In silico method for selecting residue pairs for single-molecule microscopy and spectroscopy

Abstract Obtaining (dynamic) structure related information on proteins is key for understanding their function. Methods as single-molecule Förster Resonance Energy Transfer (smFRET) and Electron Paramagnetic (EPR) that measure distances between labeled residues to obtain dynamic rely selection of suitable residue pairs chemical modification. Selection amino acids, show sufficient distance changes upon activity the protein, can be a tedious process. Here we present an in silico approach makes use two or more structures (or models) filter FRET EPR from all possible within protein. We apply method study conformational dynamics substrate-binding domain osmoregulatory ATP-Binding Cassette transporter OpuA. This speeds up process designing mutants, because its systematic nature, chances missing promising candidates are reduced.