Analysis of structure and function of putative surface-exposed proteins encoded in the Streptococcus pneumoniae genome: A bioinformatics-based approach to vaccine and drug design

Critical Reviews in Biochemistry and Molecular Biology

Volumn 38, Issue 2, 2003, Pages 143-168

  Rigden, Daniel J ^a   Galperin, Michael Y ^b   Jedrzejas, Mark J ^c  

^a EMBRAPA RECURSOS GENÉTICOS E BIOTECNOLOGIA   (Brazil)

^b NATIONAL INSTITUTES OF HEALTH   (United States)

^c CHILDREN S HOSPITAL OAKLAND RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; CHOLINE; DIPHTHERIA VACCINE; HISTIDINE; HYALURONIDASE; LIPID; MEMBRANE PROTEIN; MUCIN; PENICILLIN DERIVATIVE; PEPTIDOGLYCAN; PNEUMOCOCCUS VACCINE; POLYSACCHARIDE VACCINE; PROTEIN PSAA; PROTEIN PSPA; UNCLASSIFIED DRUG; VANCOMYCIN; VIRULENCE FACTOR;

AMINO ACID SEQUENCE; ANTIBIOTIC RESISTANCE; BACTERIAL GENOME; BACTERIAL MEMBRANE; BACTERIAL STRAIN; BACTERIAL VIRULENCE; BIOINFORMATICS; COMMUNICABLE DISEASE; DRUG APPROVAL; DRUG EFFICACY; GENOME ANALYSIS; MENINGITIS; NONHUMAN; NUCLEOTIDE SEQUENCE; OTITIS MEDIA; PATHOGENICITY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FOLDING; PROTEIN FUNCTION; PROTEIN STRUCTURE; REVIEW; SEQUENCE ANALYSIS; STREPTOCOCCUS INFECTION; STREPTOCOCCUS PNEUMONIAE; STRUCTURE ANALYSIS; THREE DIMENSIONAL IMAGING;

BACTERIA (MICROORGANISMS); NEGIBACTERIA; POSIBACTERIA; STREPTOCOCCUS; STREPTOCOCCUS PNEUMONIAE;

EID: 0038741805     PISSN: 10409238     EISSN: None     Source Type: Journal    
DOI: 10.1080/713609215     Document Type: Review

References (141)

1. Adamou, J. E., Heinrichs, J. H., Erwin, A. L., Walsh, W., Gayle, T., Dormitzer, M., Dagan, R., Brewah, Y. A, Barren, P., Lathigra, R., Langermann, S., Koenig, S., and Johnson, S. 2001. Identification and characterization of a novel family of pneumococcal proteins that are protective against sepsis. Infect. Immun. 69: 949-958.
2. Alexander, J. E., Lock, R. A., Peeters, C. C., Poolman, J. T., Andrew, P. W., Mitchell, T. J., Hansman, D., and Paton, J. C. 1994. Immunization of mice with pneumolysin toxoid confers a significant degree of protection against at least nine serotypes of Streptococcus pneumoniae. Infect. Immun. 62: 5683-5688.
3. Aloy, P., Querol, E., Aviles, F. X., and Steinberg, M.J. 2001. Automated structure-based prediction of functional sites in proteins: Applications to assessing the validity of inheriting protein function from homology in genome annotation and to protein docking. J. Mol. Biol. 311: 395-408.
4. Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D. J. 1997. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res. 25: 3389-3402.
5. Anon. 1985. Acute respiratory infections in underfives. 15 million deaths a year. Lancet 2: 699-701.
6. Banas, J. A., Russell, R. R., and Ferretti, J. J. 1990. Sequence analysis of the gene for the glucan-binding protein of Streptococcus mutans Ingbritt. Infect. Immun. 58: 667-673.
7. Bartlett, G.J., Porter, C.T., Borkakoti, N., and Thornton, J.M. 2002. Analysis of catalytic residues in enzyme active sites. J. Mol. Biol. 324: 105-121.
8. Bateman, A., Birney, E., Cerruti, L., Durbin, R., Etwiller, L., Eddy, S. R., Griffiths-Jones, S., Howe, K. L., Marshall, M., and Sonnhammer, E. L. 2002. The Pfam protein families database. Nucleic Acids Res. 30: 276-280.
9. Berks, B. C., Sargent, F., and Palmer, T. 2000. The Tat protein export pathway. Mol. Microbiol. 35: 260-274.
10. Berry, A. M. and Paton, J. C. 2000. Additive attenuation of virulence of Streptococcus pneumoniae by mutation of the genes encoding pneumolysin and other putative pneumococcal virulence proteins. Infect. Immun. 68: 133-140.
11. Berry, A. M. and Paton, J. C. 1996. Sequence heterogeneity of PsaA, a 37-kilodalton putative adhesin essential for virulence of Streptococcus pneumoniae. Infect. Immun. 64: 5255-5262.
12. Berry, A. M., Lock, R. A., and Paton, J. C. 1996. Cloning and characterization of nanB, a second Streptococcus pneumoniae neuraminidase gene, and purification of the NanB enzyme from recombinant Escherichia coli. J. Bacteriol. 178: 4854-4860.
13. Berry, A. M., Lock, R. A., Thomas, S. M., Rajan, D. P., Hansman, D., and Paton, J. C. 1994. Cloning and nucleotide sequence of the Streptococcus pneumoniae hyaluronidase gene and purification of the enzyme from recombinant Escherichia coli. Infect. Immun. 62: 1101-1108.
14. Bethe, G., Nau, R., Wellmer, A., Hakenbeck, R., Reinert, R. R., Heinz, H. P., and Zysk, G. 2001. The cell wall-associated serine protease PrtA: a highly conserved virulence factor of Streptococcus pneumoniae. FEMS Microbiol. Lett. 205: 99-104.
15. Brady, G. P. and Stouten, P. F. W. 2000. Fast prediction and visualization of protein binding pockets with PASS. J. Comp. Aided. Mol. Des. 14: 383-401.
16. Brooks-Walter, A., Briles, D. E., and Hollingshead, S. K. 1999. The pspC gene of Streptococcus pneumoniae encodes a polymorphic protein, PspC, which elicits cross-reactive antibodies to PspA and provides immunity to pneumococcal bacteremia. Infect. Immun. 67: 6533-6542.
17. Brun, E., Johnson, P. E., Creagh, A. L., Tomme, P., Webster, P., Haynes, C. A., and McIntosh, L. P. 2000. Structure and binding specificity of the second N-terminal cellulose-binding domain from Cellulomonas fimi endoglucanase C. Biochemistry 39: 2445-2458.
18. Bujnicki, J. M., Elofsson, A., Fischer, D., and Rychlewski L. 2001a. LiveBench-2: large-scale automated evaluation of protein structure prediction servers. Proteins 45 (Suppl 5): 184-191.
19. Bujnicki, J. M., Elofsson, A., Fischer, D., and Rychlewski, L. 2001b. Structure prediction meta server. Bioinformatics 17: 750-751.
20. Camara, M., Boulnois, G. J., Andrew, P. W., and Mitchell, T. J. 1994. A neuraminidase from Streptococcus pneumoniae has the features of a surface protein. Infect. Immun. 62: 3688-3695.
21. Chung, S. Y. and Subbiah, S. 1996. A structural explanation for the twilight zone of protein sequence homology. Structure 4: 1123-1127.
22. Clarke, V. A., Platt, N., and Butters, T. D. 1995. Cloning and expression of the N-acetylglucosaminidase gene from Streptococcus pneumoniae. Generation of truncated enzymes with modified aglycon specificity. J. Biol. Chem. 270: 8805-8814.
23. Cohen, J. 1994. Bumps on the vaccine road. Science 265: 1371-1373.
24. Coutinho, P. M. and Henrissat, B. 1999a. Carbohydrate-active enzymes: an integrated database approach. In: Recent Advances in Carbohydrate Bioengineering. pp. 3-12. Gilbert, H.J., Davies, G., Henrissat, B., and Svensson, B., Eds., The Royal Society of Chemistry, Cambridge.
25. Coutinho, P. M. and Henrissat, B. 1999b. The modular structure of cellulases and other carbohydrate-active enzymes: An integrated database approach. In: Genetics. Biochemistry and Ecology of Cellulose Degradation. pp. 15-23. Ohmiya, K., Hayashi, K., Sakka, K., Kobayashi, Y., Karita, S., and Kimura, T., Eds., Uni Publishers, Tokyo.
26. Coutinho, P.M. and Henrissat, B. 1999c. Carbohydrate-active Enzymes server at URL: http://afmb.cnrs-mrs.fr/~cazy/CAZY/index.html
27. Crennell, S. J., Garman, E. F., Laver, W. G., Vimr, E. R., and Taylor, G. L. 1993. Crystal structure of a bacterial sialidase (from Salmonella tryphimurium LT2) shows the same fold as an influenza virus neuraminidase. Proc. Natl. Acad. Sci. U.S.A. 90: 9852-9856.
28. Crooks, G. E., Hon, G., Chandonia, J. M., and Brenner, S. E. 2003. WebLogo: A sequence logo generator. Genome Res. 13: (in press).
29. Cundell, D. R., Gerard, N. P., Gerard, C., Idanpaan-Heikkila, I., and Tuomanen, E. I. 1995. Streptococcus pneumoniae anchor to activated human cells by the receptor for platelet-activating factor. Nature 377: 435-438.
30. Deivanayagam, C. C., Rich, R. L., Carson, M., Owens, R. T., Danthuluri, S., Bice, T., Hook, M., and Narayana, S. V. 2000. Novel fold and assembly of the repetitive B region of the Staphylococcus aureus collagen-binding surface protein. Structure 8: 67-78.
31. DeLano, W.L. 2002. The PyMOL Molecular Graphics System on World Wide Web http://www.pymol.org.
32. Devos, D. and Valencia, A. 2000. Practical limits of function prediction. Proteins 41: 98-107.
33. Devos, D. and Valencia, A. 2001. Intrinsic errors in genome annotation. Trends Genet. 17: 429-431.
34. Dintilhac, A., Alloing, G., Granadel, C., and Claverys, J. P. 1997. Competence and virulence of Streptococcus pneumoniae: Adc and PsaA mutants exhibit a requirement for Zn and Mn resulting from inactivation of putative ABC metal permeases. Mol. Microbiol. 25: 727-739.
35. Dopazo, J., Mendoza, A., Herrero, J., Caldara, F., Humbert, Y., Friedli, L., Guerrier, M., Grand-Schenk, E., Gandin, C., de Francesco, M., Polissi, A., Buell, G., Feger, G., Garcia, E., Peitsch, M., and Garcia-Bustos, J.F. 2001. Annotated draft genomic sequence from a Streptococcus pneumoniae type 19F clinical isolate. Microb. Drug Resist. 7: 99-125.
36. Durbin, R., Eddy, S., Krogh. A., and Mitchison, A. 1998. Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids. Cambridge University Press, Cambridge.
37. Fedson, D. S. and Musher, D. M. 1994. Pneumococcal vaccine. In: Vaccines. 2nd ed., pp. 517-563. Plotkin, S. A. and Mortimer, E. A., Jr., Eds.,WB Saunders, Philadelphia, PA.
38. Feldman, C., Munro, N. C., Jeffery, P. K., et al. 1992. Pneumolysin induces the salient histologic features of pneumococcal infection in the rat lung in vivo. Am. J. Respir. Cell. Mol. Biol. 5: 416-423.
39. Fernandez-Tornero, C., Garcia, E., Lopez, R., Gimenez-Gallego, G., and Romero, A. 2002. Two new crystal forms of the choline-binding domain of the major pneumococcal autolysin: Insights into the dynamics of the active homodimer. J. Mol. Biol. 321: 163-173.
40. Fernandez-Tornero, C., Lopez, R., Garcia, E., Gimenez-Gallego, G., and Romero, A. 2001. A novel solenoid fold in the cell wall anchoring domain of the pneumococcal virulence factor LytA. Nat. Struct. Biol. 8: 1020-1024.
41. Fischer, D., Elofsson, A., Rychlewski, L., Pazos, F., Valencia, A., Rost, B., Ortiz, A. R., and Dunbrack, R. L., Jr. 2001. CAFASP2: The second critical assessment of fully automated structure prediction methods. Proteins 45 (Suppl 5): 171-83.
42. Frishman, D., Albermann, K., Hani, J., Heumarm, K., Metanomski, A., Zollner, A., and Mewes, H. W. 2001. Functional and structural genomics using PED-ANT. Bioinformatics 17: 44-57.
43. Galperin, M.Y. and Koonin, E.V. 1999. Searching for drug targets in microbial genomes. Curr. Opin. Biotechnol. 10: 571-578.
44. George, R. A. and Heringa, J. 2002. SnapDRAGON: a method to delineate protein structural domains from sequence data. J. Mol. Biol. 316: 839-851.
45. Glass, J. I., Belanger, A. E., and Robertson, G. T. 2002. Streptococcus pneumoniae as a genomics platform for broad-spectrum antibiotic discovery. Curr. Opin. Microbiol. 5: 338-342.
46. Gouet, P., Courcelle, E., Stuart, D. I., and Metoz, F. 1999. ESPript: Multiple sequence alignments in PostScript. Bioinformatics 15: 305-308.
47. Gracy, J. and Argos, P. 1998. DOMO: A new database of aligned protein domains. Trends Biochem Sci. 23: 495-497.
48. Gray, B. M., Converse, G. M., 3rd, and Dillon, H. C., Jr. 1980. Epidemiologic studies of Streptococcus pneumoniae in infants: Acquisition, carriage, and infection during the first 24 months of life. J. Infect. Dis. 142: 923-933.
49. Heger, A. and Holm, L. 2000. Rapid automatic detection and alignment of repeats in protein sequences. Proteins 41: 224-237.
50. Holm, L. and Sander, C. 1997. An evolutionary treasure: unification of a broad set of amidohydrolases related to urease. Proteins 28: 72-82.
51. Hoskins, J., Alborn, W. E. Jr, Arnold, J.. Blaszczak, L. C., Burgett, S., DeHoff, B. S, Estrem, S. T., Fritz, L., Fu, D. J, Fuller, W., Geringer, C., Gilmour, R., Glass. J. S., Khoja, H., Kraft, A. R., Lagace, R. E., LeBlanc, D. J., Lee, L. N., Lefkowitz, E. J., Lu, J., Matsushima. P., McAhren, S. M., McHenney, M., McLeaster, K., Mundy, C. W., Nicas, T. I., Norris, F. H., O'Gara, M., Peery, R. B., Robertson, G. T., Rockey, P., Sun, P. M., Winkler, M. E., Yang, Y., Young-Bellido, M., Zhao, G., Zook, C. A., Baltz, R. H.. Jaskunas, S. R., Rosteck, P. R. Jr, Skatrud, P. L., and Glass J. I. 2001. Genome of the bacterium Streptococcus pneumoniae strain R6. J. Bacteriol. 183: 5709-5717.
52. Ilangovan, U., Ton-That, H., Iwahara, J., Schneewind, O., and Clubb, R. T. 2001. Structure of sortase, the transpeptidase that anchors proteins to the cell wall of Staphylococcus aurezts. Proc. Natl. Acad. Sci. USA 98: 6056-6061.
53. Inouye, S., Soberon, X., Franceschini, T., Nakamura, K., Itakura, K., and Inouye, M. 1982. Role of positive charge on the amino-terminal region of the signal peptide in protein secretion across the membrane. Proc. Natl. Acad. Sci. USA. 79: 3438-3441.
54. Jedrzejas, M. J. 2002. Three-dimensional structures of hyaluronate lyases from Streptococcus species and their mechanism of hyaluronan degradation. In: Science of Hyaluronan Today, Hascall, V.C. and Yanagishita, M. Eds., Glycoforum, www.glycoforum.gr.jp/science/hyaluronan.
55. Jedrzejas, M. J. 2001. Pneumococcal virulence factors: Structure and function. Microbiol. Mol. Biol. Rev. 65: 187-207.
56. Jedrzejas, M. J. 2000. Structural and functional comparison of polysaccharide-degrading enzymes. Crit. Rev. Biochem. Mol. Biol. 35:221-251.
57. Jedrzejas, M. J., Mello, L. V., de Groot, B. L., and Li., S. 2002. Mechanism of hyaluronan degradation by Streptococcus pneumoniae hyaluronate lyase. Structures of complexes with the substrate. J. Biol. Chem. 277: 28287-28297.
58. Jedrzejas, M. J., Lamani, E., and Becker, R. S. 2001. Biophysical characterization of selected strains of pneumococcal surface protein A. J. Biol. Chem. 276: 33121-33128.
59. Jedrzejas, M. J., Hollingshead, S. K., Lebowitz, J., Chantalat, L., Briles, D. E., and Lamani, E. 2000. Production and characterization of pneumococcal surface protein A. Arch. Biochem. Biophys. 373: 116-125.
60. Jenkins, J., Mayans, O., Smith, D., Worboys, K., and Pickersgill, R. W. 2001. Three-dimensional structure of Erwinia cho'santhemi pectin methylesterase reveals a novel esterase active site. J. Mol. Biol. 305: 951-960.
61. Johnson, P. E., Joshi, M.D., Tomme, P., Kilburn, D.G., and McIntosh, L. P. 1996. Structure of the N-terminal cellulose-binding domain of Cellulomonas fimi CenC determined by nuclear magnetic resonance spectroscopy. Biochemistry 35: 14381-14394.
62. Johnston, R. B., Jr. 1991. Pathogenesis of pneumococcal pneumonia. Rev. Infect. Dis. 13: S509-S517.
63. Jones, D. T. 1999. Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol. 29: 195-202.
64. Karplus, K., Barrett, C., and Hughey, R. 1998. Hidden Markov models for detecting remote protein homologies. Bioinformatics 14: 846-856.
65. Kelly, S. J. and Jedrzejas, M. J. 2000a. Structure and molecular mechanism of a functional form of pneumolysin: a cholesterol-dependent cytolysin from Streptococcus pnettmoniae. J. Struct. Biol. 132: 72-81.
66. Kelly, S. J. and Jedrzejas, M. J. 2000b. Crystallization and preliminary X-ray analysis of a functional form of pneumolysin, A virulence factor from Streptococcus pneumoniae. Acta Cryst. D56: 1452-1455.
67. Koonin, E. V. and Galperin, M. Y. 2002. Sequence Evolution - Function. Computational Approaches in Comparative Genomics. Kluwer Academic Publishers, Boston.
68. Kuroda, Y., Tani, K., Matsuo. Y., and Yokoyama, S. 2000. Automated search of natively folded protein fragments for high-throughput structure determination in structural genomics. Protein Sci. 9, 2313-2321.
69. Laskowski, R. A., MacArthur, M. W., Moss, D. S., and Thornton, J. M. 1993. PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Cryst., 26: 283-291.
70. Laskowski, R. A., Luscombe, N. M., Swindells, M. B., and Thornton, J. M. 1996. Protein clefts in molecular recognition and function. Protein Sci. 5: 2438-2452.
71. Lawrence, M. C., Pilling, P. A., Epa, V. C., Beery, A. M., Ogunniyi, A. D., and Paton, J. C. 1998. The crystal structure of pneumococcal surface antigen PsaA reveals a metal-binding site and a novel structure for a putative ABC-type binding protein. Structure 6: 1553-1561.
72. Li, S., Kelly, S. J., Lamani, E., Ferraroni, M., and Jedrzejas, M.J. 2000. Structural basis of hyaluronan degradation by Streptococcus pneumoniae hyaluronate lyase. EMBO J. 19: 1228-1240.
73. W., Pio, F., Pawlowski, K., and Godzik, A. 2000. Saturated BLAST: an automated multiple intermediate sequence search used to detect distant homology. Bioinformatics 16: 1105-1110.
74. Lock, R. A., Paton, J. C., and Hansman, D. 1988. Purification and immunological characterization of neuraminidase produced by Streptococcus pneumoniae. Microb. Pathog. 5: 461-467.
75. Lundstrom, J., Rychlewski, L., Bujnicki, J., and Elofsson, A. 2001. Pcons: a neural-network-based consensus predictor that improves fold recognition. Protein Sci. 10: 2354-2362.
76. Lupas, A. 1996. Prediction and analysis of coiled-coil structures. Methods Enzymol. 266: 513-525.
77. Marchler-Bauer, A., Panchenko, A. R., Shoemaker, B. A, Thiessen, P. A., Geer, L. Y., and Bryant, S. H. 2002. CDD: a database of conserved domain alignments with links to domain three-dimensional structure. Nucleic Acids Res. 30: 281-283.
78. Mark, B. L., Vocadlo, D. J., Knapp, S., Triggs-Raine, B. L., Withers, S. G., and James, M. N. 2001. Crystallographic evidence for substrate-assisted catalysis in a bacterial beta-hexosaminidase. J. Biol. Chem. 276: 10330-10337.
79. Marra, A., Asundi, J., Bartilson, M., Lawson, S., Fang, F., Christine, J., Wiesner, C., Brigham, D., Schneider, W. P., and Hromockyj, A. E. 2002. Differential fluorescence induction analysis of Streptococcus pneumoniae identifies genes involved in pathogenesis. Infect. Immun. 70: 1422-1433.
80. Mazmanian, S. K., Liu, G., Ton-That, H., and Schneewind, O. 1999. Staphylococcus aureus sortase, an enzyme that anchors surface proteins to the cell wall. Science 285, 760-763.
81. McDaniel, L. S., Sheffield, J. S., DeLucchi, P., and Briles, D. E. 1991. PspA, a surface protein of Streptococcus pneumoniae, is capable of eliciting protection against pneumococci of more than one capsular type. Infect. Immun. 59: 222-228.
82. Meddrano, F. J., Gasset, M., Lopez, Zumel, C., Usobiaga, P., Garcia, J. L., and Menendez, M. 1996. Structural characterization of the unligated and choline-bound forms of the major pneumococcal autolysin LytA amidase. Conformational transitions induced by temperature. J. Biol. Chem. 271: 29152-29161.
83. Mufson, M. A. 1990. Streptococcus pneumoniae. In: Principles and Practice of Infectious Diseases. pp. 1539-1550, Mandell, G. L., Douglas, R. G. Jr., and Bennett, J. E., Eds., Churchill Livingstone, New York.
84. Munoa, F. J., Miller, K. W., Beers, R., Graham, M., and Wu, H. C. 1991. Membrane topology of Escherichia coli prolipoprotein signal peptidase (signal peptidase II). J. Biol. Chem. 266: 17667-17672.
85. Musher, D. M. 1991. Infections caused by Streptococcus pneumoniae: Clinical spectrum, pathogenesis, immunity, and treatment. Clin. Infect. Dis. 14: 801-807.
86. Nabors, G. S., Braun, P. A., Herrmann, D. J., Heise, M. L., Pyle, D. J., Gravenstein, S., Schilling, M., Ferguson, L. M., Hollingshead, S.K., Briles, D.E., and Becker, R.S. 2000. Immunization of healthy adults with a single recombinant pneumococcal surface protein A (PspA) variant stimulates broadly cross-reactive antibodies to heterologous PspA molecules. Vaccine 18: 1743-1754.
87. Nagano, N., Porter, C. T., and Thornton, J. M. 2001. The (betaalpha)(8) glycosidases: sequence and structure analyses suggest distant evolutionary relationships. Protein Eng. 14: 845-855.
88. Nakai, K. 2001. Prediction of in vivo fates of proteins in the era of genomics and proteomics. J. Struct. Biol. 134: 103-116.
89. Nakai, K. and Horton, P. 1999. PSORT: a program for detecting sorting signals in proteins and predicting their subcellular localization. Trends Biochem. Sci. 24: 34-36.
90. Navarre, W. W. and Schneewind, O. 1999. Surface proteins of Gram-positive bacteria and mechanisms of their targeting to the cell wall envelope. Microbiol. Mol. Biol. Rev. 63: 174-229.
91. Nicholls, A., Sharp, K. A., and Honig, B. 1991. Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins 11: 281-296.
92. Nielsen, H., Engelbrecht, J., Brunak, S., and von Heijne, G. 1997. Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Protein Eng. 10: 1-6.
93. Norin, M. and Sundstrom, M. 2002. Structural proteomics: Developments in structure-to-function predictions. Trends Biotechnol. 20: 79-84.
94. Notredame, C., Higgins, D. G., and Heringa, J. 2000. T-Coffee: a novel method for fast and accurate multiple sequence alignment. J. Mol. Biol. 302: 205-217.
95. Novak R., Charpentier E., Braun J. S., Park E., Murti S., Tuomanen E., and Masure R. 2000. Extracellular targeting of choline-binding proteins in Streptococcus pneumoniae by a zinc metalloprotease. Mol. Microbiol. 36: 366-376.
96. Novak, R., Henriques, B., Charpentier, E., Normark, S., and Tuomanen, E. 1999. Emergence of vancomycin tolerance in Streptococcus pneumoniae. Nature 399: 590-593.
97. Ofran, Y. and Rost, B. 2003. Analysing six types of protein-protein interfaces. J. Mol. Biol. 325: 377-387.
98. Pallen, M. J. Lam, A. C., Antonio, M., and Dunbar, K. 2001. An embarrassment of sortases - a richness of substrates? Trends Microbiol. 9: 97-102.
99. Paton, J C. 1998. Novel pneumococcal surface proteins: role in virulence and vaccine potential. Trends Microbiol. 6: 85-87.
100. Pearson, W. R. 1990. Rapid and sensitive sequence comparison with FASTP and FASTA. Methods Enzymol. 183: 63-98.
101. Quiocho, F. A. and Vyas, N. K. 1999. Carbohydrates. In: Bioinorganic Chemistry. pp. 441-457, Oxford University Press, New York.
102. Rigden, D. J. 2002. Covariance analysis and prediction of structural domains from boundaries from multiple protein sequence alignments. Protein Eng. 15: 65-77.
103. Rigden, D. J. and Carneiro, M. 1999. A structural model for the rolA protein and its interaction with DNA. Proteins 37: 697-708.
104. Rigden, D. J., Alexeev, D., Phillips, S. E., and Fothergill-Gilmore, L. A. 1998. The 2.3 Å X-ray crystal structure of S. cerevisiae phosphoglycerate mutase. J. Mol. Biol. 276: 449-459.
105. Rigden, D. J., Bagyan, I., Lamani, E., Setlow, P., and Jedrzejas M. J. 2001b. A cofactor-dependent phosphoglycerate mutase homolog from Bacillus stearothermophilus is actually a broad specificity phosphatase. Protein Sci. 10: 1835-1846.
106. Rigden, D. J., Mello, L. V., and Bertioli, D. J. 2000. Structural modeling of a plant disease resistance gene product domain. Proteins 41: 133-143.
107. Rigden, D. J., Monteiro, A. C., and Grossi de Sa, M. F. 2001a. The protease inhibitor chagasin of Trypanosoma cruzi adopts an immunoglobulin-type fold and may have arisen by horizontal gene transfer. FEBS Lett. 504: 41-44.
108. Rigden, D. J., Setlow, P., Setlow, B., Stein, R. A., and Jedrzejas, M. J. 2002. PrfA protein of Bacillus species: Prediction and demonstration of DNA nuclease activity. Protein Sci. 11: 2370-2381.
109. Rigden, D. J. and Jedrzejas, M.J. 2003. Genome-based identification of a carbohydrate binding module in Streptococcus pneumoniae hyaluronate lyase. Proteins, in press.
110. Roos, S. and Jonsson, H. 2002. A high-molecular-mass cell-surface protein from Lactobacillus reuteri 1063 adheres to mucus components. Microbiology 148: 433-442.
111. Rosenow, C., Ryan, P., Weiser, J. N., Johnson, S., Fontan, P., Ortqvist, A., and Masure, H. R. 1997. Contribution of novel choline-binding proteins to adherence, colonization and immunogenicity of Streptococcus pneumoniae. Mol. Microb. 25: 819-829.
112. Rossjohn, J., Feil, S.C., McKinstry, W.J., Tweten, R.K., and Parker, M.W. 1997. Structure of a cholesterol-binding, thiol-activated cytolysin and a model of its membrane form. Cell 89: 685-692.
113. Rost, B., Casadio, R., Fariselli, P., and Sander, C. 1995. Transmembrane helices predicted at 95% accuracy. Protein Sci. 4: 521-533.
114. Sali, A. and Blundell, T. L. 1993. Comparative protein modeling by satisfaction of spatial restraints. J. Mol. Biol. 234: 779-815.
115. Sampson, J. S., O'Connor, S. P., Stinson, A. R., Tharpe, J. A., and Russell, H. 1994. Cloning and nucleotide sequence analysis of psaA, the Streptococcus pneumoniae gene encoding a 37-kilodalton protein homologous to previously reported Streptococcus sp. adhesins. Infect. Immun. 62: 319-324.
116. Sippl, M. J. 1993. Recognition of errors in three-dimensional structures of proteins. Proteins 17: 355-362.
117. Sippl, M. J., Lackner, P., Domingues, F. S., Prlic, A., Malik, R., Andreeva, A., and Wiederstein, M. 2001. Assessment of the CASP4 fold recognition category. Proteins 45 (Suppl 5): 55-67.
118. Stansfield, S. K. 1987. Acute respiratory infections in the developing world: Strategies for prevention, treatment and control. Pediatr. Infect. Dis. 6: 622-629.
119. Tam, R. and Saier, M. H. Jr. 1993. Structural, functional, and evolutionary relationships among extracellular solute-binding receptors of bacteria. Microbiol. Rev. 57: 320-346.
120. Tettelin, H., Nelson, K. E., Paulsen, I. T., Eisen, J. A., Read, T. D., Peterson, S., Heidelberg, J., DeBoy, R. T., Haft, D. H., Dodson, R. J., Durkin, A. S., Gwinn, M., Kolonay, J. F., Nelson, W. C., Peterson, J. D., Umayam, L. A., White, O., Salzberg, S. L., Lewis, M. R., Radune, D., Holtzapple, E., Khouri, H., Wolf, A. M., Utterback, T. R., Hansen, C. L., McDonald, L. A., Feldblyum, T. V., Angiuoli, S., Dickinson, T., Hickey, E. K., Holt, I. E, Loftus, B. J., Yang, F., Smith, H. O., Venter, J. C., Dougherty, B. A., Morrison, D. A., Hollingshead, S. K., and Fraser, C. M. 2001. Complete genome sequence of a virulent isolate of Streptococcus pneumoniae. Science 293: 498-506.
121. Tjalsma, H., Bolhuis, A., Jongbloed, J. D., Bron, S., and van Dijl, J. M. 2000. Signal peptide-dependent protein transport in Bacillus subtilis: a genome-based survey of the secretome. Microbiol. Mol. Biol. Rev. 64: 515-547.
122. Todd, A. E., Orengo, C. A., and Thornton, J. M. 2001. Evolution of function in protein superfamilies, from a structural perspective. J. Mol. Biol. 307: 1113-1143.
123. Todd, A. E., Orengo, C. A., and Thornton, J. M. 2002. Sequence and structural differences between enzyme and nonenzyme homologs. Structure 10: 1435-1451.
124. Ton-That, H., Liu, G., Mazmanian, S. K., Faull, K. F., and Schneewind, O. 1999. Purification and characterization of sortase, the transpeptidase that cleaves surface proteins of Staphylococcus aureus at the LPXTG motif. Proc. Natl. Acad. Sci. USA 96: 12424-12429.
125. Tuomanen, E. 1999. Molecular and cellular biology of pneumococcal infection. Curr. Opin. Microb. 2: 35-39.
126. Usobiaga, P., Medrando, F. J., Gasset, M., Garcia, J. L., Saiz, J. L., Rivas, G., Laynez, J., and Menendez, M. 1996. Structural organization of the major autolysin from Streptococcus pneumoniae. J. Biol. Chem. 271: 6832-6838.
127. van Dijl, J. M., Braun, P. G., Robinson, C., Quax, W. J., Antelmann, H., Hecker, M., Muller, J., Tjalsma, H., Bron, S., and Jongbloed, J. D. 2002. Functional genomic analysis of the Bacillus subtilis Tat pathway for protein secretion. J. Biotechnol. 98: 243-54.
128. von Heijne, G. 1989. Control of topology and mode of assembly of a polytopic membrane protein by positively charged residues. Nature 341: 456-458.
129. Walker, D. R. and Koonin, E. V. 1997. SEALS: a system for easy analysis of lots of sequences. ISMB 5: 333-339.
130. Wallace, A. C., Borkakoti, N., and Thornton, J. M. 1997. TESS: a geometric hashing algorithm for deriving 3D coordinate templates for searching structural databases: application to enzyme active sites. Protein Sci. 6: 2308-2323.
131. Wani, J. H., Gilbert, J. V., Plaut, A. G., and Weiser, J. N. 1996. Identification, cloning, and sequencing of the immunoglobulin A1 protease gene of Streptococcus pneumoniae. Infect. Immun. 64: 3967-3974.
132. Wheelan, S. J., Marchler-Bauer, A., and Bryant, S. H. 2000. Domain size distributions can predict domain boundaries. Bioinformatics 16: 613-618.
133. Wierenga, R. K. 2001. The TIM-barrel fold: a versatile framework for efficient enzymes. FEBS Lett. 491: 193-198.
134. Wilson, C. A., Kreychman, J., and Gerstein, M. 2000. Assessing annotation transfer for genomics: quantifying the relations between protein sequence, structure and function through traditional and probabilistic scores. J. Mol. Biol. 297: 233-249.
135. Wizemann, T. M., Heinrichs, J. H., Adamou, J. E., Enwin, A. L., Kunsch, C., Choi, G. H., Barash, S. C., Rosen, C. A., Masure, H. R., Tuomanen, E. et al. 2001. Use of a whole genome approach to identify vaccine molecules affording protection against Streptococcus pneumoniae infection. Infect. Immun. 69: 1593-1598.
136. Wootton, J. C. 1994. Non-globular domains in protein sequences: Automated segmentation using complexity measures. Comput. Chem. 18: 269-285.
137. Wootton, J. C. and Federhen, S. 1996. Analysis of compositionally biased regions in sequence databases. Methods Enzymol. 266: 554-571.
138. Wren, B. W. 1991. A family of clostridial and streptococcal ligand-binding proteins with conserved C-terminal repeat sequences. Mol. Microbiol. 5: 797-803.
139. Yoder, M. D., Lietzke, S. E., and Jurnak, F. 1993. Unusual structural features in the parallel beta-helix in pectate lyases. Structure 1: 241-251.
140. Zahner, D. and Hakenbeck, R. 2000. The Streptococcus pneumoniae beta-galactosidase is a surface protein. J. Bacteriol. 182: 5919-5921.
141. Zhou, H.X. and Shan, Y. 2001. Prediction of protein interaction sites from sequence profile and residue neighbor list. Proteins 44: 336-343.