{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,14]],"date-time":"2026-08-14T20:30:23Z","timestamp":1786739423808,"version":"build-2736575974"},"reference-count":39,"publisher":"Ovid Technologies (Wolters Kluwer Health)","issue":"2","license":[{"start":{"date-parts":[[2026,2,1]],"date-time":"2026-02-01T00:00:00Z","timestamp":1769904000000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"}],"content-domain":{"domain":["lww.com","ovid.com"],"crossmark-restriction":true},"short-container-title":[],"published-print":{"date-parts":[[2026,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background:<\/jats:title>\n                    <jats:p>\n                      <jats:italic toggle=\"yes\">Enterococcus faecium<\/jats:italic>\n                      synthesizes enterococcal surface protein (Esp), a cell wall-anchored, domain-adhesin implicated in healthcare-associated infections and persistent root canal disease. Esp may facilitate the development of strategies to inhibit surface attachment and decrease biofilm formation.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Aim:<\/jats:title>\n                    <jats:p>\n                      To\n                      <jats:italic toggle=\"yes\">in silico<\/jats:italic>\n                      characterize the secondary structure, conserved motifs, and stereochemical quality of Esp, and to relate these features to adhesion and biofilm persistence.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Materials and Methods:<\/jats:title>\n                    <jats:p>The Esp sequence was analyzed using Garnier\u2013Osguthorpe\u2013Robson (GOR) secondary structure prediction, motif and feature annotation, and stereochemical evaluation via Ramachandran plots and the overall G-factor. The study had an assessment of \u03b1-helices, \u03b2-strands, \u03b2\/\u03b3 turns, \u03b2-hairpins, and immunoglobulin-like repeats. Structural quality was defined by the proportion of favored conformations and backbone geometry metrics.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results:<\/jats:title>\n                    <jats:p>Esp is predicted to form a mostly \u03b2-sheet based structure with 35 \u03b1-helices, multiple turns, and recurring \u03b2-hairpins, consistent with Ig-like modules; stereochemical analysis (85% residues in favored Ramachandran regions; G-factor \u22120.33) supports acceptable backbone geometry, and the abundance of turns\/hairpins likely provides flexible interdomain linkers that promote surface binding and biofilm stability under root-canal stress.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusion:<\/jats:title>\n                    <jats:p>Sequence-based structural\/motif and stereochemical analyses suggest that Esp adopts a flexible, \u03b2-rich scaffold with recurrent turns and hairpins that may support adhesion and biofilm persistence in endodontic settings.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.4103\/jcde.jcde_1018_25","type":"journal-article","created":{"date-parts":[[2026,2,2]],"date-time":"2026-02-02T10:00:09Z","timestamp":1770026409000},"page":"172-178","update-policy":"https:\/\/doi.org\/10.1097\/lww.0000000000001000","source":"Crossref","is-referenced-by-count":0,"title":["Sequence-based structural\/motif and stereochemical analysis of enterococcal surface protein in endodontic"],"prefix":"10.4103","volume":"29","author":[{"given":"Nezar","family":"Boreak","sequence":"first","affiliation":[{"name":"Department of Restorative Dental Sciences, College of Dentistry, Jazan University, Jazan, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Orjwan","family":"Halawi","sequence":"additional","affiliation":[{"name":"Department of Restorative Dental Sciences, College of Dentistry, Jazan University, Jazan, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Khalid Ahmed","family":"Albulushi","sequence":"additional","affiliation":[{"name":"College of Dentistry, Taibah University, Medina, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wejdan Yahya Jaber","family":"Ghazwani","sequence":"additional","affiliation":[{"name":"Department of Restorative Dental Sciences, College of Dentistry, Jazan University, Jazan, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Roaa Mohammed","family":"Zarban","sequence":"additional","affiliation":[{"name":"Department of Restorative Dental Sciences, College of Dentistry, Jazan University, Jazan, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ahmed Saad Radi","family":"Algamdi","sequence":"additional","affiliation":[{"name":"Faculty of Dentistry, Al Baha University, Al Baha, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shadi Abdullah","family":"Hamzi","sequence":"additional","affiliation":[{"name":"College of Dentistry, Jazan University, Jazan, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Algarni Hmoud","family":"Ali","sequence":"additional","affiliation":[{"name":"Department of Restorative Dental Sciences, College of Dentistry, Jouf University, Kingdom of Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hashim","family":"Bajawi","sequence":"additional","affiliation":[{"name":"Department of Restorative Dental Sciences, College of Dentistry, Jazan University, Jazan, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"276","published-online":{"date-parts":[[2026,2,2]]},"reference":[{"key":"R1-20260202","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1016\/0022-2836(78)90297-8","article-title":"Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins","volume":"120","author":"Garnier","year":"1978","journal-title":"J Mol Biol"},{"key":"R2-20260202","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1007\/978-1-4939-6406-2_2","article-title":"The GOR method of protein secondary structure prediction and its application as a protein aggregation prediction tool","volume":"1484","author":"Kouza","year":"2017","journal-title":"Methods Mol Biol"},{"key":"R3-20260202","doi-asserted-by":"crossref","first-page":"W389","DOI":"10.1093\/nar\/gkv332","article-title":"JPred4:A protein secondary structure prediction server","volume":"43","author":"Drozdetskiy","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"R4-20260202","doi-asserted-by":"crossref","first-page":"2842","DOI":"10.1093\/bioinformatics\/btx218","article-title":"Capturing non-local interactions by long short-term memory bidirectional recurrent neural networks for improving prediction of protein secondary structure, backbone angles, contact numbers and solvent accessibility","volume":"33","author":"Heffernan","year":"2017","journal-title":"Bioinformatics"},{"key":"R5-20260202","doi-asserted-by":"crossref","first-page":"W329","DOI":"10.1093\/nar\/gky384","article-title":"IUPred2A:Context-dependent prediction of protein disorder as a function of redox state and protein binding","volume":"46","author":"M\u00e9sz\u00e1ros","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"R6-20260202","doi-asserted-by":"crossref","first-page":"6561","DOI":"10.1021\/cr400514h","article-title":"Introducing protein intrinsic disorder","volume":"114","author":"Habchi","year":"2014","journal-title":"Chem Rev"},{"key":"R7-20260202","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":"Jumper","year":"2021","journal-title":"Nature"},{"key":"R8-20260202","doi-asserted-by":"crossref","first-page":"6032","DOI":"10.1128\/IAI.72.10.6032-6039.2004","article-title":"Enterococcal surface protein, Esp, enhances biofilm formation by Enterococcus faecalis","volume":"72","author":"Tendolkar","year":"2004","journal-title":"Infect Immun"},{"key":"R9-20260202","doi-asserted-by":"crossref","first-page":"4538","DOI":"10.1128\/AEM.67.10.4538-4545.2001","article-title":"The enterococcal surface protein, Esp, is involved in Enterococcus faecalis biofilm formation","volume":"67","author":"Toledo-Arana","year":"2001","journal-title":"Appl Environ Microbiol"},{"key":"R10-20260202","doi-asserted-by":"crossref","first-page":"1185","DOI":"10.1016\/j.micinf.2011.08.006","article-title":"Contribution of the enterococcal surface protein Esp to pathogenesis of Enterococcus faecium endocarditis","volume":"13","author":"Heikens","year":"2011","journal-title":"Microbes Infect"},{"key":"R11-20260202","doi-asserted-by":"crossref","first-page":"175","DOI":"10.1007\/978-94-007-0940-9_11","article-title":"Crystallography of gram-positive bacterial adhesins","volume":"715","author":"Krishnan","year":"2011","journal-title":"Adv Exp Med Biol"},{"key":"R12-20260202","doi-asserted-by":"crossref","first-page":"200","DOI":"10.1016\/j.sbi.2012.01.009","article-title":"Structure and assembly of Gram-positive bacterial pili:Unique covalent polymers","volume":"22","author":"Kang","year":"2012","journal-title":"Curr Opin Struct Biol"},{"key":"R13-20260202","doi-asserted-by":"crossref","first-page":"633","DOI":"10.1016\/S0955-0674(03)00099-1","article-title":"Bacterial pathogenesis:Exploiting cellular adherence","volume":"15","author":"Boyle","year":"2003","journal-title":"Curr Opin Cell Biol"},{"key":"R14-20260202","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1016\/S0022-2836(63)80023-6","article-title":"Stereochemistry of polypeptide chain configurations","volume":"7","author":"Ramachandran","year":"1963","journal-title":"J Mol Biol"},{"key":"R15-20260202","doi-asserted-by":"crossref","first-page":"437","DOI":"10.1002\/prot.10286","article-title":"Structure validation by Calpha geometry:Phi, psi and Cbeta deviation","volume":"50","author":"Lovell","year":"2003","journal-title":"Proteins"},{"key":"R16-20260202","doi-asserted-by":"crossref","first-page":"345","DOI":"10.1002\/prot.340120407","article-title":"Stereochemical quality of protein structure coordinates","volume":"12","author":"Morris","year":"1992","journal-title":"Proteins"},{"key":"R17-20260202","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1023\/A:1026127927612","article-title":"From protein structure to biochemical function?","volume":"4","author":"Laskowski","year":"2003","journal-title":"J Struct Funct Genomics"},{"key":"R18-20260202","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1073\/pnas.93.1.13","article-title":"Principles of protein-protein interactions","volume":"93","author":"Jones","year":"1996","journal-title":"Proc Natl Acad Sci U S A"},{"key":"R19-20260202","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/s41586-023-05870-7","article-title":"Programmable protein delivery with a bacterial contractile injection system","volume":"616","author":"Kreitz","year":"2023","journal-title":"Nature"},{"key":"R20-20260202","doi-asserted-by":"crossref","first-page":"211","DOI":"10.1021\/bi00699a001","article-title":"Conformational parameters for amino acids in helical, beta-sheet, and random coil regions calculated from proteins","volume":"13","author":"Chou","year":"1974","journal-title":"Biochemistry"},{"key":"R21-20260202","doi-asserted-by":"crossref","first-page":"221","DOI":"10.1016\/0022-2836(88)90103-9","article-title":"Analysis and prediction of the different types of beta-turn in proteins","volume":"203","author":"Wilmot","year":"1988","journal-title":"J Mol Biol"},{"key":"R22-20260202","doi-asserted-by":"crossref","first-page":"212","DOI":"10.1002\/pro.5560050204","article-title":"PROMOTIF \u2013A program to identify and analyze structural motifs in proteins","volume":"5","author":"Hutchinson","year":"1996","journal-title":"Protein Sci"},{"key":"R23-20260202","doi-asserted-by":"crossref","first-page":"143","DOI":"10.1007\/BF03404909","article-title":"Beta-and gamma-turns in proteins revisited:A new set of amino acid turn-type dependent positional preferences and potentials","volume":"25","author":"Guruprasad","year":"2000","journal-title":"J Biosci"},{"key":"R24-20260202","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1016\/S0065-3233(08)60520-3","article-title":"The anatomy and taxonomy of protein structure","volume":"34","author":"Richardson","year":"1981","journal-title":"Adv Protein Chem"},{"key":"R25-20260202","doi-asserted-by":"crossref","first-page":"2699","DOI":"10.1093\/nar\/gky092","article-title":"UniProt:The universal protein knowledgebase","volume":"46","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"R26-20260202","first-page":"531","article-title":"Protein identification and analysis tools in the ExPASy server","volume":"112","author":"Wilkins","year":"1999","journal-title":"Methods Mol Biol"},{"key":"R27-20260202","doi-asserted-by":"crossref","first-page":"425","DOI":"10.1016\/0022-2836(87)90292-0","article-title":"Further developments of protein secondary structure prediction using information theory. New parameters and consideration of residue pairs","volume":"198","author":"Gibrat","year":"1987","journal-title":"J Mol Biol"},{"key":"R28-20260202","doi-asserted-by":"crossref","first-page":"404","DOI":"10.1093\/bioinformatics\/16.4.404","article-title":"The PSIPRED protein structure prediction server","volume":"16","author":"McGuffin","year":"2000","journal-title":"Bioinformatics"},{"key":"R29-20260202","doi-asserted-by":"crossref","first-page":"1425","DOI":"10.1002\/bip.1968.360061006","article-title":"Stereochemical criteria for polypeptides and proteins. V. Conformation of a system of three linked peptide units","volume":"6","author":"Venkatachalam","year":"1968","journal-title":"Biopolymers"},{"key":"R30-20260202","doi-asserted-by":"crossref","first-page":"726","DOI":"10.1038\/s41579-021-00569-w","article-title":"The microbiome-shaping roles of bacteriocins","volume":"19","author":"Heilbronner","year":"2021","journal-title":"Nat Rev Microbiol"},{"key":"R31-20260202","doi-asserted-by":"crossref","first-page":"505","DOI":"10.4103\/JCDE.JCDE_682_24","article-title":"Assessing the antibacterial potency of royal jelly:Minimum inhibitory concentration and minimum bactericidal concentration evaluation against Streptococcus mutans and Staphylococcus aureus","volume":"28","author":"Turbatmath","year":"2025","journal-title":"J Conserv Dent Endod"},{"key":"R32-20260202","doi-asserted-by":"crossref","first-page":"737","DOI":"10.4103\/JCDE.JCDE_215_24","article-title":"Antimicrobial efficacy of calcium silicate-based bioceramic sealers against Enterococcus faecalis and Staphylococcus aureus \u2013An in vitro study","volume":"27","author":"Kirthiga","year":"2024","journal-title":"J Conserv Dent Endod"},{"key":"R33-20260202","first-page":"560","article-title":"An in vitro evaluation of antibacterial effect of curcumin-loaded chitosan nanoparticle-coated gutta-percha against Staphylococcus aureus","volume":"26","author":"Sharma","year":"2023","journal-title":"J Conserv Dent Endod"},{"key":"R34-20260202","doi-asserted-by":"crossref","first-page":"613","DOI":"10.4103\/JCDE.JCDE_126_24","article-title":"Effect of ultrasonic and Er, Cr:YSGG laser-activated irrigation protocol on dual-species root canal biofilm removal:An in vitro study","volume":"27","author":"Datla","year":"2024","journal-title":"J Conserv Dent Endod"},{"key":"R35-20260202","doi-asserted-by":"crossref","first-page":"444","DOI":"10.4103\/JCDE.JCDE_99_25","article-title":"Evaluation of antimicrobial efficacy of sodium dichloroisocyanurate as an intracanal medicament against Enterococcus faecalis and Candida albicans","volume":"28","author":"Ilango","year":"2025","journal-title":"J Conserv Dent Endod"},{"key":"R36-20260202","doi-asserted-by":"crossref","first-page":"204","DOI":"10.1016\/j.ijbiomac.2013.03.005","article-title":"Preparation and characterization of nano chitosan for treatment wastewaters","volume":"57","author":"Sivakami","year":"2013","journal-title":"Int J Biol Macromol"},{"key":"R37-20260202","doi-asserted-by":"crossref","first-page":"477","DOI":"10.1007\/BF00228148","article-title":"AQUA and PROCHECK-NMR:Programs for checking the quality of protein structures solved by NMR","volume":"8","author":"Laskowski","year":"1996","journal-title":"J Biomol NMR"},{"key":"R38-20260202","doi-asserted-by":"crossref","first-page":"399","DOI":"10.1046\/j.1365-2591.2001.00437.x","article-title":"Enterococcus faecalis \u2013A mechanism for its role in endodontic failure","volume":"34","author":"Love","year":"2001","journal-title":"Int Endod J"},{"key":"R39-20260202","doi-asserted-by":"crossref","first-page":"1248","DOI":"10.1111\/jam.14677","article-title":"Inactivation efficacy and mechanisms of plasma activated water on bacteria in planktonic state","volume":"129","author":"Zhao","year":"2020","journal-title":"J Appl Microbiol"}],"container-title":["Journal of Conservative Dentistry and Endodontics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.ovid.com\/10.4103\/JCDE.JCDE_1018_25","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,14]],"date-time":"2026-08-14T19:28:52Z","timestamp":1786735732000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.ovid.com\/10.4103\/JCDE.JCDE_1018_25"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,2]]},"references-count":39,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2026]]}},"URL":"https:\/\/doi.org\/10.4103\/jcde.jcde_1018_25","relation":{},"ISSN":["2950-4716","2950-4708"],"issn-type":[{"value":"2950-4716","type":"print"},{"value":"2950-4708","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,2]]},"assertion":[{"value":"2025-12-05","name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2025-12-29","name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}}]}}