Correction of spin diffusion during iterative automated NOE assignment.
Indirect magnetization transfer increases the observed nuclear Overhauser enhancement (NOE) between two protons in many cases, leading to an underestimation of target distances. Wider distance bounds are necessary to account for this error. However, this leads to a loss of information and may reduce the quality of the structures generated from the inter-proton distances. Although several methods for spin diffusion correction have been published, they are often not employed to derive distance restraints. This prompted us to write a user-friendly and CPU-efficient method to correct for spin diffusion that is fully integrated in our program ambiguous restraints for iterative assignment (ARIA). ARIA thus allows automated iterative NOE assignment and structure calculation with spin diffusion corrected distances. The method relies on numerical integration of the coupled differential equations which govern relaxation by matrix squaring and sparse matrix techniques. We derive a correction factor for the distance restraints from calculated NOE volumes and inter-proton distances. To evaluate the impact of our spin diffusion correction, we tested the new calibration process extensively with data from the Pleckstrin homology (PH) domain of Mus musculus beta-spectrin. By comparing structures refined with and without spin diffusion correction, we show that spin diffusion corrected distance restraints give rise to structures of higher quality (notably fewer NOE violations and a more regular Ramachandran map). Furthermore, spin diffusion correction permits the use of tighter error bounds which improves the distinction between signal and noise in an automated NOE assignment scheme.
Linge
Jens P
JP
Unité de Bio-Informatique Structurale, Institut Pasteur, 25-28 rue du docteur Roux, F-75015 Paris, France. linge@pasteur.fr
Habeck
Michael
M
Rieping
Wolfgang
W
Nilges
Michael
M
D000465:Algorithms; D000818:Animals; D016477:Artifacts; D003198:Computer Simulation; D004058:Diffusion; D005246:Feedback; D009682:Magnetic Resonance Spectroscopy / Q000379:methods*; D051379:Mice; D008958:Models, Molecular; D011487:Protein Conformation; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D013049:Spectrin / Q000032:analysis* / Q000737:chemistry*; D013113:Spin Labels
D013113:Spin Labels; D013049:Spectrin