Discovery of novel leptospirosis vaccine candidates using reverse and structural vaccinology

Frontiers in Immunology

Volumn 8, Issue APR, 2017, Pages

  Grassmann, André Alex ^a   Kremer, Frederico Schmitt ^a   Santos, Júlia Cougo dos ^a   Souza, Jéssica Dias ^a   Pinto, Luciano da Silva ^a   McBride, Alan John Alexander ^a,b  

^a FEDERAL UNIVERSITY OF PELOTAS   (Brazil)

^b INSTITUTO OSWALDO CRUZ   (Brazil)

Author keywords

Bioinformatics; Diderm bacteria; Epitope prediction; Genome mining; Leptospira interrogans; Outer membrane protein; Structural modeling; Transport proteins

Indexed keywords

CARRIER PROTEIN; EPITOPE; HLA ANTIGEN; LEPTOSPIROSIS VACCINE; LIPOPOLYSACCHARIDE; LIPOPROTEIN; MAJOR HISTOCOMPATIBILITY ANTIGEN CLASS 2; OUTER MEMBRANE PROTEIN; PROTEIN TONB; RECOMBINANT VACCINE; TOLC PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; BACTERIAL GENOME; BACTERIAL VIRULENCE; BACTERIUM IDENTIFICATION; BIOINFORMATICS; COMPUTER MODEL; GENE ONTOLOGY; HUMAN; IMMUNE RESPONSE; LEPTOSPIRA INTERROGANS SEROVAR COPENHAGENI; LEPTOSPIROSIS; NONHUMAN; PROTEIN ANALYSIS; PROTEIN SECONDARY STRUCTURE; QUALITY CONTROL; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; VACCINATION;

EID: 85018431594     PISSN: None     EISSN: 16643224     Source Type: Journal    
DOI: 10.3389/fimmu.2017.00463     Document Type: Article

References (117)

1. Levett PN. Systematics of leptospiraceae. Curr Top Microbiol Immunol (2015) 387:11-20. doi: 10.1007/978-3-662-45059-8_2
2. Bourhy P, Collet L, Brisse S, Picardeau M. Leptospira mayottensis sp. nov., a pathogenic species of the genus Leptospira isolated from humans. Int J Syst Evol Microbiol (2014) 64(Pt 12):4061-7. doi:10.1099/ijs.0.066597-0
3. Costa F, Hagan JE, Calcagno J, Kane M, Torgerson P, Martinez-Silveira MS, et al. Global morbidity and mortality of leptospirosis: a systematic review. PLoS Negl Trop Dis (2015) 9(9):e0003898. doi:10.1371/journal.pntd.0003898
4. Ellis WA. Animal leptospirosis. Curr Top Microbiol Immunol (2015) 387:99-137. doi:10.1007/978-3-662-45059-8_6
5. Adler B. Vaccines against leptospirosis. Curr Top Microbiol Immunol (2015) 387:251-72. doi:10.1007/978-3-662-45059-8_10
6. Haake DA, Levett PN. Leptospirosis in humans. Curr Top Microbiol Immunol (2015) 387:65-97. doi:10.1007/978-3-662-45059-8_5
7. Dellagostin OA, Grassmann AA, Hartwig DD, Felix SR, da Silva EF, McBride AJ. Recombinant vaccines against leptospirosis. Hum Vaccin (2011) 7(11):1215-24. doi:10.4161/hv.7.11.17944
8. Conrad NL, Cruz McBride FW, Souza JD, Silveira MM, Felix S, Mendonca KS, et al. LigB subunit vaccine confers sterile immunity against challenge in the hamster model of leptospirosis. PLoS Negl Trop Dis (2017) 11(3):e0005441. doi:10.1371/journal.pntd.0005441
9. Coutinho ML, Choy HA, Kelley MM, Matsunaga J, Babbitt JT, Lewis MS, et al. A LigA three-domain region protects hamsters from lethal infection by Leptospira interrogans. PLoS Negl Trop Dis (2011) 5(12):e1422. doi:10.1371/journal.pntd.0001422
10. Silva EF, Medeiros MA, McBride AJ, Matsunaga J, Esteves GS, Ramos JG, et al. The terminal portion of leptospiral immunoglobulin-like protein LigA confers protective immunity against lethal infection in the hamster model of leptospirosis. Vaccine (2007) 25(33):6277-86. doi:10.1016/j.vaccine.2007.05.053
11. Koizumi N, Watanabe H. Leptospiral immunoglobulin-like proteins elicit protective immunity. Vaccine (2004) 22(11-12):1545-52. doi:10.1016/j.vaccine.2003.10.007
12. Fouts DE, Matthias MA, Adhikarla H, Adler B, Amorim-Santos L, Berg DE, et al. What makes a bacterial species pathogenic? Comparative genomic analysis of the genus Leptospira. PLoS Negl Trop Dis (2016) 10(2):e0004403. doi:10.1371/journal.pntd.0004403
13. Seixas FK, Fernandes CH, Hartwig DD, Conceicao FR, Aleixo JA, Dellagostin OA. Evaluation of different ways of presenting LipL32 to the immune system with the aim of developing a recombinant vaccine against leptospirosis. Can J Microbiol (2007) 53(4):472-9. doi:10.1139/w06-138
14. Branger C, Chatrenet B, Gauvrit A, Aviat F, Aubert A, Bach JM, et al. Protection against Leptospira interrogans sensu lato challenge by DNA immunization with the gene encoding hemolysin-associated protein 1. Infect Immun (2005) 73(7):4062-9. doi:10.1128/IAI.73.7.4062-4069.2005
15. Branger C, Sonrier C, Chatrenet B, Klonjkowski B, Ruvoen-Clouet N, Aubert A, et al. Identification of the hemolysis-associated protein 1 as a cross-protective immunogen of Leptospira interrogans by adenovirus-mediated vaccination. Infect Immun (2001) 69(11):6831-8. doi:10.1128/IAI.69.11.6831-6838.2001
16. Sonrier C, Branger C, Michel V, Ruvoen-Clouet N, Ganiere JP, Andre-Fontaine G. Evidence of cross-protection within Leptospira interrogans in an experimental model. Vaccine (2000) 19(1):86-94. doi:10.1016/S0264-410X(00)00129-8
17. Grassmann AA, Felix SR, dos Santos CX, Amaral MG, Seixas Neto AC, Fagundes MQ, et al. Protection against lethal leptospirosis after vaccination with LipL32 coupled or coadministered with the B subunit of Escherichia coli heat-labile enterotoxin. Clin Vaccine Immunol (2012) 19(5):740-5. doi:10.1128/CVI.05720-11
18. Hartwig DD, Forster KM, Oliveira TL, Amaral M, McBride AJ, Dellagostin OA. A prime-boost strategy using the novel vaccine candidate, LemA, protects hamsters against leptospirosis. Clin Vaccine Immunol (2013) 20(5):747-52. doi:10.1128/CVI.00034-13
19. Hartwig DD, Seixas FK, Cerqueira GM, McBride AJ, Dellagostin OA. Characterization of the immunogenic and antigenic potential of putative lipoproteins from Leptospira interrogans. Curr Microbiol (2011) 62(4):1337-41. doi:10.1007/s00284-010-9865-1
20. Oliveira TL, Grassmann AA, Schuch RA, Seixas Neto AC, Mendonca M, Hartwig DD, et al. Evaluation of the Leptospira interrogans outer membrane protein OmpL37 as a vaccine candidate. PLoS One (2015) 10(11):e0142821. doi:10.1371/journal.pone.0142821
21. Grassmann AA, Souza JD, McBride AJ. A universal vaccine against leptospirosis: are we going in the right direction? Front Immunol (2017) 8:256. doi:10.3389/fimmu.2017.00256
22. Rappuoli R. Reverse vaccinology, a genome-based approach to vaccine development. Vaccine (2001) 19(17-19):2688-91. doi:10.1016/S0264-410X(00)00554-5
23. Serruto D, Bottomley MJ, Ram S, Giuliani MM, Rappuoli R. The new multicomponent vaccine against meningococcal serogroup B, 4CMenB: immunological, functional and structural characterization of the antigens. Vaccine (2012) 30(Suppl 2):B87-97. doi:10.1016/j.vaccine.2012.01.033
24. Murray GL, Lo M, Bulach DM, Srikram A, Seemann T, Quinsey NS, et al. Evaluation of 238 antigens of Leptospira borgpetersenii serovar Hardjo for protection against kidney colonisation. Vaccine (2013) 31(3):495-9. doi:10.1016/j.vaccine.2012.11.028
25. Dellagostin OA, Grassmann AA, Rizzi C, Schuch RA, Jorge S, Oliveira TL, et al. Reverse vaccinology: an approach for identifying leptospiral vaccine candidates. Int J Mol Sci (2017) 18(1):158. doi:10.3390/ijms18010158
26. Schulz GE. The structure of bacterial outer membrane proteins. Biochim Biophys Acta (2002) 1565(2):308-17. doi:10.1016/S0005-2736(02)00577-1
27. Wilson MM, Bernstein HD. Surface-exposed lipoproteins: an emerging secretion phenomenon in Gram-negative bacteria. Trends Microbiol (2016) 24(3):198-208. doi:10.1016/j.tim.2015.11.006
28. Dong C, Beis K, Nesper J, Brunkan-Lamontagne AL, Clarke BR, Whitfield C, et al. Wza the translocon for E. coli capsular polysaccharides defines a new class of membrane protein. Nature (2006) 444(7116):226-9. doi:10.1038/nature05267
29. Dormitzer PR, Grandi G, Rappuoli R. Structural vaccinology starts to deliver. Nat Rev Microbiol (2012) 10(12):807-13. doi:10.1038/nrmicro2893
30. Finco O, Rappuoli R. Designing vaccines for the twenty-first century society. Front Immunol (2014) 5:12. doi:10.3389/fimmu.2014.00012
31. Koehler Leman J, Ulmschneider MB, Gray JJ. Computational modeling of membrane proteins. Proteins (2015) 83(1):1-24. doi:10.1002/prot.24703
32. Baker M. Making membrane proteins for structures: a trillion tiny tweaks. Nat Methods (2010) 7(6):429-34. doi:10.1038/nmeth0610-429
33. Khor BY, Tye GJ, Lim TS, Choong YS. General overview on structure prediction of twilight-zone proteins. Theor Biol Med Model (2015) 12:15. doi:10.1186/s12976-015-0014-1
34. Delany I, Rappuoli R, Seib KL. Vaccines, reverse vaccinology, and bacterial pathogenesis. Cold Spring Harb Perspect Med (2013) 3(5):a012476. doi:10.1101/cshperspect.a012476
35. McBride AJ, Athanazio DA, Reis MG, Ko AI. Leptospirosis. Curr Opin Infect Dis (2005) 18(5):376-86. doi:10.1097/01.qco.0000178824.05715.2c
36. Casadio R, Martelli PL, Bartoli L, Fariselli P. Topology prediction of membrane proteins: how distantly related homologs come into play. In: Frishman D, editor. Structural Bioinformatics of Membrane Proteins. New York: Springer (2010). p. 61-82. doi:10.1007/978-3-7091-0045-5_4
37. Setubal JC, Reis M, Matsunaga J, Haake DA. Lipoprotein computational prediction in spirochaetal genomes. Microbiology (2006) 152(Pt 1):113-21. doi:10.1099/mic.0.28317-0
38. Juncker AS, Willenbrock H, Von Heijne G, Brunak S, Nielsen H, Krogh A. Prediction of lipoprotein signal peptides in Gram-negative bacteria. Protein Sci (2003) 12(8):1652-62. doi:10.1110/ps.0303703
39. Gupta CL, Akhtar S, Bajpai P. In silico protein modeling: possibilities and limitations. EXCLI J (2014) 13:513-5
40. Moult J, Fidelis K, Kryshtafovych A, Schwede T, Tramontano A. Critical assessment of methods of protein structure prediction (CASP)-round x. Proteins (2014) 82(Suppl 2):1-6. doi:10.1002/prot.24452
41. Yang J, Zhang Y. Protein structure and function prediction using I-TASSER. Curr Protoc Bioinformatics (2015) 52:5.8.1-15. doi:10.1002/0471250953.bi0508s52
42. Zhang Y. I-TASSER server for protein 3D structure prediction. BMC Bioinformatics (2008) 9:40. doi:10.1186/1471-2105-9-40
43. Shaik MM, Lombardi C, Maragno Trindade D, Fenel D, Schoehn G, Di Guilmi AM, et al. A structural snapshot of type II pilus formation in Streptococcus pneumoniae. J Biol Chem (2015) 290(37):22581-92. doi:10.1074/jbc.M115.647834
44. Zuerner RL. Host response to Leptospira infection. Curr Top Microbiol Immunol (2015) 387:223-50. doi:10.1007/978-3-662-45059-8_9
45. Wang C, Peng B, Li H, Peng XX. TolC plays a crucial role in immune protection conferred by Edwardsiella tarda whole-cell vaccines. Sci Rep (2016) 6:29488. doi:10.1038/srep29488
46. Spreng S, Dietrich G, Goebel W, Gentschev I. Protection against murine listeriosis by oral vaccination with recombinant Salmonella expressing protective listerial epitopes within a surface-exposed loop of the TolC-protein. Vaccine (2003) 21(7-8):746-52. doi:10.1016/S0264-410X(02)00594-7
47. Yang TC, Ma XC, Liu F, Lin LR, Liu LL, Liu GL, et al. Screening of the Salmonella paratyphi A CMCC 50973 strain outer membrane proteins for the identification of potential vaccine targets. Mol Med Rep (2012) 5(1):78-83. doi:10.3892/mmr.2011.587
48. Higgins MK, Eswaran J, Edwards P, Schertler GF, Hughes C, Koronakis V. Structure of the ligand-blocked periplasmic entrance of the bacterial multidrug efflux protein TolC. J Mol Biol (2004) 342(3):697-702. doi:10.1016/j.jmb.2004.07.088
49. Eshghi A, Cullen PA, Cowen L, Zuerner RL, Cameron CE. Global proteome analysis of Leptospira interrogans. J Proteome Res (2009) 8(10):4564-78. doi:10.1021/pr9004597
50. Noinaj N, Guillier M, Barnard TJ, Buchanan SK. TonB-dependent transporters: regulation, structure, and function. Annu Rev Microbiol (2010) 64:43-60. doi:10.1146/annurev.micro.112408.134247
51. Nierman WC, Feldblyum TV, Laub MT, Paulsen IT, Nelson KE, Eisen JA, et al. Complete genome sequence of Caulobacter crescentus. Proc Natl Acad Sci U S A (2001) 98(7):4136-41. doi:10.1073/pnas.061029298
52. Nascimento AL, Verjovski-Almeida S, Van SMA, Monteiro-Vitorello CB, Camargo LE, Digiampietri LA, et al. Genome features of Leptospira interrogans serovar Copenhageni. Braz J Med Biol Res (2004) 37(4):459-77. doi:10.1590/S0100-879X2004000400003
53. Ferguson AD, Kodding J, Walker G, Bos C, Coulton JW, Diederichs K, et al. Active transport of an antibiotic rifamycin derivative by the outer-membrane protein FhuA. Structure (2001) 9(8):707-16. doi:10.1016/S0969-2126(01)00631-1
54. Haake DA, Matsunaga J. Leptospira: a spirochaete with a hybrid outer membrane. Mol Microbiol (2010) 77(4):805-14. doi:10.1111/j.1365-2958.2010.07262.x
55. Louvel H, Bommezzadri S, Zidane N, Boursaux-Eude C, Creno S, Magnier A, et al. Comparative and functional genomic analyses of iron transport and regulation in Leptospira spp. J Bacteriol (2006) 188(22):7893-904. doi:10.1128/JB.00711-06
56. Pinne M, Matsunaga J, Haake DA. Leptospiral outer membrane protein microarray, a novel approach to identification of host ligand-binding proteins. J Bacteriol (2012) 194(22):6074-87. doi:10.1128/JB.01119-12
57. Noinaj N, Buchanan SK, Cornelissen CN. The transferrin-iron import system from pathogenic Neisseria species. Mol Microbiol (2012) 86(2):246-57. doi:10.1111/mmi.12002
58. Greenwald J, Nader M, Celia H, Gruffaz C, Geoffroy V, Meyer JM, et al. FpvA bound to non-cognate pyoverdines: molecular basis of siderophore recognition by an iron transporter. Mol Microbiol (2009) 72(5):1246-59. doi:10.1111/j.1365-2958.2009.06721.x
59. Caimano MJ, Sivasankaran SK, Allard A, Hurley D, Hokamp K, Grassmann AA, et al. A model system for studying the transcriptomic and physiological changes associated with mammalian host-adaptation by Leptospira interrogans serovar Copenhageni. PLoS Pathog (2014) 10(3):e1004004. doi:10.1371/journal.ppat.1004004
60. Calmettes C, Ing C, Buckwalter CM, El Bakkouri M, Chieh-Lin Lai C, Pogoutse A, et al. The molecular mechanism of Zinc acquisition by the neisserial outer-membrane transporter ZnuD. Nat Commun (2015) 6:7996. doi:10.1038/ncomms8996
61. Shultis DD, Purdy MD, Banchs CN, Wiener MC. Crystallization and preliminary X-ray crystallographic analysis of the Escherichia coli outer membrane cobalamin transporter BtuB in complex with the carboxy-terminal domain of TonB. Acta Crystallogr Sect F Struct Biol Cryst Commun (2006) 62(Pt 7):638-41. doi:10.1107/S1744309106018240
62. Hu YH, Dang W, Sun L. A TonB-dependent outer membrane receptor of Pseudomonas fluorescens: virulence and vaccine potential. Arch Microbiol (2012) 194(9):795-802. doi:10.1007/s00203-012-0812-3
63. Kalbina I, Engstrand L, Andersson S, Strid A. Expression of Helicobacter pylori TonB protein in transgenic Arabidopsis thaliana: toward production of vaccine antigens in plants. Helicobacter (2010) 15(5):430-7. doi:10.1111/j.1523-5378.2010.00786.x
64. Cornelissen CN, Hollander A. TonB-dependent transporters expressed by Neisseria gonorrhoeae. Front Microbiol (2011) 2:117. doi:10.3389/fmicb.2011.00117
65. Hay ID, Rehman ZU, Rehm BH. Membrane topology of outer membrane protein AlgE, which is required for alginate production in Pseudomonas aeruginosa. Appl Environ Microbiol (2010) 76(6):1806-12. doi:10.1128/AEM.02945-09
66. Remminghorst U, Rehm BH. In vitro alginate polymerization and the functional role of Alg8 in alginate production by Pseudomonas aeruginosa. Appl Environ Microbiol (2006) 72(1):298-305. doi:10.1128/AEM.72.1.298-305.2006
67. Picardeau M, Bulach DM, Bouchier C, Zuerner RL, Zidane N, Wilson PJ, et al. Genome sequence of the saprophyte Leptospira biflexa provides insights into the evolution of Leptospira and the pathogenesis of leptospirosis. PLoS One (2008) 3(2):e1607. doi:10.1371/journal.pone.0001607
68. Noinaj N, Kuszak AJ, Gumbart JC, Lukacik P, Chang H, Easley NC, et al. Structural insight into the biogenesis of beta-barrel membrane proteins. Nature (2013) 501(7467):385-90. doi:10.1038/nature12521
69. Loosmore SM, Yang YP, Coleman DC, Shortreed JM, England DM, Klein MH. Outer membrane protein D15 is conserved among Haemophilus influenzae species and may represent a universal protective antigen against invasive disease. Infect Immun (1997) 65(9):3701-7
70. Ruffolo CG, Adler B. Cloning, sequencing, expression, and protective capacity of the oma87 gene encoding the Pasteurella multocida 87-kilodalton outer membrane antigen. Infect Immun (1996) 64(8):3161-7
71. Adler B, editor. Leptospira and Leptospirosis. Berlin, Heidelberg: Springer-Verlag (2015)
72. Botos I, Majdalani N, Mayclin SJ, McCarthy JG, Lundquist K, Wojtowicz D, et al. Structural and functional characterization of the LPS transporter LptDE from Gram-negative pathogens. Structure (2016) 24(6):965-76. doi:10.1016/j.str.2016.03.026
73. van den Berg B, Bhamidimarri SP, Winterhalter M. Crystal structure of a COG4313 outer membrane channel. Sci Rep (2015) 5:11927. doi:10.1038/srep11927
74. Belchik SM, Schaeffer SM, Hasenoehrl S, Xun L. A beta-barrel outer membrane protein facilitates cellular uptake of polychlorophenols in Cupriavidus necator. Biodegradation (2010) 21(3):431-9. doi:10.1007/s10532-009-9313-8
75. LaBauve AE, Wargo MJ. Detection of host-derived sphingosine by Pseudomonas aeruginosa is important for survival in the murine lung. PLoS Pathog (2014) 10(1):e1003889. doi:10.1371/journal.ppat.1003889
76. Hearn EM, Patel DR, van den Berg B. Outer-membrane transport of aromatic hydrocarbons as a first step in biodegradation. Proc Natl Acad Sci U S A (2008) 105(25):8601-6. doi:10.1073/pnas.0801264105
77. Black PN. The fadL gene product of Escherichia coli is an outer membrane protein required for uptake of long-chain fatty acids and involved in sensitivity to bacteriophage T2. J Bacteriol (1988) 170(6):2850-4. doi:10.1128/jb.170.6.2850-2854.1988
78. Koster S, van Pee K, Yildiz O. Purification, refolding, and crystallization of the outer membrane protein OmpG from Escherichia coli. Methods Enzymol (2015) 557:149-66. doi:10.1016/bs.mie.2015.01.018
79. Zahner D, Gandhi AR, Stuchlik O, Reed M, Pohl J, Stephens DS. Pilus backbone protein PitB of Streptococcus pneumoniae contains stabilizing intramolecular isopeptide bonds. Biochem Biophys Res Commun (2011) 409(3):526-31. doi:10.1016/j.bbrc.2011.05.038
80. Lessa-Aquino C, Borges Rodrigues C, Pablo J, Sasaki R, Jasinskas A, Liang L, et al. Identification of seroreactive proteins of Leptospira interrogans serovar Copenhageni using a high-density protein microarray approach. PLoS Negl Trop Dis (2013) 7(10):e2499. doi:10.1371/journal.pntd.0002499
81. Ruback E, Lobo LA, Franca TC, Pascutti PG. Structural analysis of Pla protein from the biological warfare agent Yersinia pestis: docking and molecular dynamics of interactions with the mammalian plasminogen system. J Biomol Struct Dyn (2013) 31(5):477-84. doi:10.1080/07391102.2012.703072
82. Suomalainen M, Haiko J, Ramu P, Lobo L, Kukkonen M, Westerlund-Wikstrom B, et al. Using every trick in the book: the Pla surface protease of Yersinia pestis. Adv Exp Med Biol (2007) 603:268-78. doi:10.1007/978-0-387-72124-8_24
83. Hritonenko V, Stathopoulos C. Omptin proteins: an expanding family of outer membrane proteases in Gram-negative enterobacteriaceae. Mol Membr Biol (2007) 24(5-6):395-406. doi:10.1080/09687680701443822
84. Verma A, Matsunaga J, Artiushin S, Pinne M, Houwers DJ, Haake DA, et al. Antibodies to a novel leptospiral protein, LruC, in the eye fluids and sera of horses with Leptospira-associated uveitis. Clin Vaccine Immunol (2012) 19(3):452-6. doi:10.1128/CVI.05524-11
85. Verma A, Artiushin S, Matsunaga J, Haake DA, Timoney JF. LruA and LruB, novel lipoproteins of pathogenic leptospira interrogans associated with equine recurrent uveitis. Infect Immun (2005) 73(11):7259-66. doi:10.1128/IAI.73.11.7259-7266.2005
86. Zhang K, Murray GL, Seemann T, Srikram A, Bartpho T, Sermswan RW, et al. Leptospiral LruA is required for virulence and modulates an interaction with mammalian apolipoprotein AI. Infect Immun (2013) 81(10):3872-9. doi:10.1128/IAI.01195-12
87. Lehmann JS, Fouts DE, Haft DH, Cannella AP, Ricaldi JN, Brinkac L, et al. Pathogenomic inference of virulence-associated genes in Leptospira interrogans. PLoS Negl Trop Dis (2013) 7(10):e2468. doi:10.1371/journal.pntd.0002468
88. Evangelista KV, Hahn B, Wunder EA Jr, Ko AI, Haake DA, Coburn J. Identification of cell-binding adhesins of Leptospira interrogans. PLoS Negl Trop Dis (2014) 8(10):e3215. doi:10.1371/journal.pntd.0003215
89. Yu NY, Wagner JR, Laird MR, Melli G, Rey S, Lo R, et al. PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes. Bioinformatics (2010) 26(13):1608-15. doi:10.1093/bioinformatics/btq249
90. Yu CS, Chen YC, Lu CH, Hwang JK. Prediction of protein subcellular localization. Proteins (2006) 64(3):643-51. doi:10.1002/prot.21018
91. Shen HB, Chou KC. Gneg-mPLoc: a top-down strategy to enhance the quality of predicting subcellular localization of Gram-negative bacterial proteins. J Theor Biol (2010) 264(2):326-33. doi:10.1016/j.jtbi.2010.01.018
92. Petersen TN, Brunak S, von Heijne G, Nielsen H. SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat Methods (2011) 8(10):785-6. doi:10.1038/nmeth.1701
93. Chou KC, Shen HB. Signal-CF: a subsite-coupled and window-fusing approach for predicting signal peptides. Biochem Biophys Res Commun (2007) 357(3):633-40. doi:10.1016/j.bbrc.2007.03.162
94. Hiller K, Grote A, Scheer M, Munch R, Jahn D. PrediSi: prediction of signal peptides and their cleavage positions. Nucleic Acids Res (2004) 32(Web Server issue):W375-9. doi:10.1093/nar/gkh378
95. Jones DT. Improving the accuracy of transmembrane protein topology prediction using evolutionary information. Bioinformatics (2007) 23(5):538-44. doi:10.1093/bioinformatics/btl677
96. Krogh A, Larsson B, von Heijne G, Sonnhammer EL. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol (2001) 305(3):567-80. doi:10.1006/jmbi.2000.4315
97. Tusnady GE, Simon I. The HMMTOP transmembrane topology prediction server. Bioinformatics (2001) 17(9):849-50. doi:10.1093/bioinformatics/17.9.849
98. Kall L, Krogh A, Sonnhammer EL. A combined transmembrane topology and signal peptide prediction method. J Mol Biol (2004) 338(5):1027-36. doi:10.1016/j.jmb.2004.03.016
99. Remmert M, Linke D, Lupas AN, Soding J. HHomp-prediction and classification of outer membrane proteins. Nucleic Acids Res (2009) 37(Web Server issue):W446-51. doi:10.1093/nar/gkp325
100. Berven FS, Flikka K, Jensen HB, Eidhammer I. BOMP: a program to predict integral beta-barrel outer membrane proteins encoded within genomes of Gram-negative bacteria. Nucleic Acids Res (2004) 32(Web Server issue):W394-9. doi:10.1093/nar/gkh351
101. Bagos PG, Liakopoulos TD, Hamodrakas SJ. Finding beta-barrel outer membrane proteins with a Markov chain model. WSEAS Trans Biol Biomed (2004) 2(1):186-9
102. Ou YY, Gromiha MM, Chen SA, Suwa M. TMBETADISC-RBF: discrimination of beta-barrel membrane proteins using RBF networks and PSSM profiles. Comput Biol Chem (2008) 32(3):227-31. doi:10.1016/j.compbiolchem.2008.03.002
103. Diaz-Mejia JJ, Babu M, Emili A. Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome. FEMS Microbiol Rev (2009) 33(1):66-97. doi:10.1111/j.1574-6976.2008.00141.x
104. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res (2004) 32(5):1792-7. doi:10.1093/nar/gkh340
105. Xu D, Zhang Y. Improving the physical realism and structural accuracy of protein models by a two-step atomic-level energy minimization. Biophys J (2011) 101(10):2525-34. doi:10.1016/j.bpj.2011.10.024
106. McGuffin LJ, Buenavista MT, Roche DB. The ModFOLD4 server for the quality assessment of 3D protein models. Nucleic Acids Res (2013) 41(Web Server issue):W368-72. doi:10.1093/nar/gkt294
107. Benkert P, Kunzli M, Schwede T. QMEAN server for protein model quality estimation. Nucleic Acids Res (2009) 37(Web Server issue):W510-4. doi:10.1093/nar/gkp322
108. Morris AL, MacArthur MW, Hutchinson EG, Thornton JM. Stereochemical quality of protein structure coordinates. Proteins (1992) 12(4):345-64. doi:10.1002/prot.340120407
109. Laskowski RA, MacArthur MW, Moss DS, Thornton JM. PROCHECK-a program to check the stereochemical quality of protein structures. J Appl Crystal (1993) 26(2):283-91. doi:10.1107/S0021889892009944
110. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, et al. UCSF Chimera-a visualization system for exploratory research and analysis. J Comput Chem (2004) 25(13):1605-12. doi:10.1002/jcc.20084
111. Schrodinger LLC. The PyMOL Molecular Graphics System, Version 1.8. (2015)
112. Mitchell A, Chang HY, Daugherty L, Fraser M, Hunter S, Lopez R, et al. The InterPro protein families database: the classification resource after 15 years. Nucleic Acids Res (2015) 43(Database issue):D213-21. doi:10.1093/nar/gku1243
113. Jones P, Binns D, Chang HY, Fraser M, Li W, McAnulla C, et al. InterProScan 5: genome-scale protein function classification. Bioinformatics (2014) 30(9):1236-40. doi:10.1093/bioinformatics/btu031
114. Roy A, Yang J, Zhang Y. COFACTOR: an accurate comparative algorithm for structure-based protein function annotation. Nucleic Acids Res (2012) 40(Web Server issue):W471-7. doi:10.1093/nar/gks372
115. Nielsen M, Lund O. NN-align. An artificial neural network-based alignment algorithm for MHC class II peptide binding prediction. BMC Bioinformatics (2009) 10:296. doi:10.1186/1471-2105-10-296
116. Nielsen M, Lund O, Buus S, Lundegaard C. MHC class II epitope predictive algorithms. Immunology (2010) 130(3):319-28. doi:10.1111/j.1365-2567.2010.03268.x
117. Crooks GE, Hon G, Chandonia JM, Brenner SE. WebLogo: a sequence logo generator. Genome Res (2004) 14(6):1188-90. doi:10.1101/gr.849004