Limits of NMR structure determination using variable target function calculations: ribonuclease T1, a case study.Pfeiffer, S., Karimi-Nejad, Y., Ruterjans, H.
(1997) J.Mol.Biol. 266: 400-423
- PubMed: 9047372
- DOI: 10.1006/jmbi.1996.0784
- PubMed Abstract:
- Conformation of Valine Side Chains in Ribonuclease T1 Determined by NMR Studies of Homonuclear and Heteronuclear 3J Coupling Constants
Karimi-Nejad, Y.,Schmidt, J.M.,Ruterjans, H.,Schwalbe, H.,Griesinger, C.
(1994) Biochemistry 33: 5481
- Complete 1H, 15N and 13C Resonance Assignment of Ribonuclease T1: Secondary Structure and Backbone Dynamics as Derived from the Chemical Shifts
Pfeiffer, S.,Engelke, J.,Ruterjans, H.
(1996) Q.Magn.Reson.Biol.Med. 3: 69
Limits of NMR structure determination using multidimensional NMR spectroscopy, variable target function calculations and relaxation matrix analysis were explored using the model protein ribonuclease T1 (RNase T1). The enzyme consists of 104 amino aci ...
Limits of NMR structure determination using multidimensional NMR spectroscopy, variable target function calculations and relaxation matrix analysis were explored using the model protein ribonuclease T1 (RNase T1). The enzyme consists of 104 amino acid residues and has a molecular mass of approximately 11 kDa. Primary experimental data comprise 1856 assigned NOE intensities, 493 3J coupling constants and 62 values of amid proton exchange rates. From these data, 2580 distance bounds, 168 allowed ranges for torsional angles and stereospecific assignments for 75% of beta-methylene protons as well as for 80% of diastereotopic methyl groups were derived. Whenever possible, the distance restraints were refined in a relaxation matrix analysis including amid proton exchange data for improvement of lower distance limits. Description of side-chain conformations were based on various models of motional averaging of 3J coupling constants. The final structure ensemble was selected from the starting ensemble comparing the global precision of structures with order parameters derived from 15N relaxation time measurements. Significant differences between the structure of RNase T1 in solution and in the crystal became apparent from a comparison of the two highly resolved structures.
Institut für Biophysikalische Chemie, Johann Wolfgang Goethe-Universität, Biozentrum, Frankfurt, Germany.