A relaxation-matrix analysis of distance-constraint ranges for NOEs in proteins at long mixing times.
Long-mixing-time data (tau m > 200 ms) from NOE spectra have largely been ignored as a source of protein structural information due to the effects of spin diffusion on calculated interproton distances when using the two-spin approximation. An effective approach for incorporating spin-diffusion effects in an average way into refinements is to choose distance bounds based on distributions of distances observed in NOE back calculations on homologous proteins from a protein structure database. We have determined distributions of interproton distances characteristic of newly observed NOE cross peaks for the proteins crambin, PTI, and echistatin at long mixing times. A relaxation-matrix analysis was used to model the effects of spin diffusion. Constraint ranges were constructed from the interproton distance distributions which can be used in standard protein-refinement programs based on the two-spin approximation. Back calculations are also used to analyze constraint ranges typically used for protein structure determinations based on NOE spectra at shorter mixing times.
Suri
A K
AK
Department of Chemistry, Rutgers University, Piscataway, New Jersey 08855-0939.
Levy
R M
RM
D004578:Electron Spin Resonance Spectroscopy; D007256:Information Systems; D036341:Intercellular Signaling Peptides and Proteins; D009682:Magnetic Resonance Spectroscopy / Q000379:methods*; D010455:Peptides; D010940:Plant Proteins / Q000032:analysis; D011487:Protein Conformation; D011506:Proteins / Q000032:analysis*; D011522:Protons; D013997:Time Factors; D014361:Trypsin Inhibitors / Q000032:analysis; D014757:Viper Venoms / Q000032:analysis
D036341:Intercellular Signaling Peptides and Proteins; D010455:Peptides; D010940:Plant Proteins; D011506:Proteins; D011522:Protons; D014361:Trypsin Inhibitors; D014757:Viper Venoms; C057986:echistatin; C024934:crambin protein, Crambe abyssinica