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 T. Harsch • C. Dasch • H. Donaubauer • K. Baskaran • W. Kremer • H. R. Kalbitzer Received: 16 September 2012 / Revised: 22 September 2012 / Published online: 25 November 2012 Ó Springer-Verlag Wien 2012 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-NH 2 and Gly-Gly-Gln-Ala-NH 2 . Nuclear Overhauser enhancement spec- troscopy (NOESY) spectra were back-calculated with the full relaxation matrix formalism implemented in AUREMOL-RELAX from molecular dynamics trajec- tories created with GROMACS and compared with experimental nuclear magnetic resonance spectra measured at 800 MHz proton resonance frequency. The com- parison of simulated with experimental NOESY spectra permitted the unambiguous stereospecific assignment of the side chain amide and H b protons of asparagine and glutamine in the random-coil peptides. 1 Introduction The interpretation of chemical shifts of proteins requires a sound empirical data basis with atom and residue data. The quality of the database mainly depends on the quality of the data deposited. Although methods for accurate stereospecific assignments of resonance lines in folded proteins exist, there is a danger that databases contain erroneous results. For biological applications the Biological Magnetic Resonance Data Bank (BMRB) [1] is the most widely used database for T. Harsch  C. Dasch  H. Donaubauer  K. Baskaran  W. Kremer  H. R. Kalbitzer (&) Institute of Biophysics and Physical Biochemistry and Centre of Magnetic Resonance in Chemistry and Biomedicine, University of Regensburg, Universita ¨tsstraße 31, 93053 Regensburg, Germany e-mail: hans-robert.kalbitzer@biologie.uniregensburg.de 123 Appl Magn Reson (2013) 44:319–331 DOI 10.1007/s00723-012-0416-8 Applied Magnetic Resonance