{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,11]],"date-time":"2026-02-11T20:29:05Z","timestamp":1770841745663,"version":"3.50.1"},"reference-count":45,"publisher":"Elsevier BV","issue":"11","license":[{"start":{"date-parts":[[2013,6,1]],"date-time":"2013-06-01T00:00:00Z","timestamp":1370044800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2013,6,1]],"date-time":"2013-06-01T00:00:00Z","timestamp":1370044800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2014,6,4]],"date-time":"2014-06-04T00:00:00Z","timestamp":1401840000000},"content-version":"vor","delay-in-days":368,"URL":"http:\/\/www.elsevier.com\/open-access\/userlicense\/1.0\/"}],"funder":[{"DOI":"10.13039\/100009578","name":"Mizutani Foundation for Glycoscience","doi-asserted-by":"publisher","award":["120012"],"award-info":[{"award-number":["120012"]}],"id":[{"id":"10.13039\/100009578","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003407","name":"Ministero dell\u2019Istruzione, dell\u2019Universit\u00e0 e della Ricerca","doi-asserted-by":"publisher","award":["200993WWF9"],"award-info":[{"award-number":["200993WWF9"]}],"id":[{"id":"10.13039\/501100003407","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["cell.com","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Biophysical Journal"],"published-print":{"date-parts":[[2013,6]]},"DOI":"10.1016\/j.bpj.2013.04.040","type":"journal-article","created":{"date-parts":[[2013,6,4]],"date-time":"2013-06-04T12:49:29Z","timestamp":1370350169000},"page":"2530-2539","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":36,"title":["Carbohydrate Recognition by RpfB from Mycobacterium tuberculosis Unveiled by Crystallographic and Molecular Dynamics Analyses"],"prefix":"10.1016","volume":"104","author":[{"given":"Flavia","family":"Squeglia","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Maria","family":"Romano","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alessia","family":"Ruggiero","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Luigi","family":"Vitagliano","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alfonso","family":"De\u00a0Simone","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rita","family":"Berisio","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"78","reference":[{"key":"10.1016\/j.bpj.2013.04.040_bib1","doi-asserted-by":"crossref","first-page":"420","DOI":"10.1378\/chest.08-2427","article-title":"Emergence of new forms of totally drug-resistant tuberculosis bacilli: super extensively drug-resistant tuberculosis or totally drug-resistant strains in Iran","volume":"136","author":"Velayati","year":"2009","journal-title":"Chest"},{"key":"10.1016\/j.bpj.2013.04.040_bib2","doi-asserted-by":"crossref","unstructured":"Rowland, K. 2012. Totally drug-resistant TB emerges in India. NATNEWS. http:\/\/www.nature.com\/news\/totally-drug-resistant-tb-emerges-in-india-1.9797.","DOI":"10.1038\/nature.2012.9797"},{"key":"10.1016\/j.bpj.2013.04.040_bib3","article-title":"First tuberculosis cases in Italy resistant to all tested drugs","volume":"12","author":"Migliori","year":"2007","journal-title":"Euro. Surveill."},{"key":"10.1016\/j.bpj.2013.04.040_bib4","doi-asserted-by":"crossref","first-page":"483","DOI":"10.1038\/nature09657","article-title":"The challenge of new drug discovery for tuberculosis","volume":"469","author":"Koul","year":"2011","journal-title":"Nature"},{"issue":"4, Suppl","key":"10.1016\/j.bpj.2013.04.040_bib5","doi-asserted-by":"crossref","first-page":"S33","DOI":"10.1038\/nm1221","article-title":"Annulling a dangerous liaison: vaccination strategies against AIDS and tuberculosis","volume":"11","author":"Kaufmann","year":"2005","journal-title":"Nat. Med."},{"key":"10.1016\/j.bpj.2013.04.040_bib6","doi-asserted-by":"crossref","first-page":"238","DOI":"10.1016\/S1369-5274(00)00082-5","article-title":"Bacterial dormancy and culturability: the role of autocrine growth factors","volume":"3","author":"Kell","year":"2000","journal-title":"Curr. Opin. Microbiol."},{"key":"10.1016\/j.bpj.2013.04.040_bib7","doi-asserted-by":"crossref","first-page":"20676","DOI":"10.1021\/ja208080r","article-title":"Chemical basis of peptidoglycan discrimination by PrkC, a key kinase involved in bacterial resuscitation from dormancy","volume":"133","author":"Squeglia","year":"2011","journal-title":"J.\u00a0Am. Chem. Soc."},{"key":"10.1016\/j.bpj.2013.04.040_bib8","doi-asserted-by":"crossref","first-page":"1184","DOI":"10.1016\/j.str.2010.06.007","article-title":"Structure and functional regulation of RipA, a mycobacterial enzyme essential for daughter cell separation","volume":"18","author":"Ruggiero","year":"2010","journal-title":"Structure"},{"key":"10.1016\/j.bpj.2013.04.040_bib9","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1042\/BJ20101643","article-title":"X-ray structural studies of the entire extracellular region of the serine\/threonine kinase PrkC from Staphylococcus aureus","volume":"435","author":"Ruggiero","year":"2011","journal-title":"Biochem.\u00a0J."},{"key":"10.1016\/j.bpj.2013.04.040_bib10","doi-asserted-by":"crossref","first-page":"623","DOI":"10.1046\/j.1365-2958.2002.03184.x","article-title":"A family of autocrine growth factors in Mycobacterium tuberculosis","volume":"46","author":"Mukamolova","year":"2002","journal-title":"Mol. Microbiol."},{"key":"10.1016\/j.bpj.2013.04.040_bib11","doi-asserted-by":"crossref","first-page":"537","DOI":"10.1038\/31159","article-title":"Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence","volume":"393","author":"Cole","year":"1998","journal-title":"Nature"},{"key":"10.1016\/j.bpj.2013.04.040_bib12","doi-asserted-by":"crossref","first-page":"2985","DOI":"10.1128\/IAI.74.5.2985-2995.2006","article-title":"Deletion of the Mycobacterium tuberculosis resuscitation-promoting factor Rv1009 gene results in delayed reactivation from chronic tuberculosis","volume":"74","author":"Tufariello","year":"2006","journal-title":"Infect. Immun."},{"key":"10.1016\/j.bpj.2013.04.040_bib13","doi-asserted-by":"crossref","first-page":"153","DOI":"10.1016\/j.jmb.2008.10.042","article-title":"Crystal structure of the resuscitation-promoting factor (DeltaDUF)RpfB from M.\u00a0tuberculosis","volume":"385","author":"Ruggiero","year":"2009","journal-title":"J.\u00a0Mol. Biol."},{"key":"10.1016\/j.bpj.2013.04.040_bib14","doi-asserted-by":"crossref","first-page":"270","DOI":"10.1038\/nsmb905","article-title":"The structure of a\u00a0resuscitation-promoting factor domain from Mycobacterium tuberculosis shows homology to lysozymes","volume":"12","author":"Cohen-Gonsaud","year":"2005","journal-title":"Nat. Struct. Mol. Biol."},{"key":"10.1016\/j.bpj.2013.04.040_bib15","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1080\/07391102.2012.698243","article-title":"Molecular determinants of inactivation of the resuscitation promoting factor B from Mycobacterium tuberculosis","volume":"31","author":"Ruggiero","year":"2013","journal-title":"J.\u00a0Biomol. Struct. Dyn."},{"key":"10.1016\/j.bpj.2013.04.040_bib16","doi-asserted-by":"crossref","first-page":"483","DOI":"10.1073\/pnas.57.3.483","article-title":"The hen egg white lysozyme molecule","volume":"57","author":"Phillips","year":"1967","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.bpj.2013.04.040_bib17","doi-asserted-by":"crossref","first-page":"416","DOI":"10.1111\/j.1469-185X.1953.tb01386.x","article-title":"Stereochemistry and mechanism of enzymatic reactions","volume":"28","author":"Koshland","year":"1953","journal-title":"Biol. Rev. Camb. Philos. Soc."},{"key":"10.1016\/j.bpj.2013.04.040_bib18","doi-asserted-by":"crossref","first-page":"835","DOI":"10.1038\/35090602","article-title":"Catalysis by hen egg-white lysozyme proceeds via a covalent intermediate","volume":"412","author":"Vocadlo","year":"2001","journal-title":"Nature"},{"key":"10.1016\/j.bpj.2013.04.040_bib19","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1016\/S0076-6879(97)76066-X","article-title":"Processing of x-ray diffraction data collected in oscillation mode","volume":"276","author":"Otwinowski","year":"1997","journal-title":"Methods Enzymol."},{"key":"10.1016\/j.bpj.2013.04.040_bib20","doi-asserted-by":"crossref","first-page":"240","DOI":"10.1107\/S0907444996012255","article-title":"Refinement of macromolecular structures by the maximum-likelihood method","volume":"53","author":"Murshudov","year":"1997","journal-title":"Acta Crystallogr. D Biol. Crystallogr."},{"key":"10.1016\/j.bpj.2013.04.040_bib21","doi-asserted-by":"crossref","first-page":"229","DOI":"10.1016\/S0076-6879(03)74011-7","article-title":"ARP\/wARP and automatic interpretation of protein electron density maps","volume":"374","author":"Morris","year":"2003","journal-title":"Methods Enzymol."},{"key":"10.1016\/j.bpj.2013.04.040_bib22","doi-asserted-by":"crossref","first-page":"622","DOI":"10.1002\/jcc.20820","article-title":"GLYCAM06: a generalizable biomolecular force field. Carbohydrates","volume":"29","author":"Kirschner","year":"2008","journal-title":"J.\u00a0Comput. Chem."},{"key":"10.1016\/j.bpj.2013.04.040_bib23","doi-asserted-by":"crossref","first-page":"855","DOI":"10.2174\/138920312804871157","article-title":"Polyproline and triple helix motifs in host-pathogen recognition","volume":"13","author":"Berisio","year":"2012","journal-title":"Curr. Protein Pept. Sci."},{"key":"10.1016\/j.bpj.2013.04.040_bib24","doi-asserted-by":"crossref","first-page":"2253","DOI":"10.1016\/j.bpj.2011.03.033","article-title":"Role of hydration in collagen recognition by bacterial adhesins","volume":"100","author":"Vitagliano","year":"2011","journal-title":"Biophys.\u00a0J."},{"key":"10.1016\/j.bpj.2013.04.040_bib25","doi-asserted-by":"crossref","first-page":"121","DOI":"10.1016\/j.bbrc.2008.04.190","article-title":"Role of hydration in collagen triple helix stabilization","volume":"372","author":"De Simone","year":"2008","journal-title":"Biochem. Biophys. Res. Commun."},{"key":"10.1016\/j.bpj.2013.04.040_bib26","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1007\/978-1-60327-058-8_8","article-title":"Protein structure modeling with MODELLER","volume":"426","author":"Eswar","year":"2008","journal-title":"Methods Mol. Biol."},{"key":"10.1016\/j.bpj.2013.04.040_bib27","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1107\/S0021889892009944","article-title":"PROCHECK: a program to check the stereochemical quality of protein structures","volume":"26","author":"Laskowski","year":"1993","journal-title":"J.\u00a0Appl. Cryst."},{"key":"10.1016\/j.bpj.2013.04.040_bib28","doi-asserted-by":"crossref","first-page":"311","DOI":"10.1073\/pnas.91.1.311","article-title":"Direct observation of\u00a0better hydration at the N-terminus of an alpha-helix with glycine rather than alanine as the N-cap residue","volume":"91","author":"Harpaz","year":"1994","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.bpj.2013.04.040_bib29","doi-asserted-by":"crossref","first-page":"1781","DOI":"10.1016\/j.carres.2010.05.026","article-title":"Conformational properties of glucose-based disaccharides investigated using molecular dynamics simulations with local elevation umbrella sampling","volume":"345","author":"Peri\u0107-Hassler","year":"2010","journal-title":"Carbohydr. Res."},{"key":"10.1016\/j.bpj.2013.04.040_bib30","doi-asserted-by":"crossref","first-page":"5545","DOI":"10.1021\/bi00139a017","article-title":"Multiple role of hydrophobicity of tryptophan-108 in chicken lysozyme: structural stability, saccharide binding ability, and abnormal pKa of glutamic acid-35","volume":"31","author":"Inoue","year":"1992","journal-title":"Biochemistry"},{"key":"10.1016\/j.bpj.2013.04.040_bib31","doi-asserted-by":"crossref","first-page":"756","DOI":"10.2174\/138920312804871201","article-title":"Bacterial cell division regulation by Ser\/Thr kinases: a structural perspective","volume":"13","author":"Ruggiero","year":"2012","journal-title":"Curr. Protein Pept. Sci."},{"key":"10.1016\/j.bpj.2013.04.040_bib32","doi-asserted-by":"crossref","first-page":"816","DOI":"10.2174\/138920312804871175","article-title":"Protein-carbohydrate interactions studied by NMR: from molecular recognition to drug design","volume":"13","author":"Fernandez-Alonso","year":"2012","journal-title":"Curr. Protein Pept. Sci."},{"key":"10.1016\/j.bpj.2013.04.040_bib33","doi-asserted-by":"crossref","first-page":"946","DOI":"10.1021\/ar300024d","article-title":"Carbohydrate-aromatic interactions","volume":"46","author":"Asensio","year":"2013","journal-title":"Acc. Chem. Res."},{"key":"10.1016\/j.bpj.2013.04.040_bib34","doi-asserted-by":"crossref","first-page":"292","DOI":"10.1021\/bi991402q","article-title":"Protein-carbohydrate interactions in human lysozyme probed by combining site-directed mutagenesis and affinity labeling","volume":"39","author":"Muraki","year":"2000","journal-title":"Biochemistry"},{"key":"10.1016\/j.bpj.2013.04.040_bib35","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1006\/jmbi.1994.0139","article-title":"Dissection of protein-carbohydrate interactions in mutant hen egg-white lysozyme complexes and their hydrolytic activity","volume":"247","author":"Maenaka","year":"1995","journal-title":"J.\u00a0Mol. Biol."},{"key":"10.1016\/j.bpj.2013.04.040_bib36","doi-asserted-by":"crossref","first-page":"4116","DOI":"10.1021\/ja3007897","article-title":"Magnitude and molecular origin of water slowdown next to a protein","volume":"134","author":"Sterpone","year":"2012","journal-title":"J.\u00a0Am. Chem. Soc."},{"key":"10.1016\/j.bpj.2013.04.040_bib37","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1007\/s10867-011-9235-7","article-title":"Understanding the role of hydrogen bonds in water dynamics and protein stability","volume":"38","author":"Bianco","year":"2012","journal-title":"J.\u00a0Biol. Phys."},{"key":"10.1016\/j.bpj.2013.04.040_bib38","doi-asserted-by":"crossref","first-page":"19873","DOI":"10.1073\/pnas.1104299108","article-title":"More than one dynamic crossover in protein hydration water","volume":"108","author":"Mazza","year":"2011","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.bpj.2013.04.040_bib39","doi-asserted-by":"crossref","first-page":"4365","DOI":"10.1073\/pnas.1116167109","article-title":"Evaporation rate of water in hydrophobic confinement","volume":"109","author":"Sharma","year":"2012","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.bpj.2013.04.040_bib40","doi-asserted-by":"crossref","first-page":"753","DOI":"10.1093\/jb\/mvn133","article-title":"Catalytic reaction mechanism of goose egg-white lysozyme by molecular modelling of enzyme-substrate complex","volume":"144","author":"Hirakawa","year":"2008","journal-title":"J.\u00a0Biochem."},{"key":"10.1016\/j.bpj.2013.04.040_bib41","doi-asserted-by":"crossref","first-page":"4404","DOI":"10.1073\/pnas.0510182103","article-title":"Three-dimensional structure of the bacterial cell wall peptidoglycan","volume":"103","author":"Meroueh","year":"2006","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.bpj.2013.04.040_bib42","doi-asserted-by":"crossref","first-page":"515","DOI":"10.1128\/IAI.72.1.515-526.2004","article-title":"Individual Mycobacterium tuberculosis resuscitation-promoting factor homologues are dispensable for growth in\u00a0vitro and in\u00a0vivo","volume":"72","author":"Tufariello","year":"2004","journal-title":"Infect. Immun."},{"key":"10.1016\/j.bpj.2013.04.040_bib43","doi-asserted-by":"crossref","first-page":"672","DOI":"10.1111\/j.1365-2958.2007.06078.x","article-title":"The resuscitation-promoting factors of Mycobacterium tuberculosis are required for virulence and resuscitation from dormancy but are collectively dispensable for growth in\u00a0vitro","volume":"67","author":"Kana","year":"2008","journal-title":"Mol. Microbiol."},{"key":"10.1016\/j.bpj.2013.04.040_bib44","doi-asserted-by":"crossref","first-page":"114","DOI":"10.1016\/j.bbrc.2007.02.094","article-title":"MD and NMR studies of alpha-bungarotoxin surface accessibility","volume":"356","author":"Venditti","year":"2007","journal-title":"Biochem. Biophys. Res. Commun."},{"key":"10.1016\/j.bpj.2013.04.040_bib45","doi-asserted-by":"crossref","first-page":"15318","DOI":"10.1021\/ja303309e","article-title":"Release of high-energy water as an essential driving force for the high-affinity binding of cucurbit[n]urils","volume":"134","author":"Biedermann","year":"2012","journal-title":"J.\u00a0Am. Chem. Soc."}],"container-title":["Biophysical Journal"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0006349513004736?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0006349513004736?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2025,9,13]],"date-time":"2025-09-13T16:26:29Z","timestamp":1757780789000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0006349513004736"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,6]]},"references-count":45,"journal-issue":{"issue":"11","published-print":{"date-parts":[[2013,6]]}},"alternative-id":["S0006349513004736"],"URL":"https:\/\/doi.org\/10.1016\/j.bpj.2013.04.040","relation":{},"ISSN":["0006-3495"],"issn-type":[{"value":"0006-3495","type":"print"}],"subject":[],"published":{"date-parts":[[2013,6]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Carbohydrate Recognition by RpfB from Mycobacterium tuberculosis Unveiled by Crystallographic and Molecular Dynamics Analyses","name":"articletitle","label":"Article Title"},{"value":"Biophysical Journal","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.bpj.2013.04.040","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"Copyright \u00a9 2013 Biophysical Society. Published by Elsevier Inc. All rights reserved.","name":"copyright","label":"Copyright"}]}}