this article; in contrast, the current article describes the WL algorithm applied to pseudoknot-free secondary structures and hybridizations.AvailabilityThe WL RNA hybridization web server is under construction at http://bioinformatics.bc.edu/clotelab/.

Dataset Information

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

Publications

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

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