Normal-mode driven exploration of protein domain motions

TL;DR

This paper introduces a novel two-step method combining normal mode analysis and distance geometry to accurately predict large protein conformational changes, leveraging low-frequency modes and the ROSETTA software.

Contribution

It presents a new approach that transforms normal mode-based conformer generation into a distance-geometry problem, enabling accurate modeling of large protein motions.

Findings

Successfully reconstructed six large amplitude conformational changes.

Low-dimensional normal coordinates suffice for near-native conformer generation.

Random exploration effectively finds low-energy conformers close to known states.

Abstract

Domain motions involved in the function of proteins can often be well described as a combination of motions along a handfull of low-frequency modes, that is, with the values of a few normal coordinates. This means that, when the functional motion of a protein is unknown, it should prove possible to predict it, since it amounts to guess a few values. However, without the help of additional experimental data, using normal coordinates for generating accurate conformers far away from the initial one is not so straightforward. To do so, a new approach is proposed: instead of building conformers directly with the values of a subset of normal coordinates, they are built in two steps, the conformer built with normal coordinates being just used for defining a set of distance constraints, the final conformer being built so as to match them. Note that this approach amounts to transform the problem of generating accurate protein conformers using normal coordinates into a better known one: the distance-geometry problem, which is herein solved with the help of the ROSETTA software. In the present study, this approach allowed to rebuild accurately six large amplitude conformational changes, using at most six low-frequency normal coordinates. As a consequence of the low-dimensionality of the corresponding subspace, random exploration also proved enough for generating low-energy conformers close to the known end-point of the conformational change of the LAO binding protein, lysozyme T4 and adenylate kinase.