Elastic network & finite element model to study actin protein mechanics & its molecular elasticity
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While there have been many recently developed Elastic Network Models (ENM) to calculate the fluctuation dynamics of proteins, e.g., Gaussian Network Model (GNM), Anisotropic Network Model (ANM), Distance Network Model (DNM), the concept of loading these models to study the molecular mechanics and constitutive behavior of structural proteins has remained relatively untouched, until very recently. This work entails using the ANM as the framework for developing a finite element model of a 9–monomer strand of actin. Critical input parameters to the model, such as the cutoff radius, r[subscript c], and spring constant, k, are generated by matching the all-atom steered molecular dynamics (SMD) residue displacements to that of the ANM. The parameters yielding the best match between the SMD and structural ENM (SENM) simulations will then be input into the finite element model (FEM) for a more in depth analysis. The finite element model incorporates a 9–monomer strand of actin. The F–actin strand is subjected axial and torsional loads comparable to those seen in vivo. Key areas of interest in the protein are examined, such as the nucleotide binding pocket (NBP) and the DNase I binding loop, to demonstrate how loading affects the protein’s conformation. Local residue displacements are tracked in an effort to garner a better understanding of how various loads are transmitted through F–actin during key events. Insights and conclusions are discussed along with the implications of this work.