MODELING MOTOR PROTEINS

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This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. We have used molecular dynamics simulations to investigate the properties of x-ray structures of actin. Actin can only be crystalized following biochemical modification that prevents polymerization. This raises the question as to whether properties deduced from the x-ray structures reflect the true properties of actin, or only of modified proteins. The support of the Computer Graphics Laboratory at UCSF is essential for visualization and interpretation of the results of our molecular dynamics simulations. Our results indicate that in many cases, the modified proteins behave differently from native actin. Actin is comprised of four subdomains, and it is important to be able to generate new putative actin structures by graphical manipulation of the spatial relationships between these sub-domains. Additionally, this project involves investigating the thermodynamic stability of putative alpha-helical coiled-coil domains that have been postulated to help regulate myosin function. The results of molecular dynamics simulations require extensive use of the graphical visualization software.