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.
Department of Chemistry, Rutgers University, Piscataway, New Jersey 08855-0939.
A K
AK
Suri
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RM
Levy
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