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Automated 2D NOESY assignment and structure calculation of Crambin(S22/I25) with the self-correcting distance
Y Xu1, J Wu, D Gorenstein
1Sealy Center for Structural Biology and Department of Human Biological Chemistry and Genetics, University of Texas Medical Branch, Galveston, Texas, 77555-1157, USA.
Journal of Magnetic Resonance (San Diego, Calif. : 1997)
|January 15, 1999
Summary
The NOAH/DIAMOD program suite successfully automated the assignment of protein nuclear Overhauser effect spectroscopy (NOESY) spectra for crambin. This method accurately determined protein structures using nuclear magnetic resonance (NMR) data.
Area of Science:
- Biochemistry
- Structural Biology
- Computational Chemistry
Background:
- Protein structure determination is crucial for understanding biological function.
- Nuclear Magnetic Resonance (NMR) spectroscopy, particularly 2D NOESY, provides vital distance constraints for structural analysis.
- Automated methods are needed to improve the efficiency and accuracy of NMR data assignment.
Purpose of the Study:
- To evaluate the efficacy of the NOAH/DIAMOD program suite for automated NOESY spectrum assignment.
- To assess the accuracy of protein structure determination using automated NMR assignments.
- To investigate the impact of incomplete chemical shift data on automated assignment and structure calculation.
Main Methods:
- Utilized the NOAH/DIAMOD program suite, incorporating feedback filtering and self-correcting distance geometry (SECODG).
- Combined automatically picked and manually assigned NOESY cross peaks to initiate calculations.
- Employed an iterative process of structure ensemble generation, filtering, and automated assignment refinement.
Main Results:
- Achieved convergence of 10 structures to 1.48 Å backbone r.m.s.d. after 60 iterations.
- Successfully assigned 426 out of 613 NOE peaks unambiguously and 59 ambiguously.
- Identified remaining unassigned peaks as likely noise or real peaks missed due to incomplete chemical shift data.
Conclusions:
- The NOAH/DIAMOD suite demonstrates significant potential for automated NOESY assignment in protein structure determination.
- Automated assignment, even with incomplete data, can yield accurate structural models.
- Further refinement of automated assignment algorithms could improve the handling of ambiguous and unassigned NOE peaks.