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Exploring the mechanism of how tvMyb2 recognizes and binds ap65-1 by molecular dynamics simulations and free energy calculations



Exploring the mechanism of how tvMyb2 recognizes and binds ap65-1 by molecular dynamics simulations and free energy calculations



Molecular Biosystems 12(1): 76-84



TvMyb2, one of the Myb-like transcriptional factors in Trichomonas vaginalis, binds to two closely spaced promoter sites, MRE-1/MRE-2r and MRE-2f, on the ap65-1 gene. However, detailed dynamical structural characteristics of the tvMyb2-ap65-1 complex and a detailed study of the protein in the complex have not been done. Focused on a specific tvMyb2-MRE-2-13 complex (PDB code: ) and a series of mutants K51A, R84A and R87A, we applied molecular dynamics (MD) simulation and molecular mechanics generalized Born surface area (MM-GBSA) free energy calculations to examine the role of the tvMyb2 protein in recognition interaction. The simulation results indicate that tvMyb2 becomes stable when it binds the DNA duplex. A series of mutants, K51A, R84A and R87A, have been followed, and the results of statistical analyses of the H-bond and hydrophobic contacts show that some residues have significant influence on recognition and binding to ap65-1 DNA. Our work gives important information to understand the interactions of tvMyb2 with ap65-1.

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Accession: 057839951

Download citation: RISBibTeXText

PMID: 26548411

DOI: 10.1039/c5mb00585j


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