Pseudo-structures for the 20 common amino acids for use in studies of protein conformations by measurements of intramolecular proton-proton distance constraints with nuclear magnetic resonance

Abstract

"Pseudo-structures" of the 20 common amino acid residues are introduced for use in protein spatial structure determinations, which rely on the use of intramolecular proton-proton distance constraints determined by nuclear Overhauser effects as input for distance geometry calculations. The proposed structures satisfy requirements for the initial structural interpretation of the nuclear magnetic resonance data that arise from the absence of stereospecific assignments and/or limited spectral resolution for certain resonance lines. The pseudo-atoms used as reference points for the experimental distance constraints can be used in conjunction with the real amino acid structures representing the van der Waals' constraints on the spatial molecular structure, or with simplified models in order to reduce the computing time for the distance geometry calculations.