A structural-informatics approach for tracing β-sheets: Building pseudo-Cα traces for β-strands in intermediate-resolution density maps

Journal of Molecular Biology

Volumn 339, Issue 1, 2004, Pages 117-130

  Kong, Yifei ^a   Zhang, Xing ^b   Baker, Timothy S ^b   Ma, Jianpeng ^a,c  

^a BAYLOR COLLEGE OF MEDICINE   (United States)

^b PURDUE UNIVERSITY   (United States)

^c Rice University   (United States)

Author keywords

bioinformatics; cryo EM, electron cryomicroscopy; D, dimensional; intermediate resolution density maps; macromolecular complexes; PDB, Protein Data Bank; rms, root mean square; secondary structural elements

Indexed keywords

ARTICLE; BETA SHEET; CRYSTAL STRUCTURE; DENSITY; MATHEMATICAL COMPUTING; PRIORITY JOURNAL; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE; QUANTITATIVE ANALYSIS; REOVIRUS; STRUCTURE ANALYSIS;

REOVIRUS SP.;

EID: 2342538953     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2004.03.038     Document Type: Article

References (51)

1. Chance M.R., Bresnick A.R., Burley S.K., Jiang J.S., Lima C.D., Sali A., et al. Structural genomics: a pipeline for providing structures for the biologist. Protein Sci. 11:2002;723-738
2. DeRosier D.J., Harrison S.C. Macromolecular assemblages. Sizing things up. Curr. Opin. Struct. Biol. 7:1997;237-238
3. Bottcher B., Wynne S.A., Crowther R.A. Determination of the fold of the core protein of hepatitis B virus by electron cryomicroscopy. Nature. 386:1997;88-91
4. Conway J.F., Cheng N., Zlotnick A., Wingfield P.T., Stahl S.J., Steven A.C. Visualization of a 4-helix bundle in the hepatitis B virus capsid by cryo-electron microscopy. Nature. 386:1997;91-94
5. Mancini E.J., Clarke M., Gowen B.E., Rutten T., Fuller S.D. Cryo-electron microscopy reveals the functional organization of an enveloped virus, Semliki Forest virus. Mol. Cell. 5:2000;255-266
6. Zhou Z.H., Dougherty M., Jakana J., He J., Rixon F.J., Chiu W. Seeing the herpesvirus capsid at 8.5 Å Science. 288:2000;877-880
7. Zhou Z.H., Liao W., Cheng R.H., Lawson J.E., McCarthy D.B., Reed L.J., Stoops J.K. Direct evidence for the size and conformational variability of the pyruvate dehydrogenase complex revealed by three-dimensional electron microscopy. The "breathing" core and its functional relationship to protein dynamics. J. Biol. Chem. 276:2001;21704-21713
8. Zhou Z.H., Baker M.L., Jiang W., Dougherty M., Jakana J., Dong G., et al. Electron cryomicroscopy and bioinformatics suggest protein fold models for rice dwarf virus. Nature Struct. Biol. 8:2001;868-873
9. Kuhn R.J., Zhang W., Rossmann M.G., Pletnev S.V., Corver J., Lenches E., et al. Structure of dengue virus: implications for flavivirus organization, maturation, and fusion. Cell. 108:2002;717-725
10. Li H., DeRosier D., Nicholson W., Nogales E., Downing K. Microtubule structure at 8 Å resolution. Structure (Camb). 10:2002;1317
11. Zhang X., Shaw A., Bates P.A., Newman R.H., Gowen B., Orlova E., et al. Structure of the AAA ATPase p97. Mol. Cell. 6:2000;1473-1484
12. Ban N., Nissen P., Hansen J., Capel M., Moore P.B., Steitz T.A. Placement of protein and RNA structures into a 5 Å-resolution map of the 50S ribosomal subunit. Nature. 400:1999;841-847
13. Ban N., Freeborn B., Nissen P., Penczek P., Grassucci R.A., Sweet R., et al. A 9 Å resolution X-ray crystallographic map of the large ribosomal subunit. Cell. 93:1998;1105-1115
14. Ban N., Nissen P., Hansen J., Moore P.B., Steitz T.A. The complete atomic structure of the large ribosomal subunit at 2.4 Å resolution. Science. 289:2000;905-920
15. Jiang W., Baker M.L., Ludtke S.J., Chiu W. Bridging the information gap: computational tools for intermediate resolution structure interpretation. J. Mol. Biol. 308:2001;1033-1044
16. Kong Y., Ma J. A structural-informatics approach for mining β-sheets: locating sheets in intermediate-resolution density maps. J. Mol. Biol. 332:2003;399-413
17. Wang Q., Buckle A.M., Fersht A.R. Stabilization of GroEL minichaperones by core and surface mutations. J. Mol. Biol. 298:2000;917-926
18. Verbeek J.J., Vlassis N., Krose B. A k-segments algorithm for finding principal curves. Pattern Recogn. Letters. 23:2002;1009-1017
19. Ludtke S.J., Baldwin P.R., Chiu W. EMAN: semiautomated software for high-resolution single-particle reconstructions. J. Struct. Biol. 128:1999;82-97
20. Rees D.C., Lewis M., Lipscomb W.N. Refined crystal structure of carboxypeptidase A at 1.54 Å resolution. J. Mol. Biol. 168:1983;367-387
21. Wittinghofer F., Krengel U., John J., Kabsch W., Pai E.F. Three-dimensional structure of p21 in the active conformation and analysis of an oncogenic mutant. Environ. Health Perspect. 93:1991;11-15
22. Hoover D.M., Ludwig M.L. A flavodoxin that is required for enzyme activation: the structure of oxidized flavodoxin from Escherichia coli at 1.8 Å resolution. Protein Sci. 6:1997;2525-2537
23. Arnold E., Rossmann M.G. The use of molecular-replacement phases for the refinement of the human rhinovirus 14 structure. Acta Crystallog. sect. A. 44:1988;270-282
24. Khan A.R., Baker B.M., Ghosh P., Biddison W.E., Wiley D.C. The structure and stability of an HLA-A*0201/octameric tax peptide complex with an empty conserved peptide-N-terminal binding site. J. Immunol. 164:2000;6398-6405
25. Eklund H., Samma J.P., Wallen L., Branden C.I., Akeson A., Jones T.A. Structure of a triclinic ternary complex of horse liver alcohol dehydrogenase at 2.9 Å resolution. J. Mol. Biol. 146:1981;561-587
26. Mayer S.M., Gormal C.A., Smith B.E., Lawson D.M. Crystallographic analysis of the MoFe protein of nitrogenase from a nifV mutant of Klebsiella pneumoniae identifies citrate as a ligand to the molybdenum of iron molybdenum cofactor (FeMoco). J. Biol. Chem. 277:2002;35263-35266
27. Steinbacher S., Seckler R., Miller S., Steipe B., Huber R., Reinemer P. Crystal structure of P22 tailspike protein: interdigitated subunits in a thermostable trimer. Science. 265:1994;383-386
28. Wilson D.K., Bohren K.M., Gabbay K.H., Quiocho F.A. An unlikely sugar substrate site in the 1.65 Å structure of the human aldose reductase holoenzyme implicated in diabetic complications. Science. 257:1992;81-84
29. Zanotti G., Panzalorto M., Marcato A., Malpeli G., Folli C., Berni R. Structure of pig plasma retinal-binding protein at 1.65 Å resolution. Acta Crystallog. sect. D. 54:1998;1049-1052
30. Gaudet R., Savage J.R., McLaughlin J.N., Willardson B.M., Sigler P.B. A molecular mechanism for the phosphorylation-dependent regulation of heterotrimeric G proteins by phosducin. Mol. Cell. 3:1999;649-660
31. Zhang X., Walker S.B., Chipman P.R., Nibert M.L., Baker T.S. Reovirus polymerase lambda 3 localized by cryo-electron microscopy of virions at a resolution of 7.6 Å Nature Struct. Biol. 10:2003;1011-1018
32. Reinisch K.M., Nibert M.L., Harrison S.C. Structure of the reovirus core at 3.6 Å resolution. Nature. 404:2000;960-967
33. Murzin A.G., Brenner S.E., Hubbard T., Chothia C. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247:1995;536-540
34. Lo Conte L., Brenner S.E., Hubbard T., Chothia C., Murzin A.G. SCOP database in 2002: refinements accommodate structural genomics. Nucl. Acids Res. 30:2002;264-267
35. Skolnick J., Kolinski A., Kihara D., Betancourt M., Rotkiewicz P., Boniecki M. Ab initio protein structure prediction via a combination of threading, lattice folding, clustering, and structure refinement. Proteins: Struct. Funct. Genet. Suppl. 5:2001;149-156
36. Miller R.T., Jones D.T., Thornton J.M. Protein fold recognition by sequence threading: tools and assessment techniques. FASEB J. 10:1996;171-178
37. Elofsson A., Fischer D., Rice D.W., Le Grand S.M., Eisenberg D. A study of combined structure/sequence profiles. Fold. Des. 1:1996;451-461
38. Lu L., Lu H., Skolnick J. MULTIPROSPECTOR: an algorithm for the prediction of protein-protein interactions by multimeric threading. Proteins: Struct. Funct. Genet. 49:2002;350-364
39. Rossmann M.G. Fitting atomic models into electron-microscopy maps. Acta Crystallog. sect. D. 56:2000;1341-1349
40. Wetzel R. Ideas of order for amyloid fibril structure. Structure (Camb). 10:2002;1031
41. Jimenez J.L., Nettleton E.J., Bouchard M., Robinson C.V., Dobson C.M., Saibil H.R. The protofilament structure of insulin amyloid fibrils. Proc. Natl Acad. Sci. USA. 99:2002;9196-9201
42. Serpell L.C., Smith J.M. Direct visualization of the β-sheet structure of synthetic Alzheimer's amyloid. J. Mol. Biol. 299:2000;225-231
43. Ankerst, M., Breunig, M. M., Kriegel, H. P. & Sander, J. (1999). OPTICS: ordering points to identify the clustering structure. Proc. ACM SIGMOD'99 Int. Conf. Management Data, pp. 49-60, ACM Press, New York, NY.
44. Kundur, D. & Hatzinakos, D. (1995). A novel recursive filtering method for blind image restoration. In Proc. IASTED Int. Conf. Signal Image Processing, pp. 428-431, IEEE/IASTED, Las Vegas, NV.
45. Volkmann N. A novel three-dimensional variant of the watershed transform for segmentation of electron density maps. J. Struct. Biol. 138:2002;123-129
46. Ayers G.R., Dainty J.C. Iterative blind deconvolution method and its applications. Opt. Letters. 13:1988;547-549
47. Davey B.L.K., Lane R.G., Bates R.H.T. Blind deconvolution of noisy complex-value image. Opt. Commun. 69:1989;353-356
48. McCallum B.C. Blind deconvolution by simulated annealing. Opt. Commun. 75:1990;101-105
49. Katsaggelos A.K. Digital Image Restoration. 1991;Springer, New York
50. Frishman D., Argos P. Knowledge-based protein secondary structure assignment. Proteins: Struct. Funct. Genet. 23:1995;566-579
51. Kraulis P.J. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallog. 24:1991;946-950