A Study on Constructing Finite Element Models for Protein Dynamics

Abstract

Proteins are essential working unit in lifes body whose functional characteristics are majorly determined by those dynamic properties. Conventional all-atom based simulation methods, such as molecular dynamics (MD) simulation or all-atom normal mode analysis (ATM-NMA) provide important insights into dynamic behaviors of proteins and their functions but those method are frequently limited due to computational complexity. As an alternative, finite element (FE) method can be used for coarse-grained simulation. Finite element method provides an efficient way of analyzing proteins dynamics related to their biological functions. The method has been successful in obtaining quite accurate results with reasonable computational time. Although there are various approaches to generating a finite element protein model for protein dynamics, it has not been critically investigated whether and how these different approaches affect the predictions. Various approaches in generating FE protein model, including different types of protein-surface definitions and those parameters, are critically investigated in this study to present the robustness of FE-based protein models. Then we provide a guideline on the construction and the use of these FE models.