(189bx) Multiscale Modeling of Actin Filaments | AIChE

(189bx) Multiscale Modeling of Actin Filaments


Katkar, H. H. - Presenter, The University of Chicago
Aydin, F., The University of Chicago
Bidone, T. C., University of Chicago
Harker, A. J., The University of Chicago
Kovar, D. R., The University of Chicago
Voth, G. A., The University of Chicago
Actin is an important protein in the cellular cytoskeleton, which polymerizes into polar filaments that form dynamic actin networks including filopodia, in which parallel actin filaments are bundled together. Each polar filament grows at its barbed end and shrinks at its pointed end under physiological conditions. The filament also ages as the nucleotide ATP bound to an actin subunit in the filament hydrolyzes and releases inorganic phosphate, modulating its mechanical properties and binding affinity towards several important actin binding proteins. Enabled/vasodilator-stimulated phosphoprotein (Ena/VASP) is an actin binding protein that assists filopodia formation by continuously associating with the growing barbed ends of predominantly short actin filaments in the bundles. The structure of a wild-type Ena/VASP loosely resembles a four-arm star polymer, with each arm consisting of several important domains responsible for interactions with actin.

In vitro microscopy experiments of purified actin filaments with Ena/VASP mutants of varying functionalities exhibit a rich phenomenology. A systematic multiscale modeling approach is used to provide insights into the experimental observations at the levels of individual arms and individual subdomains. A model based on kinetics of individual arms of Ena/VASP is constructed to understand the experimentally observed binding-unbinding rates of Ena/VASP mutants on actin filaments. Additionally, an Ultra-Coarse-Grained (UCG) model of actin is constructed, which provides a computationally efficient way to simulate long actin filaments undergoing ATP hydrolysis and growth. A systematic procedure is used to construct heterogeneous elastic networks for important domains of Ena/VASP and the actin filament including the implicit representation of subunit specific states of the bound nucleotide, using information from underlying atomistic simulations of short actin filaments interacting with Ena/VASP. Transitions between the three states of the nucleotide bound to each actin subunit are simulated in the UCG model via stochastic transitions coupled to the positions of the coarse-grained sites, and hence to the conformations of the underlying reference atomistic system. The resulting model takes into account detailed interactions at the subdomain level and is used to further study the growth of actin filament bundles in presence of Ena/VASP.