Protein structure prediction using sparse dipolar coupling data

Nucleic Acids Research

Volumn 32, Issue 2, 2004, Pages 551-561

  Qu, Youxing ^a,b   Guo, Jun Tao ^a,b   Olman, Victor ^a,b   Xu, Ying ^a,b  

^a UNIVERSITY OF GEORGIA   (United States)

^b OAK RIDGE NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; COMPUTER PROGRAM; CONTROLLED STUDY; DATA ANALYSIS; NITROGEN NUCLEAR MAGNETIC RESONANCE; PERFORMANCE; PREDICTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DATA BANK; PROTEIN DATABASE; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE; PROTEIN TARGETING; PROTON NUCLEAR MAGNETIC RESONANCE; RECORDING; REVIEW; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY;

COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; DATABASES, PROTEIN; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; SENSITIVITY AND SPECIFICITY; SOFTWARE;

EID: 1342306402     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkh204     Document Type: Review

References (100)

1. Tolman,J.R., Flanagan,J.M., Kennedy,M.A. and Prestegard,J.H. (1995) Nuclear magnetic dipole interactions in field-oriented proteins: information for structure determination in solution. Proc. Natl Acad. Sci. USA, 92, 9279-9283.
2. 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.
3. Tolman,J.R. (2001) Dipolar couplings as a probe of molecular dynamics and structure in solution. Curr. Opin. Struct. Biol., 11, 532-539.
4. Prestegard,J.H. (1998) New techniques in structural NMR-anisotropic interactions. Nature Struct. Biol., 5, 517-522.
5. Prestegard,J.H., al-Hashimi,H.M. and Tolman,J.R. (2000) NMR structures of biomolecules using field oriented media and residual dipolar couplings. Q. Rev. Biophys., 33, 371-424.
6. Bax,A., Kontaxis,G. and Tjandra.N. (2001) Dipolar couplings in macromolecular structure determination. Methods Enzymol., 339, 127-174.
7. deAlba,E. and Tjandra,N. (2002) NMR dipolar couplings for the structure determination of biopolymers in solution. Prog. Nucl. Magn. Reson. Spectrosc., 40, 175-197.
8. Bax,A. (2003) Weak alignment offers new NMR opportunities to study protein structure and dynamics. Protein Sci., 12, 1-16.
9. Briggman,K.B. and Tolman,J.R. (2003) De novo determination of bond orientations and order parameters from residual dipolar couplings with high accuracy. J. Am. Chem. Soc., 125, 10164-10165.
10. 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.
11. Hus,J.C., Marion,D. and Blackledge,M. (2001) Determination of protein backbone structure using only residual dipolar couplings. J. Am. Chem. Soc., 123, 1541-1542.
12. 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.
13. 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, 2723-2729.
14. Tolman,J.R. (2002) A novel approach to the retrieval of structural and dynamic information from residual dipolar couplings using several oriented media in biomolecular NMR spectroscopy. J. Am. Chem. Soc., 124, 12020-12030.
15. 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, 335-347.
16. Andrec,M., Harano,Y., Jacobson,M.P., Friesner,R.A. and Levy,R.M. (2002) Complete protein structure determination using backbone residual dipolar couplings and sidechain rotamer prediction. J. Struct. Funct. Genom., 2, 103-111.
17. 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, 447-460.
18. 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, 927-936.
19. Beraud,S., Bersch,B., Brutscher,B., Gans,P., Barras,F. and Blackledge,M. (2002) Direct structure determination using residual dipolar couplings: reaction-site conformation of methionine sulfoxide reductase in solution. J. Am. Chem. Soc., 124, 13709-13715.
20. Wedemeyer,W.J., Rohl,C.A. and Scherag,H.A. (2002) Exact solutions for chemical bond orientations from residual dipolar couplings. J. Biomol. NMR, 22, 137-151.
21. Annila,A., Aitio,H., Thulin,E. and Drakenberg,T. (1999) Recognition of protein folds via dipolar couplings. J. Biomol. NMR, 14, 223-230.
22. 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. Biomol. NMR, 17, 283-294.
23. Haliloglu,T., Kolinski,A. and Skolnick,J. (2003) Use of residual dipolar couplings as restraints in ab initio protein structure prediction. Biopolymers, 70, 548-562.
24. Lee,D., Grant,A., Buchan,D. and Orengo,C. (2003) A structural perspective on genome evolution. Curr. Opin. Struct. Biol., 13, 359-369.
25. Andrec,M., Du,P. and Levy,R.M. (2001) Protein structural motif recognition via NMR residual dipolar couplings. J. Am. Chem. Soc., 123, 1222-1229.
26. Valafar,H. and Prestegard,J.H. (2003) Rapid classification of a protein fold family using a statistical analysis of dipolar couplings. Bioinformatics, 19, 1549-1555.
27. Langmead,C.J. and Donald,B.R. (2003) 3D structural homology detection via unassigned residual dipolar couplings. Proceedings of IEEE Computer Society Bioinformatics Conference (CSB). Palo Alto, CA, pp. 209-217.
28. Langmead.C.J., Yan,A., Lilien,R., Wang,L. and Donald,B.R. (2003) A polynomial-time nuclear vector replacement algorithm for automated NMR resonance assignments. Proceedings of the 7th Annual International Conference on Research in Computational Molecular Biology (RECOMB). Berlin, Germany, pp. 176-187.
29. Losonczi,J.A. andrec,M.. Fischer,M.W. and Prestegard,J.H. (1999) Order matrix analysis of residual dipolar couplings using singular value decomposition. J. Magn. Reson., 138, 334-342.
30. Zweckstetter,M. and Bax,A. (2000) Prediction of sterically induced alignment in a dilute liquid crystalline phase: aid to protein structure determination by NMR. J. Am. Chem. Soc., 122, 3791-3792.
31. Dosset,P., Hus,J.C., Marion,D. and Blackledge,M. (2001) A novel interactive tool for rigid-body modeling of multi-domain macromolecules using residual dipolar couplings. J. Biomol. NMR, 20, 223-231.
32. Baker,D. and Sali,A. (2001) Protein structure prediction and structural genomics. Science, 294, 93-96.
33. Clore,G.M., Gronenborn,A.M. and Tjandra,N. (1998) Direct structure refinement against residual dipolar couplings in the presence of rhombicity of unknown magnitude. J. Magn. Reson., 131, 159-162.
34. Clore,G.M., Gronenborn,A.M. and Bax,A. (1998) A robust method for determining the magnitude of the fully asymmetric alignment tensor of oriented macromolecules in the absence of structural information. J. Magn. Reson., 133, 216-221.
35. Jones,D.T. (1999) Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol., 292, 195-202.
36. Needleman,S.B. and Wunsch,C.D. (1970) A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol., 48, 443-453.
37. Alexandrov,N.N. (1996) SARFing the PDB. Protein Eng., 9, 727-732.
38. Weisstein,N.N. (2002) CRC Concise Encyclopedia of Mathematics, 2nd Edn. CRC Press, Boca Raton, FL, pp. 2600.
39. Anton,H. and Rorres,C. (1987) Elementary Linear Algebra with Applications. John Wiley & Sons, Inc., pp. 590-591.
40. Nomura,K. and Kainosho,M. (2002) Graphical analysis of the relative orientation of molecular alignment tensors for a protein dissolved in two different anisotropic media. J. Magn. Reson., 154, 146-153.
41. Murzin,A.G., Brenner,S.E., Hubbard,T. and Chothia,C. (1995) SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol., 247, 536-540.
42. Word,J.M., Lovell,S.C., Richardson,J.S. and Richardson,D.C. (1999) Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation. J. Mol. Biol., 285, 1735-1747.
43. Carter,P., Andersen,C.A. and Rost,B. (2003) DSSPcont: continuous secondary structure assignments for proteins. Nucleic Acids Res., 31, 3293-3295.
44. Shindyalov,I.N. and Bourne,P.E. (1998) Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Eng., 11, 739-747.
45. Rost,B. and Sander,C. (1993) Prediction of protein secondary structure at better than 70% accuracy. J. Mol. Biol., 232, 584-599.
46. Wishart,D.S., Sykes,B.D. and Richards,F.M. (1991) Relationship between nuclear magnetic resonance chemical shift and protein secondary structure. J. Mol. Biol., 222, 311-333.
47. Wishart,D.S., Sykes,B.D. and Richards,F.M. (1992) The chemical shift index: a fast and simple method for the assignment of protein secondary structure through NMR spectroscopy. Biochemistry, 31, 1647-1651.
48. Wishart,D.S. and Sykes,B.D. (1994) The 13C chemical-shift index: a simple method for the identification of protein secondary structure using 13C chemical-shift data. J. Biomol. NMR, 4, 171-180.
49. Wishart,D.S. and Sykes,B.D. (1994) Chemical shifts as a tool for structure determination. Methods Enzymol., 239, 363-392.
50. 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.
51. Tolman,J.R., Al-Hashimi,H.M., Kay,L.E. and Prestegard,J.H. (2001) Structural and dynamic analysis of residual dipolar coupling data for proteins. J. Am. Chem. Soc., 123, 1416-1424.
52. Xu,Y. and Xu,D. (2000) Protein threading using PROSPECT: design and evaluation. Proteins, 40, 343-354.
53. Kim,D., Xu,D., Guo,J.T., Ellrott,K. and Xu,Y. (2003) PROSPECT II: protein structure prediction program for genome-scale applications. Protein Eng., 16, 641-650.
54. Moseley,H.N. and Montelione,G.T. (1999) Automated analysis of NMR assignments and structures for proteins. Curr. Opin. Struct. Biol., 9, 635-642.
55. Guntert,P., Salzmann,M., Braun,D. and Wuthrich,K. (2000) Sequence-specific NMR assignment of proteins by global fragment mapping with the program MAPPER. J. Biomol. NMR, 18, 129-137.
56. Atreya,H.S., Sahu,S.C., Chary,K.V. and Govil,G. (2000) A tracked approach for automated NMR assignments in proteins (TATAPRO). J. Biomol. NMR, 17, 125-136.
57. Moseley,H.N., Monleon,D. and Montelione,G.T. (2001) Automatic determination of protein backbone resonance assignments from triple resonance nuclear magnetic resonance data. Methods Enzymol., 339, 91-108.
58. Coggins,B.E. and Zhou,P. (2003) PACES: protein sequential assignment by computer-assisted exhaustive search. J. Biomol. NMR, 26, 93-111.
59. Xu,Y., Xu,D., Kim,D., Olman,V. and Razumovskaya,J. (2002) Automated assignment of backbone NMR peaks using constrained bipartite matching. IEEE Comput. Sci. Eng., 4, 50-62.
60. Sali,A. and Blundell,T.L. (1993) Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol., 234, 779-815.
61. Sayle,R.A. and Milner-White,E.J. (1995) RASMOL: biomolecular graphics for all. Trends Biochem. Sci., 20, 374.
62. Paakkonen,K., Sorsa,T., Drakenberg,T., Pollesello,P., Tilgmann,C., Permi,P., Heikkinen,S., Kilpelainen,I. and Annila,A. (2000) Conformations of the regulatory domain of cardiac troponin C examined by residual dipolar couplings. Eur. J. Biochem., 267, 6665-6672.
63. Drohat,A.C., Tjandra,N., Baldisseri,D.M. and Weber,D.J. (1999) The use of dipolar couplings for determining the solution structure of rat apo-S100B(betabeta). Protein Sci., 8, 800-809.
64. Markus,M.A., Gerstner,R.B., Draper,D.E. and Torchia,D.A. (1999) Refining the overall structure and subdomain orientation of ribosomal protein S4 delta41 with dipolar couplings measured by NMR in uniaxial liquid crystalline phases. J. Mol. Biol., 292, 375-387.
65. deAlba,E., De Vries,L., Farquhar,M.G. and Tjandra,N. (1999) Solution structure of human GAIP (Galpha interacting protein): a regulator of G protein signaling. J. Mol. Biol., 291, 927-939.
66. Wu,B., Arumugam,S., Gao,G., Lee,G.I., Semenchenko,V., Huang,W., Brew,K. and Van Doren,S.R. (2000) NMR structure of tissue inhibitor of metalloproteinases-1 implicates localized induced fit in recognition of matrix metalloproteinases. J. Mol. Biol., 295, 257-268.
67. Cornilescu,C.C., 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.
68. Wang,Y.X., Neamati,N., Jacob,J., Palmer,I., Stahl,S.J., Kaufman,J.D., Huang,P.L., Winslow,H.E., Pommier,Y., Wingfield,P.T. et al. (1999) Solution structure of anti-HIV-1 and anti-tumor protein MAP30: structural insights into its multiple functions. Cell, 99, 433-442.
69. 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.
70. Swarbrick,J.D., Bashtannyk,T., Maksel,D., Zhang,X.R., Blackburn,G.M., Gayler,K.R. and Gooley,P.R. (2000) The three-dimensional structure of the Nudix enzyme diadenosine tetraphosphate hydrolase from Lupinus angustifolius L. J. Mol. Biol., 302, 1165-1177.
71. Ramirez,B.E., Voloshin,O.N., Camerini-Otero,R.D. and Bax,A. (2000) Solution structure of DinI provides insight into its mode of RecA inactivation. Protein Sci., 9, 2161-2169.
72. Yuan,X., Shaw,A., Zhang,X., Kondo,H., Lally,J., Freemont,P.S. and Matthews,S. (2001) Solution structure and interaction surface of the C-terminal domain from p47: a major p97-cofactor involved in SNARE disassembly. J. Mol. Biol., 311, 255-263.
73. Cornilescu,G., Lee,B.R., Cornilescu,C.C., Wang,G., Peterkofsky,A. and Clore,G.M. (2002) Solution structure of the phosphoryl transfer complex between the cytoplasmic A domain of the mannitol transporter IIMannitol and HPr of the Escherichia coli phosphotransferase system. J. Biol. Chem., 277, 42289-42298.
74. Garrett,D.S., Seok,Y.J., Peterkofsky,A., Gronenborn,A.M. and Clore,G.M. (1999) Solution structure of the 40,000 Mr phosphoryl transfer complex between the N-terminal domain of enzyme I and HPr. Nature Struct. Biol., 6, 166-173.
75. Chou,J.J., Li,S., Klee,C.B. and Bax,A. (2001) Solution structure of Ca(2+)-calmodulin reveals flexible hand-like properties of its domains. Nature Struct. Biol., 8, 990-997.
76. Weigelt,J., Brown,S.E., Miles,C.S., Dixon,N.E. and Otting,G. (1999) NMR structure of the N-terminal domain of E.coli DnaB helicase: implications for structure rearrangements in the helicase hexamer. Structure Fold Design, 7, 681-690.
77. Baber,J.L., Libutti,D., Levens,D. and Tjandra,N. (1999) High precision solution structure of the C-terminal KH domain of heterogeneous nuclear ribonucleoprotein K, a c-myc transcription factor. J. Mol. Biol., 289, 949-962.
78. Bertini,I., Donaire,A., Jimenez,B., Luchinat,C., Parigi,G., Piccioli,M. and Poggi,L. (2001) Paramagnetism-based versus classical constraints: an analysis of the solution structure of Ca Ln calbindin D9k. J. Biomol. NMR, 21, 85-98.
79. Nair,M., McIntosh,P.B., Frenkiel,T.A., Kelly,G., Taylor,I.A., Smerdon,S.J. and Lane,A.N. (2003) NMR structure of the DNA-binding domain of the cell cycle protein Mbp1 from Saccharomyces cerevisiae. Biochemistry, 42, 1266-1273.
80. Polshakov,V.I., Smirnov,E.G., Birdsall,B., Kelly,G. and Feeney,J. (2002) NMR-based solution structure of the complex of Lactobacillus casei dihydrofolate reductase with trimethoprim and NADPH. J. Biomol. NMR, 24, 67-70.
81. Skelton,N.J., Koehler,M.F., Zobel,K., Wong,W.L., Yeh,S., Pisabarro,M.T., Yin,J.P., Lasky,L.A. and Sidhu,S.S. (2003) Origins of PDZ domain ligand specificity. Structure determination and mutagenesis of the Erbin PDZ domain. J. Biol. Chem., 278, 7645-7654.
82. Arumugam,S. and Van Doren,S.R. (2003) Global orientation of bound MMP-3 and N-TIMP-1 in solution via residual dipolar couplings. Biochemistry, 42, 7950-7958.
83. Wu,Y., Migliorini,M., Yu,P., Strickland,D.K. and Wang,Y.X. (2003) 1H, (13)C and (15)N resonance assignments of domain 1 of receptor associated protein. J. Biomol. NMR, 26, 187-188.
84. Ulmer,T.S., Benjamin,E., Ramirez,B.E., Delaglio,F. and Bax,A. (2003) Evaluation of backbone proton positions and dynamics in a small protein by liquid crystal NMR spectroscopy. J. Am. Chem. Soc., 125, 9179-9191.
85. Deep,S., Walker,K.P., 3rd, Shu,Z. and Hinck,A.P. (2003) Solution structure and backbone dynamics of the TGFbeta type II receptor extracellular domain. Biochemistry, 42, 10126-10139.
86. Massiah,M.A., Saraswat,V., Azurmendi,H.F. and Mildvan,A.S. (2003) Solution structure and NH exchange studies of the MutT pyrophosphohydrolase complexed with Mg(2+) and 8-oxo-dGMP, a tightly bound product. Biochemistry, 42, 10140-10154.
87. Zheng,D., Huang,Y.J., Moseley,H.N., Xiao,R., Aramini,J., Swapna,G.V. and Montelione,G.T. (2003) Automated protein fold determination using a minimal NMR constraint strategy. Protein Sci., 12, 1232-1246.
88. Cai,M., Huang,Y., Zheng,R., Wei,S.Q., Ghirlando,R., Lee,M.S., Craigie,R., Gronenborn,A.M. and Clore,G.M. (1998) Solution structure of the cellular factor BAF responsible for protecting retroviral DNA from autointegration. Nature Struct. Biol., 5, 903-909.
89. 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.
90. Kahmann,J.D., Sass,H.J., Allan,M.G., Seto,H., Thompson,C.J. and Grzesiek,S. (2003) Structural basis for antibiotic recognition by the TipA class of multidrug-resistance transcriptional regulators. EMBO J., 22, 1824-1834.
91. Tossavainen,H., Permi,P., Annila,A., Kilpelainen,I. and Drakenberg,T. (2003) NMR solution structure of calerythrin, an EF-hand calcium-binding protein from Saccharopolyspora erythraea. Eur. J. Biochem., 270, 2505-2512.
92. Brennan,L., Turner,D.L., Messias,A.C., Teodoro,M.L., LeGall,J., Santos,H. and Xavier,A.V. (2000) Structural basis for the network of functional cooperativities in cytochrome c(3) from Desulfovibrio gigas: solution structures of the oxidised and reduced states. J. Mol. Biol., 298, 61-82.
93. Bewley,C.A., Gustafson,K.R., Boyd,M.R., Covell,D.G., Bax,A., Clore,G.M. and Gronenborn,A.M. (1998) Solution structure of cyanovirin-N, a potent HIV-inactivating protein. Nature Struct. Biol., 5, 571-578.
94. Tjandra,N., Omichinski,J.G., Gronenborn,A.M., Clore,G.M. and Bax,A. (1997) Use of dipolar 1H-15N and 1H-13C couplings in the structure determination of magnetically oriented macromolecules in solution. Nature Struct. Biol., 4, 732-738.
95. Starich,M.R., Wikstrom,M., Arst,H.N.,Jr, Clore,G.M. and Gronenborn,A.M. (1998) The solution structure of a fungal AREA protein-DNA complex: an alternative binding mode for the basic carboxyl tail of GATA factors. J. Mol. Biol., 277, 605-620.
96. Starich,M.R., Wikstrom,M., Schumacher,S., Arst,H.N.,Jr, Gronenborn,A.M. and Clore,G.M. (1998) The solution structure of the Leu22→Val mutant AREA DNA binding domain complexed with a TGATAG core element defines a role for hydrophobic packing in the determination of specificity. J. Mol. Biol., 277, 621-634.
97. Chill,J.H., Quadt,S.R., Levy,R., Schreiber,G. and Anglister,J. (2003) The human type I interferon receptor: NMR structure reveals the molecular basis of ligand binding. Structure (Camb.), 11, 791-802.
98. Lauber,T., Neudecker,P., Rosch,P. and Marx,U.C. (2003) Solution structure of human proguanylin: the role of a hormone prosequence. J. Biol. Chem., 278, 24118-24124.
99. Henikoff,S. and Henikoff,J.G. (1992) Amino acid substitution matrices from protein blocks. Proc. Natl Acad. Sci. USA, 89, 10915-10919.
100. Fischer,D., Elofsson,A., Rice,D. and Eisenberg,D. (1996) Assessing the performance of fold recognition methods by means of a comprehensive benchmark. Pacific Symposium on Biocomputing. Hawaii, USA, pp. 300-318.