Large Amplitude Elastic Motions in Proteins from a Single-Parameter, Atomic Analysis

TLDR

Normal mode analysis is a leading method for studying long‑time dynamics and elasticity of biomolecules, relying on detailed semi‑empirical potentials that capture covalent and noncovalent interactions, which are essential for its success. The technique can be applied to map one crystal form to another via slow modes and to study anomalous dynamics of large proteins and complexes. A single‑parameter potential reproduces slow dynamics accurately, eliminating costly energy minimizations and allowing direct analysis of crystal coordinates.

Abstract

Normal mode analysis (NMA) is a leading method for studying long-time dynamics and elasticity of biomolecules. The method proceeds from complex semiempirical potentials characterizing the covalent and noncovalent interactions between atoms. It is widely accepted that such detailed potentials are essential to the success of NMA's. We show that a single-parameter potential is sufficient to reproduce the slow dynamics in good detail. Costly and inaccurate energy minimizations are eliminated, permitting direct analysis of crystal coordinates. The technique can be used for new applications, such as mapping of one crystal form to another by means of slow modes, and studying anomalous dynamics of large proteins and complexes.