Atomic Torsional Modal Analysis for high-resolution proteins

TL;DR

This paper presents an improved normal mode analysis method for globular proteins that incorporates torsional stiffness and atomic details, enabling accurate and stable eigenmode computation across all frequencies.

Contribution

It introduces a novel empirical potential function that enhances the accuracy of protein vibrational mode analysis by including dihedral preferences and detailed atomic interactions.

Findings

Achieves stable eigenmodes over a broad frequency spectrum

Improves upon previous models by accurately capturing slow and fast modes

Eliminates anomalous dispersion in protein vibrational spectra

Abstract

We introduce a formulation for normal mode analyses of globular proteins that significantly improves on an earlier, 1-parameter formulation (M. Tirion, PRL 77, 1905 (1996)) that characterized the slow modes associated with protein data bank structures. Here we develop that empirical potential function which is minimized at the outset to include two features essential to reproduce the eigenspectra and associated density of states over all frequencies, not merely the slow ones. First, introduction of preferred dihedral-angle configurations via use of torsional stiffness constants eliminates anomalous dispersion characteristics due to insufficiently bound surface sidechains. Second, we take into account the atomic identities and the distance of separation of all pairwise interactions. With these modifications we obtain stable, reliable eigenmodes over a wide range of frequencies.