Limits of NMR structure determination using variable target function calculations: ribonuclease T1, a case study.
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.
Pfeiffer
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Institut für Biophysikalische Chemie, Johann Wolfgang Goethe-Universität, Biozentrum, Frankfurt, Germany.
Karimi-Nejad
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Y
Rüterjans
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H
D001665:Binding Sites; D004220:Disulfides / Q000737:chemistry; D006147:Guanine / Q000378:metabolism; D006860:Hydrogen Bonding; D009682:Magnetic Resonance Spectroscopy / Q000379:methods*; D008958:Models, Molecular; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D006163:Ribonuclease T1 / Q000737:chemistry* / Q000378:metabolism*; D012984:Software; D012996:Solutions
D004220:Disulfides; D011506:Proteins; D012996:Solutions; D006147:Guanine; D006163:Ribonuclease T1