crambin-protein--crambe-abyssinica and echistatin

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.

Topics: Electron Spin Resonance Spectroscopy; Information Systems; Intercellular Signaling Peptides and Proteins; Magnetic Resonance Spectroscopy; Peptides; Plant Proteins; Protein Conformation; Proteins; Protons; Time Factors; Trypsin Inhibitors; Viper Venoms

A reduced representation of proteins has been developed for use in restraint satisfaction calculations with dynamic simulated annealing. Each amino acid residue is represented by up to four spherical virtual atoms. The virtual bonds and excluded volume of these atoms has been parameterized by analysis of 83 protein structures determined at high resolution by X-ray crystallography. The use of the new representation in NOE distance restraint satisfaction has been compared with the standard all-atom representation for the determination of the structures of crambin, echistatin, and protein G. Using the reduced representation, there is a 30-fold decrease in the computer time needed for generating a single structure, and up to a 20-fold decrease in the time taken to produce an acceptable structure compared to using the all-atom representation. The root mean square deviation between the mean structure obtained with all-atom and reduced representations is between 1.5 and 1.7 A for C alpha atoms. The new representation is adequate for describing the "low-resolution" features of protein structure such as the general fold and the positions of secondary structure elements. It can also provide an initial structure for more detailed refinement with the full all-atom representation.

Topics: Computer Simulation; Intercellular Signaling Peptides and Proteins; Magnetic Resonance Spectroscopy; Mathematical Computing; Models, Chemical; Models, Molecular; Nerve Tissue Proteins; Peptides; Plant Proteins; Platelet Aggregation Inhibitors; Protein Conformation; Thermodynamics; Viper Venoms; X-Ray Diffraction