[Determination of local conformation of proteins from 1H-NMR spectroscopy data].
A method is proposed to determine conformations of amino acid residues of the protein and effective correlation time tau c from cross-peak intensities in two-dimensional nuclear Overhauser enhancement (NOESY) spectra. The method consists in fitting complete relaxation matrix of dipeptide unit protons to experimental cross-peak intensities by varying phi, psi, chi torsional angles and tau c. To verify the method, NOESY spectra of basic pancreatic trypsin inhibitor (BPTI) were theoretically generated at mixing times tau m = 25-300 ms and tau c = 4 ns and used for local structure determination. The method works well with optimum for measurement of NOE intensities tau m 100-200 ms. As a result, the backbone phi, psi torsion angles were unambiguously determined at tau m = 100 ms for all but Gly residues of BPTI, and chi 1 angles were determined for the majority of side chains. The obtained dipeptide unit conformations are very close to the BPTI crystallographic structure: root mean square deviation (RMSD) of interproton distances within dipeptide units, on the average, is 0.08 A (maximal deviation 0.44 A), and RMSD of phi and psi angles are 18 and 9 degrees, respectively (maximal deviations are 44 and 22 degrees).
Lomize
A L
AL
Sobol'
A G
AG
Arsen'ev
A S
AS
D000596:Amino Acids / Q000032:analysis; D004151:Dipeptides / Q000032:analysis; D009682:Magnetic Resonance Spectroscopy; D008433:Mathematics; D008962:Models, Theoretical; D011487:Protein Conformation
D000596:Amino Acids; D004151:Dipeptides
Metodika opredeleniia lokal'noĭ konformatsii belkov po dannym spektroskopii 1H-IaMR.