Computer simulation of proton spin relaxation in proteins: Application to Streptomyces subtilisin inhibitor

Abstract

A computer program has been developed which can calculate the time dependence of individual proton magnetizations in a protein, for a variety of relaxation measurements in solution, using non-selective and selective excitation pulses. The basic design and capability of the program are described, together with its limitations. The program is used to simulate proton relaxation experiments by non-selective and selective excitation, and to simulate spin diffusion in a typical globular protein Streptomyces subtilisin inhibitor (SSI). The mechanism of selective spin diffusion in SSI is discussed based on a comparison of the calculated results with results of cross-saturation experiments.

Relax, a Flexible Program for the Back Calculation of NOESY Spectra Based on Complete-Relaxation-Matrix Formalism

“…In [9] this approximation the equation for the spectral density is FAST_JUMP: or in matrix notation, In [9] this approximation the equation for the spectral density is FAST_JUMP: or in matrix notation,…”

“…retical reasons (8,9). Other programs, such as MAR-DIGRAS (10, 11), NO2DI (12), and a program from Kim The quantitative analysis of nuclear Overhauser effect and Reid (13), use relaxation-matrix analysis to calculate spectra allows the determination of interatomic distances.…”