Computational analysis of artificially induced conformational changes and the effects of alternative splicing in Drosophila myosin

Makowski, Bryan Siva
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Garcia, Angel E.
Barquera, Blanca L.
Swank, Douglas M.
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Biochemistry and biophysics
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This electronic version is a licensed copy owned by Rensselaer Polytechnic Institute, Troy, NY. Copyright of original work retained by author.
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The determination of the atomic scale mechanism of protein function is crucial to treatment development for diseased states caused by the malfunction of these proteins. Here, Drosophila myosin is studied using molecular dynamics simulations in combination with experimental studies of this same system for the purpose of elucidating the function of the myosin converter region. Initially, the application of force and constraints upon the system are explored using structure-based molecular dynamics, followed by expansion to full classical mechanics simulations. Numerous unphysical behaviors in the computational system are revealed to occur in response to the applied forces and constraints. The study is then shifted to the examination of myosin converter regions constructed from different amino acid sequences. The study reveals that simple measures the motion of the alpha helix of the converter region with respect to the relay helix correlates with experimental behavior of muscle fibers containing myosin with these same sequences.
May 2015
School of Science
Biochemistry and Biophysics Program
Rensselaer Polytechnic Institute, Troy, NY
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