Species-specific protein sequence and fold optimizations

BMC Bioinformatics

Volumn 3, Issue , 2002, Pages

  Dumontier, Michel ^a,b   Michalickova, Katerina ^a,b   Hogue, Christopher W V ^a,b  

^a UNIVERSITY OF TORONTO   (Canada)

^b MOUNT SINAI HOSPITAL   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ALANINE; ARGININE; ASPARTIC ACID; GLUTAMIC ACID; GLYCINE; HISTIDINE; PHENYLALANINE; TRYPTOPHAN; TYROSINE; VALINE; ARCHAEAL PROTEIN; BACTERIAL PROTEIN; CAENORHABDITIS ELEGANS PROTEIN; FUNGAL PROTEIN; PROTEIN; PROTEOME;

AMINO ACID ANALYSIS; AMINO ACID COMPOSITION; AMINO ACID SEQUENCE; ARCHAEBACTERIUM; ARTICLE; BACTERIAL GENETICS; CELL PROLIFERATION; CELL SURVIVAL; COMPUTER PROGRAM; CONTROLLED STUDY; ECOLOGICAL NICHE; ESCHERICHIA COLI; EUKARYOTE; EVOLUTIONARY ADAPTATION; GENE SEQUENCE; HALOBACTERIUM; HYDROPHOBICITY; INTERNET; METHANOCOCCUS JANNASCHII; NONHUMAN; OPEN READING FRAME; PREDICTION; PRINCIPAL COMPONENT ANALYSIS; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN ENGINEERING; PROTEIN FOLDING; SCORING SYSTEM; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; SPECIES DIFFERENCE; ADAPTATION; ANIMAL; BACTERIAL GENOME; BIOLOGY; CHEMISTRY; COMPARATIVE STUDY; GENETICS; GENOME; HUMAN; METHODOLOGY; PREDICTION AND FORECASTING; PROTEIN SECONDARY STRUCTURE; PROTEOMICS; VALIDATION STUDY;

EUKARYOTA;

ADAPTATION, PHYSIOLOGICAL; ANIMALS; ARCHAEAL PROTEINS; BACTERIAL PROTEINS; CAENORHABDITIS ELEGANS PROTEINS; COMPUTATIONAL BIOLOGY; FUNGAL PROTEINS; GENOME; GENOME, ARCHAEAL; GENOME, BACTERIAL; GENOME, FUNGAL; GENOME, HUMAN; HUMANS; PREDICTIVE VALUE OF TESTS; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; PROTEINS; PROTEOME; PROTEOMICS; SPECIES SPECIFICITY;

EID: 0242365841     PISSN: 14712105     EISSN: None     Source Type: Journal    
DOI: 10.1186/1471-2105-3-39     Document Type: Article

References (57)

1. Martin DD, Ciulla RA, Roberts MF: Osmoadaptation in archaea. Appl Environ Microbiol 1999, 65:1815-25
2. Gross M, Jaenicke R: Proteins under pressure. The influence of high hydrostatic pressure on structure, function and assembly of proteins and protein complexes. Eur J Biochem 1994, 221:617-30
3. Vieille C, Zeikus GJ: Hyperthermophilic enzymes: sources, uses, and molecular mechanisms for thermostability. Microbiol Mol Biol Rev 2001, 65:1-43
4. Audia JP, Webb CC, Foster JW: Breaking through the acid barrier: an orchestrated response to proton stress by enteric bacteria. Int J Med Microbiol 2001, 291:97-106
5. May BJ, Zhang Q, Li LL, Paustian ML, Whittam TS, Kapur V: Complete genomic sequence of Pasteurella multocida, Pm70. Proc Natl Acad Sci U S A 2001, 98:3460-5
6. Oren A: Bioenergetic aspects of halophilism. Microbiol Mol Biol Rev 1999, 63:334-48
7. Baudouin-Cornu P, Surdin-Kerjan Y, Marliere P, Thomas D: Molecular evolution of protein atomic composition. Science 2001, 293:297-300
8. Kreil DP, Ouzounis CA: Identification of thermophilic species by the amino acid compositions deduced from their genomes. Nucleic Acids Res 2001, 29:1608-15
9. Nelson KE, Clayton RA, Gill SR, Gwinn ML, Dodson RJ, Haft DH, Hickey EK, Peterson JD, Nelson WC, Ketchum KA, McDonald L, Utterback TR, Malek JA, KD Linher, Garrett MM, Stewart AM, Cotton MD, Pratt MS, Phillips CA, D Richardson, Heidelberg J, Sutton GG, Fleischmann RD, Eisen JA, Fraser CM, et al: Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima. Nature 1999, 399:323-9
10. She Q, Singh RK, Confalonieri F, Zivanovic Y, Allard G, Awayez MJ, Chan-Weiher CC, Clausen IG, Curtis BA, De Moors A, Erauso G, Fletcher C, Gordon PM, Heikamp-de Jong I, Jeffries AC, Kozera CJ, Medina N, Peng X, Thi-Ngoc HP, Redder P, Schenk ME, Theriault C, Tolstrup N, Charlebois RL, Doolittle WF, Duguet M, Gaasterland T, Garrett RA, Ragan MA, Sensen CW, Van der Oost J: The complete genome of the crenarchaeon Sulfolobus solfataricus P2. Proc Natl Acad Sci U S A 2001, 98:7835-40
11. White O, Eisen JA, Heidelberg JF, Hickey EK, Peterson JD, Dodson RJ, Haft DH, Gwinn ML, Nelson WC, Richardson DL, Moffat KS, Qin H, Jiang L, Pamphile W, Crosby M, Shen M, Vamathevan JJ, Lam P, McDonald L, Utterback T, Zalewski C, Makarova KS, Aravind L, Daly MJ, Fraser CM, et al: Genome sequence of the radioresistant bacterium Deinococcus radiodurans R1. Science 1999, 286:1571-7
12. Makarova KS, Aravind L, Wolf YI, Tatusov RL, Minton KW, Koonin EV, Daly MJ: Genome of the extremely radiation-resistant bacterium Deinococcus radiodurans viewed from the perspective of comparative genomics. Microbiol Mol Biol Rev 2001, 65:44-79
13. Shigenobu S, Watanabe H, Hattori M, Sakaki Y, Ishikawa H: Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp. APS. Nature 2000, 407:81-6
14. Goodner B, Hinkle G, Gattung S, Miller N, Blanchard M, Qurollo B, Goldman BS, Cao Y, Askenazi M, Halling C, Mullin L, Houmiel K, Gordon J, Vaudin M, Iartchouk O, Epp A, Liu F, Wollam C, Allinger M, Doughty D, Scott C, Lappas C, Markelz B, Flanagan C, Crowell C, Gurson J, Lomo C, Sear C, Strub G, Cielo C, Slater S: Genome sequence of the plant pathogen and biotechnology agent Agrobacterium tumefaciens C58. Science 2001, 294:2323-8
15. Galibert F, Finan TM, Long SR, Puhler A, Abola P, Ampe F, Barloy-Hubler F, Barnett MJ, Becker A, Boistard P, Bothe G, Boutry M, Bowser L, Buhrmester J, Cadieu E, Capela D, Chain P, Cowie A, Davis RW, Dreano S, Federspiel NA, Fisher RF, Gloux S, Godrie T, Goffeau A, Golding B, Gouzy J, Gurjal M, Hernandez-Lucas I, Hong A, Huizar L, Hyman RW, Jones T, Kahn D, Kahn ML, Kalman S, Keating DH, Kiss E, Komp C, Lelaure V, Masuy D, Palm C, Peck MC, Pohl TM, Portetelle D, Purnelle B, Ramsperger U, Surzycki R, Thebault P, Vandenbol M, Vorholter FJ, Weidner S, Wells DH, Wong K, Yeh KC, Batut J: The composite genome of the legume symbiont Sinorhizobium meliloti. Science 2001, 293:668-72
16. Houry WA: Mechanism of substrate recognition by the chaperonin GroEL. Biochem Cell Biol 2001, 79:569-77
17. Kim R, Kim KK, Yokota H, Kim SH: Small heat shock protein of Methanococcus jannaschii, a hyperthermophile. Proc Natl Acad Sci U S A 1998, 95:9129-33
18. Mogk A, Tomoyasu T, Goloubinoff P, Rudiger S, Roder D, Langen H, Bukau B: Identification of thermolabile Escherichia coli proteins: prevention and reversion of aggregation by DnaK and ClpB. Embo J 1999, 18:6934-49
19. Kowalski JM, Kelly RM, Konisky J, Clark DS, Wittrup KD: Purification and functional characterization of a chaperone from Methanococcus jannaschii. Syst Appl Microbiol 1998, 21:173-8
20. Bock AK, Glasemacher J, Schmidt R, Schonheit P: Purification and characterization of two extremely thermostable enzymes, phosphate acetyltransferase and acetate kinase, from the hyperthermophilic eubacterium Thermotoga maritima. J Bacteriol 1999, 181:1861-7
21. Russell RJ, Ferguson JM, Hough DW, Danson MJ, Taylor GL: The crystal structure of citrate synthase from the hyperthermophilic archaeon pyrococcus furiosus at 1.9 A resolution. Biochemistry 1997, 36:9983-94
22. Lobry JR: Influence of genomic G+C content on average amino-acid composition of proteins from 59 bacterial species. Gene 1997, 205:309-16
23. Lynn DJ, Singer GA, Hickey DA: Synonymous codon usage is subject to selection in thermophilic bacteria. Nucleic Acids Res 2002, 30:4272-7
24. Chakravarty S, Varadarajan R: Elucidation of determinants of protein stability through genome sequence analysis. FEBS Lett 2000, 470:65-9
25. Chakravarty S, Varadarajan R: Elucidation of factors responsible for enhanced thermal stability of proteins: a structural genomics based study. Biochemistry 2002, 41:8152-61
26. Tekaia F, Yeramian E, Dujon B: Amino acid composition of genomes, lifestyles of organisms, and evolutionary trends: a global picture with correspondence analysis. Gene 2002, 297:51
27. Maes D, Zeelen JP, Thanki N, Beaucamp N, Alvarez M, Thi MH, Backmann J, Martial JA, Wyns L, Jaenicke R, Wierenga RK: The crystal structure of triosephosphate isomerase (TIM) from Thermotoga maritima: a comparative thermostability structural analysis of ten different TIM structures. Proteins 1999, 37:441-53
28. Szilagyi A, Zavodszky P: Structural differences between mesophilic, moderately thermophilic and extremely thermophilic protein subunits: results of a comprehensive survey. Structure Fold Des 2000, 8:493-504
29. Wootton JC, Federhen S: Analysis of compositionally biased regions in sequence databases. Methods Enzymol 1996, 266:554-71
30. Tusnady GE, Simon I: The HMMTOP transmembrane topology prediction server. Bioinformatics 2001, 17:849-50
31. Nielsen H, Engelbrecht J, S Brunak, von Heijne G: Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Protein Eng 1997, 10:1-6
32. Lupas A, Van Dyke M, Stock J: Predicting coiled coils from protein sequences. Science 1991, 252:1162-4
33. Rost B, Fariselli P, Casadio R: Topology prediction for helical transmembrane proteins at 86% accuracy. Protein Sci 1996, 5:1704-18
34. Chou KC, Maggiora GM: Domain structural class prediction. Protein Eng 1998, 11:523-38
35. Kyte J, Doolittle RF: A simple method for displaying the hydropathic character of a protein. J Mol Biol 1982, 157:105-32
36. Cai YD, Liu XJ, Xu XB, Chou KC: Support vector machines for prediction of protein subcellular location by incorporating quasi-sequence-order effect. J Cell Biochem 2002, 84:343-8
37. Wilkins MR, Pasquali C, Appel RD, Ou K, Golaz O, Sanchez JC, Yan JX, Gooley AA, Hughes G, Humphery-Smith I, Williams KL, Hochstrasser DF: From proteins to proteomes: large scale protein identification by two-dimensional electrophoresis and amino acid analysis. Biotechnology (N Y) 1996, 14:61-5
38. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25:3389-402
39. Burge C, Karlin S: Prediction of complete gene structures in human genomic DNA. J Mol Biol 1997, 268:78-94
40. Uberbacher EC, Mural RJ: Locating protein-coding regions in human DNA sequences by a multiple sensor-neural network approach. Proc Natl Acad Sci U S A 1991, 88:11261-5
41. Gelfand MS: Prediction of function in DNA sequence analysis. J Comput Biol 1995, 2:87-115
42. Dennis PP, Shimmin LC: Evolutionary divergence and salinity-mediated selection in halophilic archaea. Microbiol Mol Biol Rev 1997, 61:90-104
43. Katinka MD, Duprat S, Cornillot E, Metenier G, Thomarat F, Prensier G, Barbe V, Peyretaillade E, Brottier P, Wincker P, Delbac F, El Alaoui H, Peyret P, Saurin W, Gouy M, Weissenbach J, Vivares CP: Genome sequence and gene compaction of the eukaryote parasite Encephalitozoon cuniculi. Nature 2001, 414:450-3
44. Clarke GD, Beiko RG, Ragan MA, Charlebois RL: Inferring genome trees by using a filter to eliminate phylogenetically discordant sequences and a distance matrix based on mean normalized BLASTP scores. J Bacteriol 2002, 184:2072-80
45. Wolf YI, Rogozin IB, Grishin NV, Tatusov RL, Koonin EV: Genome trees constructed using five different approaches suggest new major bacterial clades. BMC Evol Biol 2001, 1:8
46. Ahern TJ, Klibanov AM: The mechanisms of irreversible enzyme inactivation at 100C. Science 1985, 228:1280-4
47. Tomazic SJ, Klibanov AM: Mechanisms of irreversible thermal inactivation of Bacillus alpha-amylases. J Biol Chem 1988, 263:3086-91
48. Fukuchi S, Nishikawa K: Protein surface amino acid compositions distinctively differ between thermophilic and mesophilic bacteria. J Mol Biol 2001, 309:835-43
49. Bryant SH, Lawrence CE: The frequency of ion-pair substructures in proteins is quantitatively related to electrostatic potential: a statistical model for nonbonded interactions. Proteins 1991, 9:108-19
50. Wheeler DL, Church DM, Lash AE, Leipe DD, Madden TL, Pontius JU, Schuler GD, Schriml LM, Tatusova TA, Wagner L, Rapp BA: Database resources of the National Center for Biotechnology Information: 2002 update. Nucleic Acids Res 2002, 30:13-6
51. Michalickova K, Bader GD, Dumontier M, Lieu HC, Betel D, Isserlin R, Hogue CW: SeqHound: biological sequence and structure database as a platform for bioinformatics research. BMC Bioinformatics 2002, 3:32
52. Dumontier M, Hogue CWV: NBLAST: a Cluster Variant of BLAST for NxN Comparisons. BMC Bioinformatics 2002, 3:13
53. Wang Y, Bryant S, Tatusov R, Tatusova T: Links from genome proteins to known 3-D structures. Genome Res 2000, 10:1643-7
54. Higgins DG, Sharp PM: CLUSTAL: a package for performing multiple sequence alignment on a microcomputer. Gene 1988, 73:237-44
55. Hogue CW, Ohkawa H, Bryant SH: A dynamic look at structures: WWW-Entrez and the Molecular Modeling Database. Trends Biochem Sci 1996, 21:226-9
56. Melo F, Sanchez R, Sali A: Statistical potentials for fold assessment. Protein Sci 2002, 11:430-48
57. Marti-Renom MA, Stuart AC, Fiser A, Sanchez R, Melo F, Sali A: Comparative protein structure modeling of genes and genomes. Annu Rev Biophys Biomol Struct 2000, 29:291-325