A polynomial-time nuclear vector replacement algorithm for automated NMR resonance assignments

Journal of Computational Biology

Volumn 11, Issue 2-3, 2004, Pages 277-298

  Langmead, Christopher James ^a   Yan, Anthony ^a   Lilien, Ryan ^a   Wang, Lincong ^a   Donald, Bruce Randall ^a,b,c  

^a Dartmouth Department of Computer Science_Dartmouth College   (United States)

^b Dartmouth Department of Chemistry   (United States)

^c Dartmouth College   (United States)

Author keywords

Automated NMR resonance assignments; Molecular replacement; Nuclear vector replacement; Protein fold determination; Residual dipolar couplings; Structural genomics; Structural homology detection

Indexed keywords

PROTEIN G; UBIQUITIN;

ACCURACY; ALGORITHM; AMINO ACID SEQUENCE; AUTOMATION; CALCULATION; CONFERENCE PAPER; DATA BASE; GENE STRUCTURE; GENOMICS; LIGAND BINDING; MEASUREMENT; MOLECULAR DYNAMICS; MOLECULAR MODEL; MOLECULAR PROBE; NITROGEN NUCLEAR MAGNETIC RESONANCE; NUCLEAR MAGNETIC RESONANCE; NUCLEAR OVERHAUSER EFFECT; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; SEQUENCE HOMOLOGY; THREE DIMENSIONAL IMAGING; TIME; X RAY CRYSTALLOGRAPHY;

ALGORITHMS; COMPUTATIONAL BIOLOGY; MAGNETIC RESONANCE SPECTROSCOPY; PROTEIN STRUCTURE, TERTIARY;

EID: 3142588772     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/1066527041410436     Document Type: Conference Paper

References (74)

1. Al-Hashimi, H.M., Gorin, A., Majumdar, A., Gosser, Y., and Patel, D.J. 2002. Towards structural genomics of RNA: Rapid NMR resonance assignment and simultaneous RNA tertiary structure determination using residual dipolar couplings. J. Mol. Biol. 318, 637-649.
2. Altschul, S.F., Gish, W., Miller, W., Myers, E.W., and Lipman, D.J. 1990. Basic local alignment search tool. J. Mol. Biol. 215, 403-410.
3. Andrec, M., Du, P., and Levy, R.M. 2001. Protein backbone structure determination using only residual dipolar couplings from one ordering medium. J. Biomol. NMR 21(4), 335-347.
4. Annila, A., Aitio, H., Thulin, E., and Drakenberg, T. 1999. Recognition of protein folds via dipolar couplings. J. Biom. NMR 14, 223-230.
5. Artymiuk, P.J., Blake, C.C.F., Rice, D.W., and Wilson, K.S. 1982. The structures of the monoclinic and orthorhombic forms of hen egg-white lysozyme at 6 angstroms resolution. Acta Crystal. B Biol. Crystal. 38, 778.
6. Babu, C.R., Flynn, P.F., and Wand, A.J. 2001. Validation of protein structure from preparations of encapsulated proteins dissolved in low viscosity fluids. J. Am. Chem. Soc. 123, 2691.
7. Bailey-Kellogg, C., Widge, A., Kelley III, J.J., Berardi, M.J., Bushweller, J.H., and Donald, B.R. 2000. The NOESY Jigsaw: Automated protein secondary structure and main-chain assignment from sparse, unassigned NMR data. J. Comp. Biol. 7(3-4), 537-558.
8. Basu, S. 1997. An improved algorithm for quantifier elimination over real closed fields. IEEE FOCS, 56-65.
9. Basu, S., and Roy, M.F. 1996. On the combinatorial and algebraic complexity of quantifier elimination. J. ACM 43(6), 1002-1045.
10. Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N., and Bourne, P.E. 2000. The Protein Data Bank. Nucl. Acids Res. 28, 235-242.
11. Blundell, T.L., Sibanda, B.L., Sternberg, M.J., and Thornton, J.M. 1987. Knowledge-based prediction of protein structures and the design of novel molecules. Nature 326, 347-352.
12. Chen, Y., Reizer, J., Saier Jr., M.H., Fairbrother, W.J., and Wright, P.E. 1993. Mapping of the binding interfaces of the proteins of the bacterial phosphotransferase system, HPr and IIAglc. Biochemistry 32(1), 32-37.
13. Chou, J.J., Li, S., and Bax, A. 2000. Study of conformational rearrangement and refinement of structural homology models by the use of heteronuclear dipolar couplings. J. Biom. NMR 18, 217-227.
14. Cornilescu, G., Marquardt, J.L., Ottiger, M., and Bax, A. 1998. Validation of protein structure from anisotropic carbonyl chemical shifts in a dilute liquid crystalline phase. J. Am. Chem. Soc. 120, 6836-6837.
15. Cuff, J.A., Clamp, M.E., Siddiqui, A.S., Finlay, M., and Barton, G.J. 1998. Jpred: A consensus secondary structure prediction server. Bioinformatics 14, 892-893.
16. Delaglio, F., Kontaxis, G., and Bax, A. 2000. Protein structure determination using molecular fragment replacement and NMR dipolar couplings. J. Am. Chem. Soc. 122, 2142-2143.
17. Diamond, R. 1974. Real-space refinement of the structure of hen egg-white lysozyme. J. Mol. Biol. 82, 371-391.
18. Fejzo, J., Lepre, C.A., Peng, J.W., Bemis, G.W., Ajay, Murcko, M.A., and Moore, J.M. 1999. The SHAPES strategy: An NMR-based approach for lead generation in drug discovery. Chem. Biol. 6, 755-769.
19. Fetrow, J.S., and Bryant, S.H. 1993. New programs for protein tertiary structure prediction. Bio/Technology 11, 479-484.
20. Fiaux, J., Bertelsen, E.B., Horwich, A.L., and Wüthrich, K. 2002. NMR analysis of a 900K GroELGroES complex. Nature 418, 207-211.
21. Fowler, C.A., Tian, F., Al-Hashimi, H.M., and Prestegard, J.H. 2000. Rapid determination of protein folds using residual dipolar couplings. J. Mol. Biol. 304(3), 447-460.
22. Gallagher, T., Alexander, P., Bryan, P., and Gilliland, G.L. 1994. Two crystal structures of the B1 immunoglobulin-binding domain of streptococcal protein G and comparison with NMR. Biochemistry 33, 4721-4729.
23. Girard, E., Chantalat, L., Vicat, J., and Kahn, R. 2001. Gd-HPDO3A, a complex to obtain high-phasing-power heavy atom derivatives for SAD and MAD experiments: Results with tetragonal hen egg-white lysozyme. Acta Crystal. D Biol. Crystal. 58, 1-9.
24. Golub, G.H., and Van Loan, C.F. 1996. Matrix Computations, 3rd ed., 253-254, Johns Hopkins Univeristy Press, Baltimore, MD.
25. Greer, J. 1991. Comparative modeling of homologous proteins. Meth. Enzymol. 202, 239-252.
26. Grigor'ev, D.Y. 1988. Complexity of deciding Tarski algebra. J. Symbolic Computation 5(1-2), 65-108.
27. Grigor'ev, D.Y., and Vorobjov, N.N. 1988. Solving systems of polynomial inequalities in subexponential time. J. Symbolic Computation 5(1-2), 37-64.
28. Gronenborn, A.M., Filpula, D.R., Essig, N.Z., Achari, A., Whitlow, M., Wingfield, P.T., and Clore, G.M. 1991. A novel, highly stable fold of the immunoglobulin binding domain of streptococcal protein G. Science 253, 657.
29. Harris, R. 2002. The Ubiquitin NMR Resource Page, BBSRC Bloomsbury Center for Structural Biology, www.biochem. ucl.ac.uk/bsm/nmr/ubq/index.html.
30. Hoch, J., Burns, M.M., and Redfield, C. 1990. Frontiers of NMR in Molecular Biology, 167-175, Alan R. Liss, NY.
31. Hus, J.C., Marion, D., and Blackledge, M. 2000. De novo determination of protein structure by NMR using orientational and long-range order restraints. J. Mol. Biol. 298(5), 927-936.
32. Hus, J.C., Prompers, J., and Brüschweiler, R. 2002. Assignment strategy for proteins of known structure. J. Mag. Res. 157, 119-125.
33. Johnson, E.C., Lazar, G.A., Desjarlais, J.R., and Handel, T.M. 1999. Solution structure and dynamics of a designed hydrophobic core variant of ubiquitin. Structure Fold Des. 7, 967-976.
34. Johnson, M.S., Srinivasan, N., Sowdhamini, R., and Blundell, T.L. 1994. Knowledge-based protein modeling. Mol. Biochem. 29, 1-68.
35. Kuhn, H.W. 1955. Hungarian method for the assignment problem. Nav. Res. Logist. Quarterly 2, 83-97.
36. Kullback, S., and Leibler, R.A. 1951. On information and sufficiency. Annals Math. Statist. 22, 79-86.
37. Kurinov, I.V., and Harrison, R.W. 1995. The influence of temperature on lysozyme crystals - structure and dynamics of protein and water. Acta Crystal. D Biol. Crystal. 51, 98-109.
38. Kuszewski, J., Gronenborn, A.M., and Clore, G.M. 1999. Improving the packing and accuracy of NMR structures with a pseudopotential for the radius of gyration. J. Am. Chem. Soc. 121, 2337-2338.
39. Langmead, C., and Donald, B.R. 2003. 3D Structural homology detection via unassigned residual dipolar couplings, Proc. IEEE Computer Society Bioinformatics Conference (CSB), Stanford CA. (August 10, 2003), pp. 209-217. ISBN 0-7695-2000-6.
40. Langmead, C., and Donald, B.R. 2004a. An expectation/maximization nuclear vector replacement algorithm for automated NMR resonance assignments. J. Biomol. NMR 29, 111-138.
41. Langmead, C., and Donald, B.R. 2004b. An improved nuclear vector replacement algorithm for nuclear magnetic resonance assignment. Dartmouth Computer Science Technical Report TR2004-494, Hanover, NH. http://www.cs. dartmouth.edu/reports/abstracts/TR2004-494/
42. Langmead, C., and Donald, B.R. 2004c. High-throughput 3D homology detection via NMR resonance assignment. Dartmouth Computer Science Technical Report TR2004-487, Hanover, NH. http://www.cs.dartmouth.edu/reports/ abstracts/TR2004-487/
43. Lathrop, R.H., and Smith, T.F. 1996. Global optimum protein threading with gapped alignment and empirical pair score functions. J. Mol. Biol. 255, 641-665.
44. Lim, K., Nadarajah, A., Forsythe, E.L., and Pusey, M.L. 1998. Locations of bromide ions in tetragonal lysozyme crystals. Acta Crystal. D Biol. Crystal. 54, 899-904.
45. Losonczi, J.A., Andrec, M., Fischer, W.F., and Prestegard, J.H. 1999. Order matrix analysis of residual dipolar couplings using singular value decomposition. J. Magn. Reson. 138(2), 334-342.
46. Meiler, J., Peti, W., and Griesinger, C. 2000. DipoCoup: A versatile program for 3D-structure homology comparison based on residual dipolar couplings and pseudocontact shifts. J. Biom. NMR 17, 283-294.
47. Mueller, G.A., Choy, W.Y., Yang, D., Forman-Kay, J.D., Venters, R.A., and Kay, L.E. 2000. Global folds of proteins with low densities of NOEs using residual dipolar couplings: Application to the 370-residue maltodextrin-binding protein. J. Mol. Biol. 300, 197-212.
48. National Institute of General Medical Sciences. 2002. The Protein Structure Initiative. URL: www.nigms.nih.gov/psi/.
49. Oki, H., Matsuura, Y., Komatsu, H., and Chernov, A.A. 1999. Refined structure of orthorhombic lysozyme crystallized at high temperature: Correlation between morphology and intermolecular contacts. Acta Crystal. D Biol. Crystal. 55, 114.
50. Osapay, K., and Case, D.A. 1991. A new analysis of proton chemical shifts in proteins. J. Am. Chem. Soc. 113, 9436-9444.
51. Palmer III, A.G. 1997. Probing molecular motion by NMR. Curr. Opin. Struct. Biol. 7, 732-737.
52. Pearlman, D.A., Case, D.A., Caldwell, J.W., Ross, W.S., Cheatham, T.E., DeBolt, S., Ferguson, D., Seibel, G., and Kollman, P. 1995. AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structures and energies of molecules. Comp. Phy. Comm. 91, 1-41.
53. Ramage, R., Green, J., Muir, T.W., Ogunjobi, O.M., Love, S., and Shaw, K. 1994. Synthetic, structural and biological studies of the ubiquitin system: The total chemical synthesis of ubiquitin. J. Biochem. 299, 151-158.
54. Redfield, C., Hoch, J., and Dobson, C. 1983. Chemical shifts of aromatic protons in protein NMR spectra. FEBS Lett. 159, 132-136.
55. Rohl, C.A., and Baker, D. 2002. De novo determination of protein backbone structure from residual dipolar couplings using Rosetta. J. Am. Chem. Soc. 124(11), 2723-2729.
56. Rossman, M.G., and Blow, D.M. 1962. The detection of sub-units within the crystallographic asymmetric unit. Acta Crystal. 15, 24-31.
57. Sali, A., Overington, J.P., Johnson, M.S., and Blundell, T.L. 1990. From comparisons of protein sequences and structures to protein modelling and design. Trends Biochem. Sci. 15, 235-240.
58. Saupe, A. 1968. Recent results in the field of liquid crystals. Angew. Chem. 7, 97-112.
59. Schneider, D.M., Dellwo, M.J., and Wand, A.J. 1992. Fast internal main-chain dynamics of human ubiquitin. Biochemistry 31(14), 3645-3652.
60. Schwalbe, H., Grimshaw, S.B., Spencer, A., Buck, M., Boyd, J., Dobson, C.M., Redfield, C., and Smith, L.J. 2001. A refined solution structure of hen lysozyme determined using residual dipolar coupling data. Protein Sci. 10, 677-688.
61. Shuker, S.B., Hajduk, P.J., Meadows, R.P., and Fesik, S.W. 1996. Discovering high affinity ligands for proteins: SAR by NMR. Science 274, 1531-1534.
62. Tian, F., Valafar, H., and Prestegard, J.H. 2001. A dipolar coupling based strategy for simultaneous resonance assignment and structure determination of protein backbones. J. Am. Chem. Soc. 123, 11791-11796.
63. Tjandra, N., and Bax, A. 1997. Direct measurement of distances and angles in biomolecules by NMR in a dilute liquid crystalline medium. Science 278, 1111-1114.
64. Vaney, M.C., Maignan, S., Ries-Kautt, M., and Ducruix, A. 1996. High-resolution structure (1.33 Angstrom) of a HEW lysozyme tetragonal crystal grown in the APCF apparatus. Data and structural comparison with a crystal grown under microgravity from SpaceHab-01 mission. Acta Crystal. D Biol. Crystal. 52, 505-517.
65. Vijay-Kumar, S., Bugg, C.E., and Cook, W.J. 1987. Structure of ubiquitin refined at 1.8 Å resolution. J. Mol. Biol. 194, 531-544.
66. Wang, L., and Donald, B.R. 2004. Exact solutions for internuclear vectors and backbone dihedral angles from NH residual dipolar couplings in two media, and their application in a systematic search algorithm for determining protein backbone structure. J. Biomol. NMR. In press.
67. Weber, P.L., Brown, S.C., and Mueller, L. 1987. Sequential 1H NMR assignments and secondary structure identification of human ubiquitin. Biochemistry 26, 7282-7290.
68. Wedemeyer, W.J., Rohl, C.A., and Scheraga, H.A. 2002. Exact solutions for chemical bond orientations from residual dipolar couplings. J. Biom. NMR 22, 137-151.
69. Wishart, D.S., Watson, M.S., Boyko, R.F., and Sykes, B.D. 1997. Automated 1H and 13C chemical shift prediction using the BioMagResBank. J. Biomol. NMR 10, 329-336.
70. Wüthrich, K. 2000. Protein recognition by NMR. Nat. Struct. Biol. 7(3), 188-189.
71. Xu, Y., Xu, D., Crawford, O.H., Einstein, J.R., and Serpersu, E. 2000. Protein structure determination using protein threading and sparse NMR data. RECOMB'00.
72. Xu, Y., Xu, D., Kim, D., Olman, V., Razumovskaya, J., and Jiang, T. 2002. Automated assignment of backbone NMR peaks using constrained bipartite matching. IEEE Comput. Sci. Eng. 4(1), 50-62.
73. Yan, A., Langmead, C., and Donald, B.R. 2003. A probability-based similarity measure for saupe alignment tensors with applications to residual dipolar couplings in NMR structural biology. Dartmouth Computer Science Technical Report TR2003-474, Hanover, NH. http://www.cs.dartmouth.edu/reports/ abstracts/TR2003-474/
74. Zweckstetter, M., and Bax, A. 2001. Single-step determination of protein substructures using dipolar couplings: Aid to structural genomics. J. Am. Chem. Soc. 123(38), 9490-9491.