Extracting the Dynamic Motion of Proteins Using Normal Mode Analysis

• DOI: 10.1007/978-1-0716-2095-3_9
• Publication Date: 2022-05-04T06:03:29Z
• Authors: Jacob A. Bauer; Vladena Bauerová-...
• Keywords: Motion; Protein Conformation; Molecular Conformation; Proteins; Molecular Dynamics Simulation; Software

Normal mode analysis (NMA) is a technique for describing the conformational states accessible to a protein in a minimum energy conformation. NMA gives results similar to those produced by principal components analysis of a molecular dynamics simulation, but with only a fraction of the computational effort. Here, we provide a brief overview of the theory and describe three methods for carrying out NMA, including the use of one of the on-line services, the use of off-line software for calculating the projection of the modes calculated from one conformation onto another, and an all-atom NMA calculated using GROMACS. For all three methods, we will use the E1·2Ca2+ form of the Ca2+-ATPase as a concrete example.