Challenges at the frontiers of structural biology

Trends in Cell Biology

Volumn 9, Issue 12, 1999, Pages

  Sali, Andrej ^a   Kuriyan, John ^a  

^a ROCKEFELLER UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

M PROTEIN;

GENE SEQUENCE; GENOME; MACROMOLECULE; MOLECULAR SIZE; PRIORITY JOURNAL; PROTEIN ASSEMBLY; PROTEIN DOMAIN; PROTEIN STRUCTURE; REVIEW;

ANIMALS; BIOLOGY; HUMANS; PROTEIN CONFORMATION; PROTEINS;

EID: 0033400935     PISSN: 09628924     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0962-8924(99)01685-2     Document Type: Review

References (44)

1. Orengo C.A.et al. Protein superfamilies and domain superfolds. Nature. 372:1994;631-634.
2. Holm L., Sander C. Mapping the protein universe. Science. 273:1996;595-602.
3. Brenner S.E.et al. Population statistics of protein structures: lessons from structural classifications. Curr. Opin. Struct. Biol. 7:1997;369-376.
4. Hubbard T.J.P.et al. SCOP: A structural classification of proteins database. Nucleic Acids Res. 27:199;254-256.
5. Holm L., Sander C. Protein folds and families: sequence and structure alignments. Nucleic Acids Res. 27:1999;244-247.
6. Orengo C.A.et al. The CATH database provides insights into protein-structure-function relationship. Nucleic Acids Res. 27:1999;275-279.
7. Terwilliger T.C.et al. Class-directed structure determination: Foundation for a Protein Structure Initiative. Protein Sci. 7:1998;1851-1856.
8. Sali A. 100,000 protein structures for the biologist. Nat. Struct. Biol. 5:1998;1029-1032.
9. Zarembinski T.I.et al. Structure-based assignment of the biochemical function of a hypothetical protein: a test case of structural genomics. Proc. Natl. Acad. Sci. U. S. A. 95:1998;15189-15193.
10. Burley S.K.et al. Structural genomics: beyond the Human Genome Project. Nat. Genet. 23:1999;151-157.
11. Cort J.R.et al. A phylogenetic approach to target selection for structural genomics: solution structure of YciH. Nucleic Acids Res. 27:1999;4018-4027.
12. Fischer D., Eisenberg D. Fold recognition using sequence-derived predictions. Protein Sci. 5:1996;947-955.
13. Sánchez R., Sali A. Large-scale protein structure modeling of the Saccharomyces cerevisiae genome. Proc. Natl. Acad. Sci. U. S. A. 95:1998;13597-13602.
14. Teichmann S.A.et al. Structural assignments to the Mycoplasma genitalium proteins show extensive gene duplications and domain rearrangements. Proc. Natl. Acad. Sci. U. S. A. 22:1998;14658-14663.
15. Huynen M.et al. Homology-based fold predictions for Mycoplasma genitalium proteins. J. Mol. Biol. 280:1998;323-326.
16. Rychlewski L.et al. Fold and function predictions for Mycoplasma genitalium proteins. Fold. Des. 3:1998;229-238.
17. Jones D.T. Genthreader: An efficient and reliable protein fold recognition method for genomic sequences. J. Mol. Biol. 287:1999;797-815.
18. Guex N.et al. Protein modelling for all. Trends Biochem. Sci. 24:1999;364-367.
19. Wüthrich K. The second decade - into the third millennium. Nat. Struct. Biol. 5:1998;492-495.
20. Hendrickson W.A. Determination of macromolecular structures from anomalous diffraction of synchrotron data. Science. 254:1991;51-58.
21. Walsh M.A.et al. Taking MAD to the extreme: ultrafast protein structure determination. Acta Crystallogr. D55:1999;1168-1173.
22. Blundell T.L.et al. Knowledge-based prediction of protein structures and the design of novel molecules. Nature. 326:1987;347-352.
23. Martí-Renom M.A.et al. Comparative protein structure modeling of genes and genomes. Annu. Rev. Biophys. Biomol. Struct. 1999;. in press.
24. Ring C.S.et al. Structure-based inhibitor design by using protein models for the development of antiparasitic agents. Proc. Natl. Acad. Sci. U. S. A. 90:1993;3583-3587.
25. Sánchez R., Sali A. ModBase: A database of comparative protein structure models. Bioinformatics. 1999;. in press.
26. Conte L.L.et al. The atomic structure of protein-protein recognition sites. J. Mol. Biol. 285:1999;2177-2198.
27. Nadassy K.et al. Structural features of protein-nucleic acid recognition sites. Biochemistry. 38:1999;1999-2017.
28. Sicheri F., Kuriyan J. Structures of Src-family tyrosine kinases. Curr. Opin. Struct. Biol. 7:1997;777-785.
29. Gopaul D.N.et al. Structure of the Holliday junction intermediate in Cre-loxP site-specific recombination. EMBO J. 17:1998;4175-4187.
30. Garboczi D.N.et al. Structure of the complex between human T-cell receptor, viral peptide and HLA-A2. Nature. 384:1996;134-141.
31. Garcia K.C.et al. An αβ T cell receptor structure at 2.5 Å and its orientation in the TCR-MHC complex. Science. 274:1996;209-219.
32. Doublie S.et al. An open and closed case for all polymerases. Struct. Fold. Des. 7:1999;R31-R35.
33. Patikoglou G., Burley S.K. Eukaryotic transcription factor-DNA complexes. Annu. Rev. Biophys. Biomol. Struct. 26:1997;289-325.
34. Doyle D.A.et al. The structure of the potassium channel: molecular basis of conduction and selectivity. Science. 280:1998;69-77.
35. von Bohlen K.et al. Characterization and preliminary attempts for derivatization of crystals of large ribosomal subunits from Haloarcula marismortui diffracting to 3 Å resolution. J. Mol. Biol. 222:1991;11-15.
36. Ban N.et al. Placement of protein and RNA structures into a 5 Å-resolution map of the 50S ribosomal subunit. Nature. 400:1999;841-847.
37. Gouet P.et al. The highly ordered double-stranded RNA genome of bluetongue virus revealed by crystallography. Cell. 97:1999;481-490.
38. Iwata S.et al. Structure at 2.8 Å resolution of cytochrome c oxidase from Paracoccus denitrificans. Nature. 376:1995;660-669.
39. Tsukihara T.et al. Structures of metal sites of oxidized bovine heart cytochrome c oxidase at 2.8 Å Science. 269:1995;1069-1074.
40. 1-ATPase from bovine heart mitochondria. Nature. 370:1994;621-628.
41. Luger K.et al. Crystal structure of the nucleosome core particle at 2.8 Å resolution. Nature. 389:1997;251-260.
42. Schindler T.et al. Crystal structure of Hck in complex with a Src family-selective tyrosine kinase inhibitor. Mol. Cell. 3:1999;639-648.
43. Xu W.et al. Crystal structures of c-Src reveal features of its autoinhibitory mechanism. Mol. Cell. 3:1999;629-638.
44. Yamaguchi H., Hendrickson W.A. Structural basis for activation of the human lymphocyte kinase Lck upon tyrosine phosphorylation. Nature. 384:1996;484-489.