Model-free analysis for large proteins at high magnetic field strengths.
Protein backbone dynamics is often characterized using model-free analysis of three sets of (15)N relaxation data: longitudinal relaxation rate (R1), transverse relaxation rate (R2), and (15)N-{H} NOE values. Since the experimental data is limited, a simplified model-free spectral density function is often used that contains one Lorentzian describing overall rotational correlation but not one describing internal motion. The simplified spectral density function may be also used in estimating the overall rotational correlation time, by making the R2/R1 largely insensitive to internal motions, as well as used as one of the choices in the model selection protocol. However, such approximation may not be valid for analysis of relaxation data of large proteins recorded at high magnetic field strengths since the contribution to longitudinal relaxation from the Lorentzian describing the overall rotational diffusion of the molecule is comparably small relative to that describing internal motion. Here, we quantitatively estimate the errors introduced by the use of the simplified spectral density in model-free analysis for large proteins at high magnetic field strength.
Chang
Shou-Lin
SL
Institute of Bioinformatics and Structural Biology, Department of Life Science, National Tsing Hua University, HsinChu 30055, Taiwan.
Hinck
Andrew P
AP
Ishima
Rieko
R
D019295:Computational Biology / Q000379:methods; D003198:Computer Simulation; D004058:Diffusion; D004574:Electromagnetic Fields; D008954:Models, Biological; D008958:Models, Molecular; D015233:Models, Statistical; D008962:Models, Theoretical; D008968:Molecular Conformation; D015394:Molecular Structure; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods*; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D013997:Time Factors
D011506:Proteins