Stereospecific Assignment of the Asparagine and Glutamine Side Chain Amide Protons in Random-Coil Peptides by Combination of Molecular Dynamic Simulations with Relaxation Matrix Calculations

Abstract

A database with correct stereospecific assignment is also important for accurate chemical shift prediction. Here, usually chemical shifts of random-coil model peptides or from a protein database are used for correct parameterization. However, an analysis of the data stored in the Biological Magnetic Resonance Data Bank (BMRB) shows that a substantial part of all stereospecific assignments stored is not correct. Here, we provide the stereospecific assignment of amide side chain protons in the amino acids glutamine and asparagine in the model peptides Gly-Gly-Asn-Ala-NH2 and Gly-Gly-Gln-Ala-NH2. Nuclear Overhauser enhancement spectroscopy (NOESY) spectra were back-calculated with the full relaxation matrix formalism implemented in AUREMOL-RELAX from molecular dynamics trajectories created with GROMACS and compared with experimental nuclear magnetic resonance spectra measured at 800 MHz proton resonance frequency. The comparison of simulated with experimental NOESY spectra permitted the unambiguous stereospecific assignment of the side chain amide and Hβ protons of asparagine and glutamine in the random-coil peptides.