  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.
