A structural-informatics approach for mining β-sheets: Locating sheets in intermediate-resolution density maps

Journal of Molecular Biology

Volumn 332, Issue 2, 2003, Pages 399-413

  Kong, Yifei ^a   Ma, Jianpeng ^a,b  

^a BAYLOR COLLEGE OF MEDICINE   (United States)

^b Rice University   (United States)

Author keywords

Bioinformatics; Intermediate resolution density maps; Macromolecular complexes; Secondary structural elements

Indexed keywords

AMYLOID;

ALGORITHM; ARTICLE; BETA SHEET; CRYOELECTRON MICROSCOPY; CRYSTAL STRUCTURE; DENSITY; GENE MAPPING; GENOMICS; MORPHOLOGY; PRIORITY JOURNAL; PROTEIN STRUCTURE;

EID: 0041507094     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0022-2836(03)00859-3     Document Type: Article

References (51)

1. DeRosier D.J., Harrison S.C. Macromolecular assemblages. Sizing things up. Curr. Opin. Struct. Biol. 7:1997;237-238.
2. 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.
3. 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.
4. 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.
5. 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.
6. 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.
7. 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.
8. 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.
9. Li H., DeRosier D., Nicholson W., Nogales E., Downing K. Microtubule structure at 8 Å resolution. Structure (Camb). 10:2002;1317.
10. 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.
11. 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 50 S ribosomal subunit. Nature. 400:1999;841-847.
12. 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.
13. 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.
14. 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.
15. 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.
16. 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. 2001;149-156.
17. 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.
18. Kihara D., Lu H., Kolinski A., Skolnick J. TOUCHSTONE: an ab initio protein structure prediction method that uses threading-based tertiary restraints. Proc. Natl Acad. Sci. USA. 98:2001;10125-10130.
19. 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.
20. Wetzel R. Ideas of order for amyloid fibril structure. Structure (Camb). 10:2002;1031.
21. 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.
22. 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.
23. 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.
24. 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.
25. 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.
26. Wang Q., Buckle A.M., Fersht A.R. Stabilization of GroEL minichaperones by core and surface mutations. J. Mol. Biol. 298:2000;917-926.
27. 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.
28. 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.
29. 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.
30. 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.
31. 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.
32. 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.
33. 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.
34. Ludtke S.J., Baldwin P.R., Chiu W. EMAN: semiautomated software for high-resolution single-particle reconstructions. J. Struct. Biol. 128:1999;82-97.
35. Samatey F.A., Imada K., Nagashima S., Vonderviszt F., Kumasaka T., Yamamoto M., Namba K. Structure of the bacterial flagellar protofilament and implications for a switch for supercoiling. Nature. 410:2001;331-337.
36. Mimori Y., Yamashita I., Murata K., Fujiyoshi Y., Yonekura K., Toyoshima C., Namba K. The structure of the R-type straight flagellar filament of Salmonella at 9 Å resolution by electron cryomicroscopy. J. Mol. Biol. 249:1995;69-87.
37. Vaidehi N., Floriano W.B., Trabanino R., Hall S.E., Freddolino P., Choi E.J. Prediction of structure and function of G protein-coupled receptors. Proc. Natl Acad. Sci. USA. 99:2002;12622-12627.
38. Baker D., Sali A. Protein structure prediction and structural genomics. Science. 294:2001;93-96.
39. Bonneau R., Strauss C.E., Rohl C.A., Chivian D., Bradley P., Malmstrom L., Robertson T., Baker D. De novo prediction of three-dimensional structures for major protein families. J. Mol. Biol. 322:2002;65-78.
40. Bonneau R., Ruczinski I., Tsai J., Baker D. Contact order and ab initio protein structure prediction. Protein Sci. 11:2002;1937-1944.
41. Ruczinski I., Kooperberg C., Bonneau R., Baker D. Distributions of beta sheets in proteins with application to structure prediction. Proteins: Struct. Funct. Genet. 48:2002;85-97.
42. Mallick P., Weiss R., Eisenberg D. The directional atomic solvation energy: an atom-based potential for the assignment of protein sequences to known folds. Proc. Natl Acad. Sci. USA. 99:2002;16041-16046.
43. Simons K.T., Strauss C., Baker D. Prospects for ab initio protein structural genomics. J. Mol. Biol. 306:2001;1191-1199.
44. Fischer D., Eisenberg D. Protein fold recognition using sequence-derived predictions. Protein Sci. 5:1996;947-955.
45. Sánchez R., Sali A. Comparative protein structure modeling in genomics. J. Comput. Phys. 151:1999;388-401.
46. 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.
47. 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.
48. Zerovnik E. Amyloid-fibril formation. Proposed mechanisms and relevance to conformational disease. Eur. J. Biochem. 269:2002;3362-3371.
49. Raghava G.P.S. Protein secondary structure prediction using nearest neighbor and neural network approach. Fourth Community Wide Experiment on the Critical Assessmant of Techniques for Protein Structure Prediction, December 3-7. 2000;. pp. 75-76.
50. Ankerst M., Breunig M.M., Kriegel H.P., Sander J. OPTICS: ordering points to identify the clustering structure. Proc. ACM SIGMOD'99 Int. Conf. on Management of Data. 1999;. pp. 49-60.
51. Frishman D., Argos P. Knowledge-based protein secondary structure assignment. Proteins: Struct. Funct. Genet. 23:1995;566-579.