Spectral density function mapping using 15N relaxation data exclusively.
A method is presented for the determination of values of the spectral density function, J(omega), describing the dynamics of amide bond vectors from 15N relaxation parameters alone. Assuming that the spectral density is given by the sum of Lorentzian functions, the approach allows values of J(omega) to be obtained at omega = 0, omega N and 0.870 omega H, where omega N and omega H are Larmor frequencies of nitrogen and proton nuclei, respectively, from measurements of 15N T1, T2 and 1H-15N steady-state NOE values at a single spectrometer frequency. Alternatively, when measurements are performed at two different spectrometer frequencies of i and j MHz, J(omega) can be mapped at omega = 0, omega iN, omega jN, 0.870 omega iH and 0.870 omega iH, where omega iN, for example, is the 15N Larmor frequency for a spectrometer operating at 1 MHz. Additionally, measurements made at two different spectrometer frequencies enable contributions to transverse relaxation from motions on millisecond-microsecond time scales to be evaluated and permit assessment of whether a description of the internal dynamics is consistent with a correlation function consisting of a sum of exponentials. No assumptions about the specific form of the spectral density function describing the dynamics of the 15N-NH bond vector are necessary, provided that dJ(omega)/d omega is relatively constant between omega = omega H + omega N to omega = omega H - omega N. Simulations demonstrate that the method is accurate for a wide range of protein motions and correlation times, and experimental data establish the validity of the methodology. Results are presented for a folded and an unfolded form of the N-terminal SH3 domain of the protein drk.
Farrow
N A
NA
Protein Engineering Network of Centre of Excellence, University of Toronto, ON, Canada.
Zhang
O
O
Szabo
A
A
Torchia
D A
DA
Kay
L E
LE
D000818:Animals; D055598:Chemical Phenomena; D002627:Chemistry, Physical; D029721:Drosophila Proteins; D007301:Insect Hormones / Q000737:chemistry; D009682:Magnetic Resonance Spectroscopy / Q000379:methods*; D009587:Nitrogen Isotopes; D011506:Proteins / Q000737:chemistry*; D018909:src Homology Domains
D029721:Drosophila Proteins; D007301:Insect Hormones; D009587:Nitrogen Isotopes; D011506:Proteins; C080530:drk protein, Drosophila