{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,26]],"date-time":"2026-08-26T10:21:14Z","timestamp":1787739674254,"version":"build-2784847793"},"reference-count":74,"publisher":"MDPI AG","issue":"23","license":[{"start":{"date-parts":[[2023,11,26]],"date-time":"2023-11-26T00:00:00Z","timestamp":1700956800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"CONAHCYT","award":["387325"],"award-info":[{"award-number":["387325"]}]},{"name":"CONAHCYT","award":["988721"],"award-info":[{"award-number":["988721"]}]},{"name":"CONAHCYT","award":["739485"],"award-info":[{"award-number":["739485"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>CagY is the largest and most complex protein from Helicobacter pylori\u2019s (Hp) type IV secretion system (T4SS), playing a critical role in the modulation of gastric inflammation and risk for gastric cancer. CagY spans from the inner to the outer membrane, forming a channel through which Hp molecules are injected into human gastric cells. Yet, a tridimensional structure has been reported for only short segments of the protein. This intricate protein was modeled using different approaches, including homology modeling, ab initio, and deep learning techniques. The challengingly long middle repeat region (MRR) was modeled using deep learning and optimized using equilibrium molecular dynamics. The previously modeled segments were assembled into a 1595 aa chain and a 14-chain CagY multimer structure was assembled by structural alignment. The final structure correlated with published structures and allowed to show how the multimer may form the T4SS channel through which CagA and other molecules are translocated to gastric cells. The model confirmed that MRR, the most polymorphic and complex region of CagY, presents numerous cysteine residues forming disulfide bonds that stabilize the protein and suggest this domain may function as a contractile region playing an essential role in the modulating activity of CagY on tissue inflammation.<\/jats:p>","DOI":"10.3390\/ijms242316781","type":"journal-article","created":{"date-parts":[[2023,11,27]],"date-time":"2023-11-27T03:32:03Z","timestamp":1701055923000},"page":"16781","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["A Proposal for a Consolidated Structural Model of the CagY Protein of Helicobacter pylori"],"prefix":"10.3390","volume":"24","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1843-9922","authenticated-orcid":false,"given":"Mario Angel","family":"L\u00f3pez-Luis","sequence":"first","affiliation":[{"name":"Laboratorio de Biotecnolog\u00eda y Bioinform\u00e1tica Gen\u00f3mica, Departamento de Bioqu\u00edmica, Escuela Nacional de Ciencias Biol\u00f3gicas, Instituto Polit\u00e9cnico Nacional, Campus L\u00e1zaro C\u00e1rdenas, Mexico City 11340, Mexico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5171-8862","authenticated-orcid":false,"given":"Eva Elda","family":"Soriano-P\u00e9rez","sequence":"additional","affiliation":[{"name":"Laboratorio de Biotecnolog\u00eda y Bioinform\u00e1tica Gen\u00f3mica, Departamento de Bioqu\u00edmica, Escuela Nacional de Ciencias Biol\u00f3gicas, Instituto Polit\u00e9cnico Nacional, Campus L\u00e1zaro C\u00e1rdenas, Mexico City 11340, Mexico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jos\u00e9 Carlos","family":"Parada-Fabi\u00e1n","sequence":"additional","affiliation":[{"name":"Laboratorio de Biotecnolog\u00eda y Bioinform\u00e1tica Gen\u00f3mica, Departamento de Bioqu\u00edmica, Escuela Nacional de Ciencias Biol\u00f3gicas, Instituto Polit\u00e9cnico Nacional, Campus L\u00e1zaro C\u00e1rdenas, Mexico City 11340, Mexico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3945-4221","authenticated-orcid":false,"given":"Javier","family":"Torres","sequence":"additional","affiliation":[{"name":"Unidad de Investigaci\u00f3n en Enfermedades Infecciosas, UMAE Pediatr\u00eda, Instituto Mexicano del Seguro Social, Mexico City 06720, Mexico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rogelio","family":"Maldonado-Rodr\u00edguez","sequence":"additional","affiliation":[{"name":"Laboratorio de Biotecnolog\u00eda y Bioinform\u00e1tica Gen\u00f3mica, Departamento de Bioqu\u00edmica, Escuela Nacional de Ciencias Biol\u00f3gicas, Instituto Polit\u00e9cnico Nacional, Campus L\u00e1zaro C\u00e1rdenas, Mexico City 11340, Mexico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1871-4311","authenticated-orcid":false,"given":"Alfonso","family":"M\u00e9ndez-Tenorio","sequence":"additional","affiliation":[{"name":"Laboratorio de Biotecnolog\u00eda y Bioinform\u00e1tica Gen\u00f3mica, Departamento de Bioqu\u00edmica, Escuela Nacional de Ciencias Biol\u00f3gicas, Instituto Polit\u00e9cnico Nacional, Campus L\u00e1zaro C\u00e1rdenas, Mexico City 11340, Mexico"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2023,11,26]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"1582","DOI":"10.1126\/science.1080857","article-title":"Traces of human migrations in Helicobacter pylori populations","volume":"299","author":"Falush","year":"2003","journal-title":"Science"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"449","DOI":"10.1128\/CMR.00054-05","article-title":"Pathogenesis of Helicobacter pylori infection","volume":"19","author":"Kusters","year":"2006","journal-title":"Clin. 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