AlloPathFinder allows users to compute likely allosteric pathways in proteins. The underlying assumption is that residues participating in allosteric communication should be fairly conserved and that communication happens through residues that are close in space.The initial application for the code provided was to study the allosteric communication in myosin. Myosin is a well-studied molecular motor protein that walks along actin filaments to achieve cellular tasks such as movement of cargo proteins.It couples ATP hydrolysis to highly-coordinated conformational changes that result in a power-stroke motion, or ”walking” of myosin. Communication between a set of residues must link the three functional regions of myosin and transduce energy: the catalytic ATP binding region, the lever arm, and the actin-binding domain. We are investigating which residues are likely to participate in allosteric communication pathways.
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Tang S, Liao JC, Dunn A, Spudich JA, Altman RB, Schmidt J.
“Predicting allosteric communication in myosin via a pathway of conserved residues.”
Journal of Molecular Biology, 373, 1361–1373. (2007)