Effects of experimentally achievable improvements in the quality of NMR distance constraints on the accuracy of calculated protein structures

Journal of Molecular Biology

Volumn 258, Issue 2, 1996, Pages 334-348

  Hoogstraten, Charles G ^a,b   Markley, John L ^a  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

^b UNIVERSITY OF COLORADO   (United States)

Author keywords

Magnetization exchange network editing; NOESY; Protein solution structure; Spin diffusion; Structural accuracy

Indexed keywords

OVOMUCOID; PROTEIN;

ACCURACY; ARTICLE; COMPUTER ANALYSIS; METHODOLOGY; MOLECULAR MODEL; NONHUMAN; NUCLEAR MAGNETIC RESONANCE; NUCLEAR OVERHAUSER EFFECT; PRIORITY JOURNAL; PROTEIN CONFORMATION; TURKEY (BIRD); X RAY ANALYSIS;

EID: 0029881076     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1996.0254     Document Type: Article

References (33)

1. Bax, A. & Grzesiek, S. (1993). Methodological advances in protein NMR. Acct. Chem. Res. 26, 131-138.
2. Borgias, B. A., Gochin, M., Kerwood, D. J. & James, T. L. (1990). Relaxation matrix analysis of 2D NMR data. Prog. NMR Spectrosc. 22, 83-100.
3. Brünger, A. T. (1992). X-PLOR Version 3.1: A System for X-ray Crystallography and NMR, Yale University Press, New Haven.
4. Clore, G. M. & Gronenborn, A. M. (1991). Structures of larger proteins in solution: three-and four-dimensional heteronuclear NMR spectroscopy Science, 252, 1390-1399.
5. Clore, G. M. & Gronenborn, A. M. (1993). Determination of structures of larger proteins in solution by three-and four-dimensional heteronuclear magnetic resonance spectroscopy In NMR of Proteins (Clore, G. M. & Gronenborn, A. M., eds), pp. 1-32, CRC Press, Boca Raton.
6. Clore, G. M., Robien, M. A. & Gronenborn, A. M. (1993). Exploring the limits of precision and accuracy of protein structures determined by nuclear magnetic resonance spectroscopy J. Mol. Biol. 231, 82-102.
7. Fejzo, J., Krezel, A. M., Westler, W. M., Macura, S. & Markley J. L. (1991). Refinement of the NMR solution structure of a protein to remove distortions arising from neglect of internal motion. Biochemistry, 30, 3807-3811.
8. Forman-Kay J. D., Clore, G. M., Wingfield, P. T. & Gronenborn, A. M. (1991). High-resolution three-dimensional structure of reduced recombinant human thioredoxin in solution. Biochemistry, 30, 2685-2698.
9. Fujinaga, M., Sielecki, A. R., Read, R. J., Ardelt, W., Laskowski, M. Jr & James, M. N. G. (1987). Crystal and molecular structures of the complex of α-chymotrypsin with its inhibitor turkey ovomucoid third domain at 1.8 Å resolution. J. Mol. Biol. 195, 397-418.
10. Havel, T. F. (1991). An evaluation of computational strategies for use in the determination of protein structure from distance constraints obtained by nuclear magnetic resonance. Prog. Biophys. Mol. Biol. 56, 43-78.
11. Havel, T. F. & Wüthrich, K. (1985). An evaluation of the combined use of nuclear magnetic resonance and distance geometry for the determination of protein conformation in solution. J. Mol. Biol. 182, 281-294.
12. Hoogstraten, C. G., Westler, W. M., Macura, S. & Markley J. L. (1993). Improved measurement of longer protonproton distances in proteins by relaxation network editing. J. Magn. Reson. B, 102, 232-235.
13. Hoogstraten, C. G., Choe, S., Westler, W. M. & Markley J. L. (1995a). Comparison of the accuracy of protein solution structures derived from conventional and network-edited NOESY data. Protein Sci. 4, 2289-2299.
14. Hoogstraten, C. G., Westler, W. M., Macura, S. & Markley, J. L. (1995b). NOE measurements in the absence of spin diffusion: application to methylene groups in proteins and effects on local structural parameters. J. Am. Chem. Soc. 117, 5610-5611.
15. Hoogstraten, C. G., Westler, W. M., Mooberry, E. S., Macura, S. & Markley, J. L. (1995c). Analysis of transverse cross relaxation within a simplified relaxation submatrix: BD-ROESY. J. Magn. Reson. B, 109, 76-79.
16. James, T. L. (1994). Assessment of quality of derived macromolecular structures. Methods Enzymol. 239, 416-439.
17. Jardetzky, O. (1991). Interpretation of NMR data in terms of protein structure: summary of a round table discussion. In Computational Aspects of the Study of Biological Macromolecules by Nuclear Magnetic Resonance Spectroscopy (Hoch, J. C., Poulsen, F. M. & Redfield, C., eds), pp. 375-389, Plenum Press, New York.
18. Keepers, J. W. & James, T. L. (1984). A theoretical study of distance determinations from NMR. Two-dimensional nuclear Overhauser effect spectra. J. Magn. Reson. 57, 404-426.
19. Kominos, D., Suri, A. K., Kitchen, D. B., Bassolino, D. & Levy R. M. (1992). Simulating the effect of the two-spin approximation on the generation of protein structures from NOE data. J. Magn. Reson. 97, 398-410.
20. Krezel, A. M., Darba, P., Robertson, A. D., Fejzo, J., Macura, S. & Markley, J. L. (1994). Solution structure of turkey ovomucoid third domain as determined from nuclear magnetic resonance data. J. Mol. Biol. 242, 203-214.
21. Liu, H., Anil Kumar, Borgias, B. A., Thomas, P. D. & James, T. L. (1994). CORMA 5.0/MARDIGRAS 3.0 (UCSF), University of California, San Francisco.
22. Liu, Y., Zhao, D., Altman, R. & Jardetzky, O. (1992). A systematic comparison of three structure determination methods from NMR data: Dependence upon quality and quantity of data. J. Biomol. NMR, 2, 373-388.
23. Macura, S. & Ernst, R. R. (1980). Elucidation of cross relaxation in liquids by two-dimensional N. M. R. spectroscopy Mol. Phys. 41, 95-117.
24. Macura, S., Fejzo, J., Hoogstraten, C. G., Westler, W. M. & Markley, J. L. (1992). Topological editing of cross-relaxation networks. Israel J. Chem. 32, 245-256.
25. Macura, S., Westler, W. M. & Markley, J. L. (1994). Two-dimensional exchange spectroscopy of proteins. Methods Enzymol. 239, 106-144.
26. Neuhaus, D. & Williamson, M. (1989). The Nuclear Overhauser Effect in Structural and Conformational Analysis, VCH, New York.
27. Nilges, M., Clore, G. M. & Gronenborn, A. M. (1988). Determination of three-dimensional structures of proteins from interproton distance data by hybrid distance geometry-dynamical simulated annealing calculations. FEBS Letters, 229, 317-324.
28. Press, W. H., Flannery B. P., Teukolsky, S. A. & Vetterling, W. T. (1988). Numerical Recipes in C, Cambridge University Press, Cambridge.
29. Robertson, A. D., Westler, W. M. & Markley, J. L. (1988). Two-dimensional NMR studies of Kazal proteinase inhibitors. 1. Sequence-specific assignments and secondary structure of turkey ovomucoid third domain. Biochemistry, 27, 2519-2529.
30. Thomas, P. D., Basus, V. J. & James, T. L. (1991). Protein solution structure determination using distances from two-dimensional nuclear Overhauser effect experiments: effect of approximations on the accuracy of derived structures. Proc. Natl Acad. Sci. USA, 88, 1237-1241.
31. Wijmenga, S. S., Mooren, M. M. W. & Hilbers, C. W. (1993). NMR of nucleic acids; from spectrum to structure. In NMR of Macromolecules: A Practical Approach (Roberts, G. C. K., ed.), pp. 217-288, Oxford University Press, Oxford.
32. Zhao, D. & Jardetzky, O. (1994). An assessment of the precision and accuracy of protein structures determined by NMR: Dependence on distance errors. J. Mol. Biol. 239, 601-607.
33. Zolnai, Zs., Juranic, N., Markley, J. L. & Macura, S. (1995). Magnetization exchange network editing: Mathematical principles and experimental demonstration. J. Chem. Phys. 200, 161-179.