Identifying the minimal sets of distance restraints for FRET-assisted protein structural modeling

TL;DR

This study identifies the minimal number of FRET-derived distance restraints needed in molecular dynamics simulations to accurately model protein structures in vivo, demonstrating that a small fraction of restraints can induce conformational changes.

Contribution

The paper introduces methods to select key FRET pairs and determines the minimal restraints required for effective in vivo protein structural modeling.

Findings

A small fraction (less than 8%) of restraints can induce conformational changes.

FRET-assisted MD simulations are effective for atomic-scale protein modeling in vivo.

Optimal restraint selection enhances the accuracy of structural predictions.

Abstract

Proteins naturally occur in crowded cellular environments and interact with other proteins, nucleic acids, and organelles. Since most previous experimental protein structure determination techniques require that proteins occur in idealized, non-physiological environments, the effects of realistic cellular environments on protein structure are largely unexplored. Recently, F\"{o}rster resonance energy transfer (FRET) has been shown to be an effective experimental method for investigating protein structure in vivo. Inter-residue distances measured in vivo can be incorporated as restraints in molecular dynamics (MD) simulations to model protein structural dynamics in vivo. Since most FRET studies only obtain inter-residue separations for a small number of amino acid pairs, it is important to determine the minimum number of restraints in the MD simulations that are required to achieve a given root-mean-square deviation (RMSD) from the experimental structural ensemble. Further, what is the optimal method for selecting these inter-residue restraints? Here, we implement several methods for selecting the most important FRET pairs and determine the number of pairs $N_{r}$ that are needed to induce conformational changes in proteins between two experimentally determined structures. We find that enforcing only a small fraction of restraints, $N_{r}/N \lesssim 0.08$, where $N$ is the number of amino acids, can induce the conformational changes. These results establish the efficacy of FRET-assisted MD simulations for atomic scale structural modeling of proteins in vivo.