PROTEIN BACKBONE DYNAMICS REVEALED BY QUASI SPECTRAL DENSITY-FUNCTION ANALYSIS OF AMIDE N-15 NUCLEI

Spectral density functions J(0), J(omega(N)), and J(omega(H)+omega(N)) Of individual amide N-15 nuclei in proteins were approximated by a quasi spectral density function (QSDF). Using this function, the backbone dynamics were analyzed for seven protein systems on which data have been published. We defined J(0; omega(N)) as the difference between the J(0) and the J(omega(N)) values, which describes motions slower than 50 (or 60) MHz, and J(omega(N); omega(H+N)) as the difference between the J(omega(N)) and the J((omega)(H)+omega(N)) values, which describes motions slower than 450 (or 540) MHz. The QSDF analysis can easily extract the J(0; omega(N)) of protein backbones, which have often some relation to biologically relevant reactions. Flexible N-terminal regions in eglin c and glucose permease IIA and a loop region in eglin c showed smaller values of both the J(0; omega(N)) and the J(omega(N); omega(H+N)) as compared with the other regions, indicating increases in motions faster than nanosecond. The values of the J(0; omega(N)) for the backbone of the FK506 binding protein showed a large variation in the apoprotein but fell in a very narrow range after the binding of FK506. Characteristic increase or decrease in the values of J(0) and J(omega(N)) was observed in two or three residues located between secondary structures.