NMR structural inference of symmetric homo-oligomers

Journal of Computational Biology

Volumn 18, Issue 12, 2011, Pages 1757-1775

  Chandola, Himanshu ^a   Yan, Anthony K ^b   Potluri, Shobha ^a,c   Donald, Bruce R ^b,d   Bailey Kellogg, Chris ^a  

^a Dartmouth College   (United States)

^b Duke University   (United States)

^c PFIZER INC   (United States)

^d DUKE UNIVERSITY MEDICAL CENTER   (United States)

Author keywords

Bayesian inference; distance restraint; posterior distribution characterization; protein complex structure determination

Indexed keywords

PROTEIN;

ALGORITHM; ARTICLE; CELL SIZE; CHEMISTRY; METHODOLOGY; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PROTEIN MULTIMERIZATION; PROTEIN QUATERNARY STRUCTURE; PROTEIN SUBUNIT;

ALGORITHMS; CELL SIZE; MAGNETIC RESONANCE SPECTROSCOPY; PROTEIN MULTIMERIZATION; PROTEIN STRUCTURE, QUATERNARY; PROTEIN SUBUNITS; PROTEINS;

EID: 82755173940     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2010.0327     Document Type: Article

References (32)

1. Berman, H.M., Westbrook, J., Feng, Z., et al. 2000. The Protein Data Bank. Nuclic Acids Res. 28, 235-242. (Pubitemid 30047768)
2. Brünger, A.T. 1993. XPLOR: A System for X-Ray Crystallography and NMR. Yale University Press, New Havern, CT.
3. Dean, J., and Ghemawat, S. 2004. MapReduce: simplified data processing on large clusters. Proc. OSDI'04: Sixth Symp. Operating System Design Implement.
4. Desmet, J., De Maeyer, M., Hazes, B., et al. 1992. The dead-end elimination theorem and its use in protein side-chain positioning. Nature 356, 539-542.
5. Georgiev, I., Lilien, R.H., and Donald, B.R. 2008. The minimized dead-end elimination criterion and its application to protein redesign in a hybrid scoring and search algorithm for computing partition functions over molecular ensembles. J. Comput. Chem. 29, 1527-1542.
6. Goodsell, D.S., and Olson, A.J. 2000. Structural symmetry and protein function. Annu. Rev. Biophys. Biomol. Struct. 29, 105-153. (Pubitemid 30599590)
7. Güntert, P., Braun, W., and Wüthrich, K. 1991. Efficient computation of three-dimensional protein structures in solution from nuclear magnetic resonance data using the program DIANA and the supporting programs CALIBA, HABAS and GLOMSA. J. Mol. Biol. 217, 517-530. (Pubitemid 121003298)
8. Güntert, P., Mumenthaler, C., and Wüthrich, K. 1997. Torsion angle dynamics for NMR structure calculation with the new program DYANA. J. Mol. Biol. 273, 283-298. (Pubitemid 27460230)
9. Habeck, M., Nilges, M., and Rieping, W. 2005. Replica-exchange Monte Carlo scheme for Bayesian data analysis. Phys. Rev. 94, 01805.
10. Habeck, M., Rieping, W., and Nilges, M. 2006. Weighting of experimental evidence in macromolecular structure determination. Proc. Natl. Acad. Sci. USA 103, 1756-1761. (Pubitemid 43228766)
11. Ikura, M., and Bax, A. 1992. Isotope-filtered 2D NMR of a protein peptide complex: study of a skeletal-muscle myosin light chain kinase fragment bound to calmodulin. J. Am. Chem. Soc. 114, 2433-2440.
12. Jeffreys, H. 1946. An invariant form for the prior probability in estimation problems. Proc. R. Soc. A 186, 453-461.
13. Kass, R.E., and Wasserman, L.A. 1996. The selection of prior distributions by formal rules. J. Am. Stat. Assoc. 91, 1343-1370.
14. King, G.F., Shih, Y.L., Maciejewski, M.W., et al. 2000. Structural basis for the topological specificity function of MinE. Nat. Struct. Biol. 7, 1013-1017.
15. Lee, W., Revington, M.J., Arrowsmith, C., et al. 1994. A pulsed-field gradient isotope-filtered 3D C-13 HMQCNOESY experiment for extracting intermolecular NOE contacts in molecular-complexes. FEBS Lett. 350, 87-90.
16. Lipari, G., and Szabo, A. 1982. Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 1. Theory and range of validity. J. Am. Chem. Soc. 104, 4546-4559.
17. MacKenzie, K.R., Prestegard, J.H., and Engelman, D.M. 1996. Leucine side-chain rotamers in a glycophorin A transmembrane peptide as revealed by three-bond carboncarbon couplings and 13C chemical shifts. J. Biomol. NMR 7, 256-260. (Pubitemid 126709565)
18. Macura, S., and Ernst, R.R. 1980. Elucidation of cross relaxation in liquids by two-dimensional NMR spectroscopy. Mol. Phys. 41, 95-117.
19. Moran, M.G., and Kendall, P.A.P. 1963. Geometrical Probability. Charles Griffin & Co. Ltd., London.
20. Nilges, M., Habeck, M., O'Donoghue, S.L., et al. 2006. Error distribution derived NOE distance restraints. Proteins 64, 652-664. (Pubitemid 44100731)
21. Oxenoid, K., and Chou, J.J. 2005. The structure of phospholamban pentamer reveals a channel-like architecture in membranes. Proc. Natl. Acad. Sci. USA 102, 10870-10875. (Pubitemid 41105959)
22. Potluri, S., Yan, A.K., Chou, J.J., et al. 2006. Structure determination of symmetric protein complexes by a complete search of symmetry configuration space using NMR distance restraints and van der Waals packing. Proteins 65, 203-219. (Pubitemid 44320629)
23. Potluri, S., Yan, A.K., Donald, B.R., et al. 2007. A complete algorithm to resolve ambiguity for inter-subunit NOE assignment in structure determination of symmetric homo-oligomers. Protein Sci. 16, 69-81. (Pubitemid 46036499)
24. Rieping, W., Habeck, M., and Nilges, M. 2005a. Modeling errors in NOE data with a log-normal distribution improves the quality of NMR structures. J. Am. Chem. Soc. 127, 16026-16027. (Pubitemid 41689221)
25. Rieping, W., Michael, H., and Nilges, M. 2005b. Inferential structure determination. Science 309, 303-306.
26. Santaló , L.A. 2002. Integral Geometry and Geometric Probability, 2nd ed. Cambridge University Press, New York.
27. Schnell, J.R., and Chou, J.J. 2008. Structure and mechanism of the M2 proton channel of influenza A virus. Nature 451, 591-595. (Pubitemid 351186272)
28. Seavey, B.R., Farr, E.A., Westler, W.M., et al. 1991. A relational database for sequence-specific protein NMR data. J. Biomol. NMR 1, 217-236.
29. Walters, K.J., Matsuo, H., and Wagner, G. 1997. A simple method to distinguish intermonomer nuclear overhauser effects in homodimeric proteins with C2 symmetry. J. Am. Chem. Soc. 119, 5958-5959.
30. Wang, J., Pielak, R.M., McClintock, M.A., et al. 2009. Solution structure and functional analysis of the influenza B proton channel. Nat. Struct. Mol. Biol. 16, 1267-1271.
31. Wiltscheck, R., Kammerer, R.A., Dames, S.A., et al. 1997. Heteronuclear NMR assignments and secondary structure of the coiled coil trimerization domain from cartilage matrix protein in oxidized and reduced forms. Protein Sci. 6, 1734-1745. (Pubitemid 27333076)
32. Zwahlen, C., Legaulte, P., Vincent, S.J.F., et al. 1997. Methods for measurement of intermolecular NOEs by multinuclear NMR spectroscopy: application to a bacteriophage labda N-Peptide/boxB RNA complex. J. Am. Chem. Soc. 119, 6711-6721. (Pubitemid 27343493)