DETERMINATION OF LOCAL STRUCTURE OF PROTEINS FROM TWO-DIMENSIONAL 1 H NMR DATA
A. L. LOMIZE, A. G. SOBOL, A. S. ARSENIEV
M. M. Shemyakin Institute of Bioorganic Chemistry, Academy of Sciences of the USSR, Moscow
Abstract: A method is proposed to determine conformations of ammo acid residues of the protein and effective correlation time τc 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 φ, ψ, χ torsional angles and τc. To verify the method, NOESY spectra of basic pancreatic trypsin inhibitor (BPTI) were theoretically generated at mixing times Tm=25—300 ms and τc=4 ns and used for local structure determination. The method works well with optimum for measurement of NOB intensities τm 100—200 ms. As a result, the backbone φ, ψ torsion angles were unambiguously determined at τm =100 ms for all but Gly residues of BPTI, and χ1 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 φ and ψ angles are 18 and 9°, respectively (maximal deviations are 44 and 22°).
Russian Journal of Bioorganic Chemistry 1990, 16 (2):179-201