Accurate relaxation parameters for large proteins.
The practical applicability, performance, and robustness of three-way decomposition (TWD) for the extraction of relaxation parameters are demonstrated for a large protein with 370 residues, the maltose binding protein. An ordinary set of seven relaxation-modulated (15)N HSQC spectra, recorded at another site, is systematically analyzed. For all 341 assigned backbone amide groups, including 21 pairs and one group of three overlapped peaks, T1 decay values were determined. On isolated peaks, TWD extracts T1 values with systematically lower error bounds compared to conventional tools, although for these simple cases the improvements remain limited. However, in the presence of spectral artifacts, the decrease in errors can become significant, demonstrating the higher robustness of TWD. For about half of the peaks in overlapped regions, the decomposition allowed separation of the signals, yielding significantly different T1 values between overlapping signals. For the rest, similarity of the decay times for the two or three overlapping signals could be confirmed within usually low error bounds. The use of TWD thus leads to a significant increase in the number of accessible relaxation probes in large proteins. With a newly implemented graphical user interface, the application of TWD requires merely a peak list, and thus no additional effort compared to conventional approaches is needed.
Gutmanas
Aleksandras
A
Biophysics Group, Department of Chemistry, Göteborg University, Box 462, 405 30 Göteborg, Sweden.
Tu
Luan
L
Orekhov
Vladislav Yu
VY
Billeter
Martin
M
D000465:Algorithms; D002352:Carrier Proteins / Q000032:analysis* / Q000737:chemistry*; D058619:Maltose-Binding Proteins; D008956:Models, Chemical; D008958:Models, Molecular; D009038:Motion; D009587:Nitrogen Isotopes; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods*; D011786:Quality Control
D002352:Carrier Proteins; D058619:Maltose-Binding Proteins; D009587:Nitrogen Isotopes