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Here we show that the characteristic GGA(I,L,V) and FxxN tetrapeptide repeats fit into a larger repeat sequence, which correspond to the coils of a large beta-helical domain in high quality structure predictions. Analysis of the protein using structure prediction algorithms provided novel insight to the chlamydial Pmp family of proteins. While the tetrapeptide motifs themselves are predicted to play a structural role in folding and close stacking of the beta-helical backbone of the passenger domain, we found many of the interesting features of Pmps are localized to the side loops jutting out from the beta helix including protease cleavage, host cell adhesion, and B-cell epitopes; while T-cell epitopes are predominantly found in the beta-helix itself. This analysis more accurately defines the Pmp family of <jats:italic>Chlamydia<\/jats:italic> and may better inform rational vaccine design and functional studies.<\/jats:p>","DOI":"10.1371\/journal.pone.0304525","type":"journal-article","created":{"date-parts":[[2024,6,11]],"date-time":"2024-06-11T18:10:06Z","timestamp":1718129406000},"page":"e0304525","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":6,"title":["Sequence, structure prediction, and epitope analysis of the polymorphic membrane protein family in Chlamydia trachomatis"],"prefix":"10.1371","volume":"19","author":[{"given":"Patrick W.","family":"Cervantes","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Brent W.","family":"Segelke","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Edmond 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Gupta","year":"2021","journal-title":"Sex Transm Dis."},{"key":"pone.0304525.ref003","doi-asserted-by":"crossref","first-page":"1795","DOI":"10.3390\/diagnostics12081795","article-title":"Chlamydia trachomatis as a Current Health Problem: Challenges and Opportunities.","volume":"12","author":"R Rodrigues","year":"2022","journal-title":"Diagnostics"},{"key":"pone.0304525.ref004","doi-asserted-by":"crossref","first-page":"1116","DOI":"10.1038\/s41564-022-01177-x","article-title":"Sexually transmitted infections and female reproductive health.","volume":"7","author":"OT Van Gerwen","year":"2022","journal-title":"Nat Microbiol"},{"key":"pone.0304525.ref005","doi-asserted-by":"crossref","first-page":"18327","DOI":"10.1038\/s41598-019-54886-5","article-title":"Chlamydia trachomatis serovars in urogenital and ocular samples collected 2014\u20132017 from Austrian patients.","volume":"9","author":"I Lesiak-Markowicz","year":"2019","journal-title":"Sci 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Pilo","year":"2021","journal-title":"BMC Microbiol"},{"key":"pone.0304525.ref009","doi-asserted-by":"crossref","first-page":"S126","DOI":"10.1086\/652398","article-title":"Chlamydia trachomatis Strains and Virulence: Rethinking Links to Infection Prevalence and Disease Severity","volume":"201","author":"GI Byrne","year":"2010","journal-title":"J Infect Dis"},{"key":"pone.0304525.ref010","doi-asserted-by":"crossref","first-page":"e0258759","DOI":"10.1371\/journal.pone.0258759","article-title":"Human genital antibody-mediated inhibition of Chlamydia trachomatis infection and evidence for ompA genotype-specific neutralization.","volume":"16","author":"CM Ardizzone","year":"2021","journal-title":"PLoS ONE"},{"key":"pone.0304525.ref011","doi-asserted-by":"crossref","first-page":"865","DOI":"10.1128\/iai.41.2.865-868.1983","article-title":"Immunotypes of Chlamydia trachomatis isolates in Seattle, Washington.","volume":"41","author":"C Kuo","year":"1983","journal-title":"Infect 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M\u00fcller","year":"2017","journal-title":"Vaccine"},{"key":"pone.0304525.ref018","doi-asserted-by":"crossref","first-page":"e0144380","DOI":"10.1371\/journal.pone.0144380","article-title":"Delivery of a Chlamydial Adhesin N-PmpC Subunit Vaccine to the Ocular Mucosa Using Particulate Carriers.","volume":"10","author":"A Inic-Kanada","year":"2015","journal-title":"PLOS ONE."},{"key":"pone.0304525.ref019","doi-asserted-by":"crossref","first-page":"2543","DOI":"10.1016\/j.vaccine.2017.03.070","article-title":"Comparison of the nine polymorphic membrane proteins of Chlamydia trachomatis for their ability to induce protective immune responses in mice against a C. muridarum challenge","volume":"35","author":"S Pal","year":"2017","journal-title":"Vaccine"},{"key":"pone.0304525.ref020","doi-asserted-by":"crossref","first-page":"609","DOI":"10.3390\/vaccines9060609","article-title":"Prophylactic Multi-Subunit Vaccine against Chlamydia trachomatis: In Vivo Evaluation in Mice.","volume":"9","author":"C Lanfermann","year":"2021","journal-title":"Vaccines"},{"key":"pone.0304525.ref021","doi-asserted-by":"crossref","first-page":"3218","DOI":"10.1128\/IAI.01566-08","article-title":"Chlamydia trachomatis-Infected Patients Display Variable Antibody Profiles against the Nine-Member Polymorphic Membrane Protein Family","volume":"77","author":"C Tan","year":"2009","journal-title":"Infect Immun"},{"key":"pone.0304525.ref022","doi-asserted-by":"crossref","first-page":"1670","DOI":"10.4049\/jimmunol.1001240","article-title":"A Genome-Wide Profiling of the Humoral Immune Response to Chlamydia trachomatis Infection Reveals Vaccine Candidate Antigens Expressed in Humans","volume":"185","author":"J Wang","year":"2010","journal-title":"J Immunol"},{"key":"pone.0304525.ref023","doi-asserted-by":"crossref","first-page":"246","DOI":"10.1128\/IAI.00626-10","article-title":"Identification of Immunodominant Antigens by Probing a Whole Chlamydia trachomatis Open Reading Frame 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spp.\u2013autotransporters beyond the Proteobacteria","volume":"9","author":"IR Henderson","year":"2001","journal-title":"Trends Microbiol"},{"key":"pone.0304525.ref030","doi-asserted-by":"crossref","first-page":"1163","DOI":"10.3389\/fmicb.2019.01163","article-title":"Type V Secretion Systems: An Overview of Passenger Domain Functions.","volume":"10","author":"I Meuskens","year":"2019","journal-title":"Front Microbiol."},{"key":"pone.0304525.ref031","doi-asserted-by":"crossref","first-page":"544","DOI":"10.1002\/mbo3.186","article-title":"All subtypes of the Pmp adhesin family are implicated in chlamydial virulence and show species-specific function.","volume":"3","author":"E Becker","year":"2014","journal-title":"MicrobiologyOpen."},{"key":"pone.0304525.ref032","doi-asserted-by":"crossref","first-page":"1004","DOI":"10.1111\/j.1365-2958.2010.07386.x","article-title":"Members of the Pmp protein family of Chlamydia pneumoniae mediate adhesion to human cells via short repetitive peptide motifs","volume":"78","author":"K Molleken","year":"2010","journal-title":"Mol Microbiol"},{"key":"pone.0304525.ref033","doi-asserted-by":"crossref","first-page":"22806","DOI":"10.1074\/jbc.M116.728915","article-title":"The Chlamydia pneumoniae Adhesin Pmp21 Forms Oligomers with Adhesive Properties","volume":"291","author":"SET Luczak","year":"2016","journal-title":"J Biol Chem"},{"key":"pone.0304525.ref034","first-page":"12","article-title":"Chlamydia trachomatis Polymorphic Membrane Proteins (Pmps) Form Functional Homomeric and Heteromeric Oligomers.","author":"A Favaroni","year":"2021","journal-title":"Front Microbiol."},{"key":"pone.0304525.ref035","doi-asserted-by":"crossref","first-page":"656209","DOI":"10.3389\/fmicb.2021.656209","article-title":"Pmp Repertoires Influence the Different Infectious Potential of Avian and Mammalian Chlamydia psittaci Strains.","volume":"12","author":"A Favaroni","year":"2021","journal-title":"Front Microbiol."},{"key":"pone.0304525.ref036","doi-asserted-by":"crossref","first-page":"629","DOI":"10.1101\/gr.3684805","article-title":"The Chlamydophila abortus genome sequence reveals an array of variable proteins that contribute to interspecies variation","volume":"15","author":"NR Thomson","year":"2005","journal-title":"Genome Res"},{"key":"pone.0304525.ref037","doi-asserted-by":"crossref","first-page":"508","DOI":"10.1128\/IAI.01173-08","article-title":"Chlamydia trachomatis Polymorphic Membrane Protein D Is an Oligomeric Autotransporter with a Higher-Order Structure","volume":"77","author":"KA Swanson","year":"2009","journal-title":"Infect Immun"},{"key":"pone.0304525.ref038","doi-asserted-by":"crossref","first-page":"174","DOI":"10.1111\/j.1462-5822.2009.01389.x","article-title":"Variable expression of surface-exposed polymorphic membrane proteins in in vitro-grown Chlamydia trachomatis","volume":"12","author":"C Tan","year":"2010","journal-title":"Cell Microbiol"},{"key":"pone.0304525.ref039","doi-asserted-by":"crossref","first-page":"1185","DOI":"10.1111\/j.1365-2958.2011.07877.x","article-title":"Quantitative proteomics reveals metabolic and pathogenic properties of Chlamydia trachomatis developmental forms","volume":"82","author":"HA Saka","year":"2011","journal-title":"Mol Microbiol"},{"key":"pone.0304525.ref040","doi-asserted-by":"crossref","first-page":"2686","DOI":"10.1128\/JB.183.8.2686-2690.2001","article-title":"Characterization of Outer Membrane Proteins in Chlamydia trachomatis LGV Serovar L2","volume":"183","author":"J Tanzer R","year":"2001","journal-title":"J Bacteriol"},{"key":"pone.0304525.ref041","doi-asserted-by":"crossref","first-page":"275","DOI":"10.1128\/JB.188.1.275-286.2006","article-title":"Polymorphisms in the Nine Polymorphic Membrane Proteins of Chlamydia trachomatis across All Serovars: Evidence for Serovar Da Recombination and Correlation with Tissue Tropism","volume":"188","author":"JP Gomes","year":"2006","journal-title":"J Bacteriol"},{"key":"pone.0304525.ref042","first-page":"333","article-title":"The Number, Organization, and Size of Polymorphic Membrane Protein Coding Sequences as well as the Most Conserved Pmp Protein Differ within and across Chlamydia Species","volume":"26","author":"S Van Lent","year":"2016","journal-title":"J Mol Microbiol Biotechnol"},{"key":"pone.0304525.ref043","doi-asserted-by":"crossref","first-page":"1200","DOI":"10.1128\/IAI.71.3.1200-1208.2003","article-title":"Polymorphic membrane protein H has evolved in parallel with the three disease-causing groups of Chlamydia trachomatis","volume":"71","author":"DR Stothard","year":"2003","journal-title":"Infect Immun"},{"key":"pone.0304525.ref044","doi-asserted-by":"crossref","first-page":"14819","DOI":"10.1073\/pnas.251267298","article-title":"BETAWRAP: Successful prediction of parallel -helices from primary sequence reveals an association with many microbial pathogens","volume":"98","author":"P Bradley","year":"2001","journal-title":"Proc Natl Acad Sci"},{"key":"pone.0304525.ref045","doi-asserted-by":"crossref","first-page":"e03242","DOI":"10.1128\/spectrum.03242-23","article-title":"A structural foundation for studying chlamydial polymorphic membrane proteins","volume":"11","author":"AM Debrine","year":"2023","journal-title":"Microbiol Spectr"},{"key":"pone.0304525.ref046","doi-asserted-by":"crossref","first-page":"e0198662","DOI":"10.1371\/journal.pone.0198662","article-title":"The Chlamydia trachomatis PmpD adhesin forms higher order structures through disulphide-mediated covalent interactions.","volume":"13","author":"W Paes","year":"2018","journal-title":"PLoS ONE."},{"key":"pone.0304525.ref047","doi-asserted-by":"crossref","first-page":"36","DOI":"10.1186\/1471-2180-2-36","article-title":"The expression, processing and localization of polymorphic membrane proteins in Chlamydia pneumoniae strain CWL029","volume":"2","author":"BB Vandahl","year":"2002","journal-title":"BMC Microbiol"},{"key":"pone.0304525.ref048","doi-asserted-by":"crossref","first-page":"319","DOI":"10.1046\/j.1365-2958.2003.03838.x","article-title":"From the inside out\u2014processing of the Chlamydial autotransporter PmpD and its role in bacterial adhesion and activation of human host cells","volume":"51","author":"W Wehrl","year":"2004","journal-title":"Mol Microbiol"},{"key":"pone.0304525.ref049","doi-asserted-by":"crossref","first-page":"e568","DOI":"10.1371\/journal.pone.0000568","article-title":"Expression, Processing, and Localization of PmpD of Chlamydia trachomatis Serovar L2 during the Chlamydial Developmental Cycle.","volume":"2","author":"AO Kiselev","year":"2007","journal-title":"PLoS ONE"},{"key":"pone.0304525.ref050","doi-asserted-by":"crossref","first-page":"e5191","DOI":"10.1371\/journal.pone.0005191","article-title":"Analysis of pmpD Expression and PmpD Post-Translational Processing during the Life Cycle of Chlamydia trachomatis Serovars A, D, and L2.","volume":"4","author":"AO Kiselev","year":"2009","journal-title":"PLoS ONE."},{"key":"pone.0304525.ref051","doi-asserted-by":"crossref","first-page":"D344","DOI":"10.1093\/nar\/gks1067","article-title":"New and continuing developments at PROSITE","volume":"41","author":"CJA Sigrist","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"pone.0304525.ref052","doi-asserted-by":"crossref","first-page":"772","DOI":"10.1093\/molbev\/mst010","article-title":"MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability","volume":"30","author":"K Katoh","year":"2013","journal-title":"Mol Biol Evol"},{"key":"pone.0304525.ref053","doi-asserted-by":"crossref","first-page":"W200","DOI":"10.1093\/nar\/gky448","article-title":"HMMER web server: 2018 update","volume":"46","author":"SC Potter","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"pone.0304525.ref054","article-title":"Protein tertiary structure prediction and refinement using deep learning and Rosetta in CASP14","author":"I Anishchenko","year":"2021","journal-title":"Proteins"},{"key":"pone.0304525.ref055","doi-asserted-by":"crossref","first-page":"871","DOI":"10.1126\/science.abj8754","article-title":"Accurate prediction of protein structures and interactions using a 3-track neural network","volume":"373","author":"M Baek","year":"2021","journal-title":"Science"},{"key":"pone.0304525.ref056","doi-asserted-by":"crossref","first-page":"1605","DOI":"10.1002\/jcc.20084","article-title":"UCSF Chimera\u2014a visualization system for exploratory research and analysis","volume":"25","author":"EF Pettersen","year":"2004","journal-title":"J Comput Chem"},{"key":"pone.0304525.ref057","doi-asserted-by":"crossref","first-page":"583","DOI":"10.1038\/s41586-021-03819-2","article-title":"Highly accurate protein structure prediction with AlphaFold","volume":"596","author":"J Jumper","year":"2021","journal-title":"Nature"},{"key":"pone.0304525.ref058","doi-asserted-by":"crossref","first-page":"D439","DOI":"10.1093\/nar\/gkab1061","article-title":"AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models","volume":"50","author":"M Varadi","year":"2022","journal-title":"Nucleic Acids Res"},{"key":"pone.0304525.ref059","doi-asserted-by":"crossref","first-page":"1123","DOI":"10.1126\/science.ade2574","article-title":"Evolutionary-scale prediction of atomic-level protein structure with a language model","volume":"379","author":"Z Lin","year":"2023","journal-title":"Science"},{"key":"pone.0304525.ref060","doi-asserted-by":"crossref","first-page":"bbab518","DOI":"10.1093\/bib\/bbab518","article-title":"Predicting protein\u2013membrane interfaces of peripheral membrane proteins using ensemble machine learning","volume":"23","author":"A Chatzigoulas","year":"2022","journal-title":"Brief Bioinform"},{"key":"pone.0304525.ref061","doi-asserted-by":"crossref","first-page":"7812","DOI":"10.1021\/jp071097f","article-title":"The MARTINI Force Field:\u2009 Coarse Grained Model for Biomolecular Simulations","volume":"111","author":"SJ Marrink","year":"2007","journal-title":"J Phys Chem B"},{"key":"pone.0304525.ref062","doi-asserted-by":"crossref","first-page":"687","DOI":"10.1021\/ct300646g","article-title":"Improved Parameters for the Martini Coarse-Grained Protein Force Field.","volume":"9","author":"DH de Jong","year":"2013","journal-title":"J Chem Theory Comput."},{"key":"pone.0304525.ref063","doi-asserted-by":"crossref","first-page":"4486","DOI":"10.1021\/acs.jctc.5b00513","article-title":"CHARMM-GUI Martini Maker for Coarse-Grained Simulations with the Martini Force Field.","volume":"11","author":"Y Qi","year":"2015","journal-title":"J Chem Theory Comput."},{"key":"pone.0304525.ref064","doi-asserted-by":"crossref","first-page":"e1000810","DOI":"10.1371\/journal.pcbi.1000810","article-title":"Polarizable Water Model for the Coarse-Grained MARTINI Force Field.","volume":"6","author":"SO Yesylevskyy","year":"2010","journal-title":"PLOS Comput Biol."},{"key":"pone.0304525.ref065","doi-asserted-by":"crossref","first-page":"1701","DOI":"10.1002\/jcc.20291","article-title":"GROMACS: Fast, flexible, and free","volume":"26","author":"D Van Der Spoel","year":"2005","journal-title":"J Comput Chem"},{"key":"pone.0304525.ref066","doi-asserted-by":"crossref","first-page":"014101","DOI":"10.1063\/1.2408420","article-title":"Canonical sampling through velocity rescaling","volume":"126","author":"G Bussi","year":"2007","journal-title":"J Chem Phys"},{"key":"pone.0304525.ref067","doi-asserted-by":"crossref","first-page":"7182","DOI":"10.1063\/1.328693","article-title":"Polymorphic transitions in single crystals: A new molecular dynamics method","volume":"52","author":"M Parrinello","year":"1981","journal-title":"J Appl Phys"},{"key":"pone.0304525.ref068","doi-asserted-by":"crossref","first-page":"D339","DOI":"10.1093\/nar\/gky1006","article-title":"The Immune Epitope Database (IEDB): 2018 update.","volume":"47","author":"R Vita","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"pone.0304525.ref069","doi-asserted-by":"crossref","first-page":"W24","DOI":"10.1093\/nar\/gkx346","article-title":"BepiPred-2.0: improving sequence-based B-cell epitope prediction using conformational epitopes","volume":"45","author":"MC Jespersen","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"pone.0304525.ref070","doi-asserted-by":"crossref","first-page":"e1002829","DOI":"10.1371\/journal.pcbi.1002829","article-title":"Reliable B cell epitope predictions: impacts of method development and improved benchmarking","volume":"8","author":"JV Kringelum","year":"2012","journal-title":"PLoS Comput Biol"},{"key":"pone.0304525.ref071","first-page":"3363","article-title":"Several common HLA-DR types share largely overlapping peptide binding repertoires","volume":"160","author":"S Southwood","year":"1998","journal-title":"J Immunol Baltim Md 1950."},{"key":"pone.0304525.ref072","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1586\/14760584.2015.955478","article-title":"Time for TImmunoinformatics addresses vaccine design for neglected tropical and emerging infectious diseases.","volume":"14","author":"FE Terry","year":"2014","journal-title":"Expert Rev Vaccines."},{"key":"pone.0304525.ref073","doi-asserted-by":"crossref","first-page":"28","DOI":"10.1016\/j.jim.2015.03.022","article-title":"Development and validation of a broad scheme for prediction of HLA class II restricted T cell epitopes","volume":"422","author":"S Paul","year":"2015","journal-title":"J Immunol Methods"},{"key":"pone.0304525.ref074","doi-asserted-by":"crossref","first-page":"1340","DOI":"10.1038\/s41467-021-21511-x","article-title":"Improved protein structure refinement guided by deep learning based accuracy estimation","volume":"12","author":"N Hiranuma","year":"2021","journal-title":"Nat Commun"},{"key":"pone.0304525.ref075","doi-asserted-by":"crossref","first-page":"4239","DOI":"10.1038\/ncomms5239","article-title":"A mortise-tenon joint in the transmembrane domain modulates autotransporter assembly into bacterial outer membranes.","volume":"5","author":"DL Leyton","year":"2014","journal-title":"Nat Commun"},{"key":"pone.0304525.ref076","doi-asserted-by":"crossref","first-page":"1395","DOI":"10.1038\/s41467-018-03593-2","article-title":"Molecular basis for the folding of \u03b2-helical autotransporter passenger domains.","volume":"9","author":"X Yuan","year":"2018","journal-title":"Nat Commun"},{"key":"pone.0304525.ref077","doi-asserted-by":"crossref","first-page":"323","DOI":"10.1016\/j.bbamem.2010.07.036","article-title":"Lipid chain branching at the iso- and anteiso-positions in complex Chlamydia membranes: a molecular dynamics study","volume":"1808","author":"JB Lim","year":"2011","journal-title":"Biochim Biophys Acta"},{"key":"pone.0304525.ref078","doi-asserted-by":"crossref","first-page":"2607","DOI":"10.3389\/fmicb.2017.02607","article-title":"Identification of the Autochaperone Domain in the Type Va Secretion System (T5aSS): Prevalent Feature of Autotransporters with a \u03b2-Helical Passenger.","volume":"8","author":"M Rojas-Lopez","year":"2017","journal-title":"Front Microbiol."},{"key":"pone.0304525.ref079","doi-asserted-by":"crossref","first-page":"163","DOI":"10.1111\/j.1574-6968.2007.00833.x","article-title":"Autotransporter proteins: novel targets at the bacterial cell surface","volume":"274","author":"TJ Wells","year":"2007","journal-title":"FEMS Microbiol Lett"},{"key":"pone.0304525.ref080","doi-asserted-by":"crossref","first-page":"111","DOI":"10.1016\/S0079-6107(01)00013-X","article-title":"The architecture of parallel \u03b2-helices and related folds","volume":"77","author":"J Jenkins","year":"2001","journal-title":"Prog Biophys Mol Biol"},{"key":"pone.0304525.ref081","doi-asserted-by":"crossref","first-page":"241","DOI":"10.1016\/0969-2126(93)90013-7","article-title":"Unusual structural features in the parallel \u03b2-helix in pectate lyases","volume":"1","author":"MD Yoder","year":"1993","journal-title":"Structure"},{"key":"pone.0304525.ref082","doi-asserted-by":"crossref","first-page":"849","DOI":"10.1126\/science.3775366","article-title":"Loops in Globular Proteins: A Novel Category of Secondary Structure","volume":"234","author":"JF Leszczynski","year":"1986","journal-title":"Science"},{"key":"pone.0304525.ref083","article-title":"Role of adhesin proteins in Chlamydia infection","author":"A. Favaroni","year":"2017","journal-title":"Dissertation, Heinrich Heine University"},{"key":"pone.0304525.ref084","doi-asserted-by":"crossref","first-page":"249","DOI":"10.1042\/bj2970249","article-title":"The structure and function of proline-rich regions in proteins","volume":"297","author":"MP Williamson","year":"1994","journal-title":"Biochem J"},{"key":"pone.0304525.ref085","doi-asserted-by":"crossref","first-page":"2852","DOI":"10.1002\/anie.200400618","article-title":"Recognition of proline-rich motifs by protein-protein-interaction domains","volume":"44","author":"LJ Ball","year":"2005","journal-title":"Angew Chem Int Ed Engl"},{"key":"pone.0304525.ref086","doi-asserted-by":"crossref","first-page":"3940","DOI":"10.1128\/IAI.00632-08","article-title":"Pmp-Like Proteins Pls1 and Pls2 Are Secreted into the Lumen of the Chlamydia trachomatis Inclusion","volume":"76","author":"I Jorgensen","year":"2008","journal-title":"Infect Immun"},{"key":"pone.0304525.ref087","first-page":"87","article-title":"Trichomonas vaginalis Pathobiology.","volume-title":"Advances in Parasitology.","author":"RP Hirt","year":"2011"},{"key":"pone.0304525.ref088","doi-asserted-by":"crossref","first-page":"406","DOI":"10.1186\/s13071-019-3660-z","article-title":"Characterization of the BspA and Pmp protein family of trichomonads.","volume":"12","author":"MR Handrich","year":"2019","journal-title":"Parasit Vectors."},{"key":"pone.0304525.ref089","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1038\/nrmicro2733","article-title":"From self sufficiency to dependence: mechanisms and factors important for autotransporter biogenesis","volume":"10","author":"DL Leyton","year":"2012","journal-title":"Nat Rev Microbiol"},{"key":"pone.0304525.ref090","doi-asserted-by":"crossref","first-page":"1592","DOI":"10.1016\/j.bbamcr.2013.11.006","article-title":"Type V secretion: from biogenesis to biotechnology","volume":"1843","author":"P van Ulsen","year":"2014","journal-title":"Biochim Biophys Acta"},{"key":"pone.0304525.ref091","first-page":"8","article-title":"Type V Secretion in Gram-Negative Bacteria.","author":"HD Bernstein","year":"2019","journal-title":"EcoSal Plus."},{"key":"pone.0304525.ref092","doi-asserted-by":"crossref","first-page":"457","DOI":"10.1073\/pnas.1311592111","article-title":"The antigen 43 structure reveals a molecular Velcro-like mechanism of autotransporter-mediated bacterial clumping","volume":"111","author":"B Heras","year":"2014","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pone.0304525.ref093","first-page":"80","volume-title":"Proceedings of the Julius Schachter Fifteenth International Symposium on Human Chlamydial Infections.","author":"RJ Suchland","year":"2022"},{"key":"pone.0304525.ref094","doi-asserted-by":"crossref","first-page":"e1003325","DOI":"10.1371\/journal.ppat.1003325","article-title":"The Chlamydia pneumoniae Invasin Protein Pmp21 Recruits the EGF Receptor for Host Cell Entry","volume":"9","author":"K M\u00f6lleken","year":"2013","journal-title":"PLOS Pathog"},{"key":"pone.0304525.ref095","first-page":"177","volume-title":"Proceedings of the Julius Schachter Fifteenth International Symposium on Human Chlamydial Infections","author":"X Li","year":"2022"},{"key":"pone.0304525.ref096","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1016\/j.bj.2018.04.007","article-title":"In silico prediction of T- and B-cell epitopes in PmpD: First step towards to the design of a Chlamydia trachomatis vaccine","volume":"41","author":"RC Russi","year":"2018","journal-title":"Biomed J"}],"container-title":["PLOS ONE"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0304525","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,6,11]],"date-time":"2024-06-11T18:10:47Z","timestamp":1718129447000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0304525"}},"subtitle":[],"editor":[{"given":"Agathe","family":"Subtil","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2024,6,11]]},"references-count":96,"journal-issue":{"issue":"6","published-online":{"date-parts":[[2024,6,11]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0304525","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,6,11]]}}}