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MCPath: Monte Carlo (MC) path generation approach to predict likely allosteric pathways and functional residues
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Allosteric mechanism of proteins is essential in biomolecular signaling. An important aspect underlying this mechanism is the communication pathways connecting functional residues. Here, a Monte Carlo (MC) path generation approach is proposed and implemented to define likely allosteric pathways through generating an ensemble of maximum probability paths, where the protein structure is considered as a network of amino acid residues and inter-residue interactions are described by an atomistic potential function. The suggested pathways and the residues constituting the pathways that are maximally probable are mostly agrees the previous studies. Overall, it is demonstrated that the communication pathways could be multiple and intrinsically disposed and the MC path generation approach provides an effective tool for the prediction of key residues that mediate the allosteric communication in an ensemble of pathways and functionally plausible residues.

Keywords: allostery, Monte Carlo path generation, functional residue

References

1. Lockless, SW, Ranganathan SJ, Evolutionarily conserver pathways of energetic connectivity in protein families”, Science, 1999, 286. 295-299.
2. Goodey NM, Benkovic SJ, Allosteric regulation and catalysis emerge via a common route, Nat Chem Biol, 2008, 4, 474–482.
3. del Sol, A, Tsai, C-J, Ma, B and Nussinov, R, The Origin of Allosteric Functional Modulation: Multiple Pre-existing Pathways, Structure, 2009, 17, 1042–1050.

 


Please cite: Kaya, C., Armutlulu, A., Ekesan, S., & Haliloglu, T. (2013). MCPath: Monte
Carlo path generation approach to predict likely allosteric pathways and
functional residues. Nucleic acids research, 41(W1), W249-W255.


For questions and comments: "mcpath AT prc.boun.edu.tr"