{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,9]],"date-time":"2026-09-09T06:13:41Z","timestamp":1788934421454,"version":"build-2803163510"},"reference-count":86,"publisher":"Elsevier BV","issue":"11","license":[{"start":{"date-parts":[[2024,11,1]],"date-time":"2024-11-01T00:00:00Z","timestamp":1730419200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2024,11,1]],"date-time":"2024-11-01T00:00:00Z","timestamp":1730419200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2024,9,27]],"date-time":"2024-09-27T00:00:00Z","timestamp":1727395200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100009193","name":"Royal Society of New Zealand Marsden Fund","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100009193","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["jbc.org","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Journal of Biological Chemistry"],"published-print":{"date-parts":[[2024,11]]},"DOI":"10.1016\/j.jbc.2024.107851","type":"journal-article","created":{"date-parts":[[2024,9,30]],"date-time":"2024-09-30T13:58:38Z","timestamp":1727704718000},"page":"107851","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":7,"title":["On the function of TRAP substrate-binding proteins: Conformational variation of the sialic acid binding protein\u00a0SiaP"],"prefix":"10.1016","volume":"300","author":[{"given":"Te-Rina J.","family":"King-Hudson","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4029-1650","authenticated-orcid":false,"given":"James S.","family":"Davies","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Senwei","family":"Quan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael J.","family":"Currie","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zachary D.","family":"Tillett","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5482-8052","authenticated-orcid":false,"given":"Jack","family":"Copping","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Santosh","family":"Panjikar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rosmarie","family":"Friemann","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jane R.","family":"Allison","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rachel A.","family":"North","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5506-4939","authenticated-orcid":false,"given":"Renwick C.J.","family":"Dobson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.jbc.2024.107851_bib1","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1128\/JB.181.1.47-54.1999","article-title":"Convergent pathways for utilization of the amino sugars N-acetylglucosamine, N-acetylmannosamine, and N-acetylneuraminic acid by Escherichia coli","volume":"181","author":"Plumbridge","year":"1999","journal-title":"J.\u00a0Bacteriol."},{"key":"10.1016\/j.jbc.2024.107851_bib2","doi-asserted-by":"crossref","first-page":"1173","DOI":"10.1111\/j.1365-2958.2005.04901.x","article-title":"Sialic acid transport in Haemophilus influenzae is essential for lipopolysaccharide sialylation and serum resistance and is dependent on a novel tripartite ATP-independent periplasmic transporter","volume":"58","author":"Severi","year":"2005","journal-title":"Mol. Microbiol."},{"key":"10.1016\/j.jbc.2024.107851_bib3","doi-asserted-by":"crossref","first-page":"118","DOI":"10.1186\/1471-2148-9-118","article-title":"Insights into the evolution of sialic acid catabolism among bacteria","volume":"9","author":"Almagro-Moreno","year":"2009","journal-title":"BMC Evol. Biol."},{"key":"10.1016\/j.jbc.2024.107851_bib4","doi-asserted-by":"crossref","first-page":"760","DOI":"10.1042\/BST20160056","article-title":"Sialic acid acquisition in bacteria-one substrate, many transporters","volume":"44","author":"Thomas","year":"2016","journal-title":"Biochem. Soc. Trans."},{"key":"10.1016\/j.jbc.2024.107851_bib5","doi-asserted-by":"crossref","first-page":"219","DOI":"10.1007\/s12551-017-0343-x","article-title":"\u201cJust a spoonful of sugar\u2026\u201d: import of sialic acid across bacterial cell membranes","volume":"10","author":"North","year":"2018","journal-title":"Biophysical Rev."},{"key":"10.1016\/j.jbc.2024.107851_bib6","doi-asserted-by":"crossref","first-page":"2158","DOI":"10.1099\/mic.0.059659-0","article-title":"The VC1777\u2013VC1779 proteins are members of a sialic acid-specific subfamily of TRAP transporters (SiaPQM) and constitute the sole route of sialic acid uptake in the human pathogen Vibrio cholerae","volume":"158","author":"Chowdhury","year":"2012","journal-title":"Microbiology"},{"key":"10.1016\/j.jbc.2024.107851_bib7","doi-asserted-by":"crossref","first-page":"48","DOI":"10.1186\/1471-2180-10-48","article-title":"Sialic acid mediated transcriptional modulation of a highly conserved sialometabolism gene cluster in Haemophilus influenzae and its effect on virulence","volume":"10","author":"Jenkins","year":"2010","journal-title":"BMC Microbiol."},{"key":"10.1016\/j.jbc.2024.107851_bib8","doi-asserted-by":"crossref","first-page":"855","DOI":"10.1074\/jbc.M706603200","article-title":"Characterization of the N-acetyl-5-neuraminic acid-binding site of the extracytoplasmic solute receptor (SiaP) of nontypeable Haemophilus influenzae strain 2019","volume":"283","author":"Johnston","year":"2008","journal-title":"J.\u00a0Biol. Chem."},{"key":"10.1016\/j.jbc.2024.107851_bib9","doi-asserted-by":"crossref","DOI":"10.1073\/pnas.2301115120","article-title":"Sialic acid plays a pivotal role in licensing Citrobacter rodentium\u2019s transition from the intestinal lumen to a mucosal adherent niche","volume":"120","author":"Liang","year":"2023","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"10.1016\/j.jbc.2024.107851_bib10","doi-asserted-by":"crossref","first-page":"3301","DOI":"10.1074\/jbc.RA119.010526","article-title":"The basis for non-canonical ROK family function in the N-acetylmannosamine kinase from the pathogen Staphylococcus aureus","volume":"295","author":"Coombes","year":"2020","journal-title":"J.\u00a0Biol. Chem."},{"key":"10.1016\/j.jbc.2024.107851_bib11","doi-asserted-by":"crossref","DOI":"10.1016\/j.jbc.2021.101113","article-title":"N-Acetylmannosamine-6-phosphate 2-epimerase uses a novel substrate-assisted mechanism to catalyze amino sugar epimerization","volume":"297","author":"Currie","year":"2021","journal-title":"J.\u00a0Biol. Chem."},{"key":"10.1016\/j.jbc.2024.107851_bib12","doi-asserted-by":"crossref","first-page":"30923","DOI":"10.1021\/acsomega.0c03699","article-title":"Structure and function of N-acetylmannosamine kinases from pathogenic bacteria","volume":"5","author":"Setty","year":"2020","journal-title":"ACS Omega"},{"key":"10.1016\/j.jbc.2024.107851_bib13","doi-asserted-by":"crossref","first-page":"654","DOI":"10.1002\/prot.25846","article-title":"On the structure and function of Escherichia coli YjhC: an oxidoreductase involved in bacterial sialic acid metabolism","volume":"88","author":"Horne","year":"2020","journal-title":"Proteins"},{"key":"10.1016\/j.jbc.2024.107851_bib14","doi-asserted-by":"crossref","first-page":"4414","DOI":"10.1002\/1873-3468.12462","article-title":"Structure and inhibition of N-acetylneuraminate lyase from methicillin-resistant Staphylococcus aureus","volume":"590","author":"North","year":"2016","journal-title":"FEBS Lett."},{"key":"10.1016\/j.jbc.2024.107851_bib15","doi-asserted-by":"crossref","first-page":"405","DOI":"10.1111\/j.1574-6976.2001.tb00584.x","article-title":"The tripartite ATP-independent periplasmic (TRAP) transporters of bacteria and archaea","volume":"25","author":"Kelly","year":"2001","journal-title":"Fems. Microbiol. Rev."},{"key":"10.1016\/j.jbc.2024.107851_bib16","doi-asserted-by":"crossref","first-page":"68","DOI":"10.1111\/j.1574-6976.2010.00236.x","article-title":"Tripartite ATP-independent periplasmic (TRAP) transporters in bacteria and archaea","volume":"35","author":"Mulligan","year":"2011","journal-title":"Fems. Microbiol. Rev."},{"key":"10.1016\/j.jbc.2024.107851_bib17","doi-asserted-by":"crossref","first-page":"1120","DOI":"10.1038\/s41467-023-36590-1","article-title":"Structure and mechanism of a tripartite ATP-independent periplasmic TRAP transporter","volume":"14","author":"Davies","year":"2023","journal-title":"Nat. Commun."},{"key":"10.1016\/j.jbc.2024.107851_bib18","doi-asserted-by":"crossref","first-page":"4471","DOI":"10.1038\/s41467-022-31907-y","article-title":"Structural and mechanistic analysis of a tripartite ATP-independent periplasmic TRAP transporter","volume":"13","author":"Peter","year":"2022","journal-title":"Nat. Commun."},{"key":"10.1016\/j.jbc.2024.107851_bib19","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.92307.3","article-title":"Structural and biophysical analysis of a Haemophilus influenzae tripartite ATP-independent periplasmic (TRAP) transporter","volume":"12","author":"Currie","year":"2024","journal-title":"eLife"},{"key":"10.1016\/j.jbc.2024.107851_bib20","article-title":"Molecular determinants of Neu5Ac binding to a tripartite ATP independent periplasmic (TRAP) transporter","volume":"1","author":"Goyal","year":"2024","journal-title":"eLife"},{"key":"10.1016\/j.jbc.2024.107851_bib21","doi-asserted-by":"crossref","first-page":"134","DOI":"10.1016\/j.tibs.2023.11.006","article-title":"TRAPs: the \u2018elevator-with-an-operator\u2019 mechanism","volume":"49","author":"Davies","year":"2023","journal-title":"Trends Biochem. Sci."},{"key":"10.1016\/j.jbc.2024.107851_bib22","doi-asserted-by":"crossref","first-page":"1011","DOI":"10.1042\/BST20150135","article-title":"The substrate-binding protein in bacterial ABC transporters: dissecting roles in the evolution of substrate specificity","volume":"43","author":"Maqbool","year":"2015","journal-title":"Biochem. Soc. Trans."},{"key":"10.1016\/j.jbc.2024.107851_bib23","doi-asserted-by":"crossref","first-page":"471","DOI":"10.1016\/j.tim.2010.06.009","article-title":"Caught in a TRAP: substrate-binding proteins in secondary transport","volume":"18","author":"Fischer","year":"2010","journal-title":"Trends Microbiol."},{"key":"10.1016\/j.jbc.2024.107851_bib24","doi-asserted-by":"crossref","first-page":"1778","DOI":"10.1073\/pnas.0809979106","article-title":"The substrate-binding protein imposes directionality on an electrochemical sodium gradient-driven TRAP transporter","volume":"106","author":"Mulligan","year":"2009","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"10.1016\/j.jbc.2024.107851_bib25","doi-asserted-by":"crossref","first-page":"15818","DOI":"10.1021\/jacs.9b06275","article-title":"Water networks can determine the affinity of ligand binding to proteins","volume":"141","author":"Darby","year":"2019","journal-title":"J.\u00a0Am. Chem. Soc."},{"key":"10.1016\/j.jbc.2024.107851_bib26","doi-asserted-by":"crossref","first-page":"27113","DOI":"10.1074\/jbc.M115.656603","article-title":"Tripartite ATP-independent Periplasmic (TRAP) transporters use an arginine-mediated selectivity filter for high affinity substrate binding","volume":"290","author":"Fischer","year":"2015","journal-title":"J.\u00a0Biol. Chem."},{"key":"10.1016\/j.jbc.2024.107851_bib27","doi-asserted-by":"crossref","first-page":"22212","DOI":"10.1074\/jbc.M603463200","article-title":"Conservation of structure and mechanism in primary and secondary transporters exemplified by SiaP, a sialic acid binding virulence factor from Haemophilus influenzae","volume":"281","author":"M\u00fcller","year":"2006","journal-title":"J.\u00a0Biol. Chem."},{"key":"10.1016\/j.jbc.2024.107851_bib28","doi-asserted-by":"crossref","first-page":"1801","DOI":"10.1107\/S139900471400830X","article-title":"Bacterial periplasmic sialic acid-binding proteins exhibit a conserved binding site","volume":"70","author":"Setty","year":"2014","journal-title":"Acta Crystallogr. D Biol. Crystallogr."},{"key":"10.1016\/j.jbc.2024.107851_bib29","doi-asserted-by":"crossref","first-page":"2606","DOI":"10.1016\/j.febslet.2010.04.043","article-title":"A\u00a0structural classification of substrate-binding proteins","volume":"584","author":"Berntsson","year":"2010","journal-title":"FEBS Lett."},{"key":"10.1016\/j.jbc.2024.107851_bib30","doi-asserted-by":"crossref","first-page":"1131","DOI":"10.1016\/S0021-9258(19)68161-5","article-title":"Hinge-bending in L-arabinose-binding protein. The \u201cVenus\u2019s-flytrap\u201d model","volume":"257","author":"Mao","year":"1982","journal-title":"J.\u00a0Biol. Chem."},{"key":"10.1016\/j.jbc.2024.107851_bib31","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1208\/ps010202","article-title":"The venus flytrap of periplasmic binding proteins: an ancient protein module present in multiple drug receptors","volume":"1","author":"Felder","year":"1999","journal-title":"AAPS PharmSci"},{"key":"10.1016\/j.jbc.2024.107851_bib32","doi-asserted-by":"crossref","first-page":"8931","DOI":"10.1016\/S0021-9258(17)37057-6","article-title":"The 1.9 A x-ray structure of a closed unliganded form of the periplasmic glucose\/galactose receptor from Salmonella typhimurium","volume":"269","author":"Flocco","year":"1994","journal-title":"J.\u00a0Biol. Chem."},{"key":"10.1016\/j.jbc.2024.107851_bib33","doi-asserted-by":"crossref","first-page":"17881","DOI":"10.1074\/jbc.271.30.17881","article-title":"Maltose-binding protein containing an interdomain disulfide bridge confers a dominant-negative phenotype for transport and chemotaxis","volume":"271","author":"Zhang","year":"1996","journal-title":"J.\u00a0Biol. Chem."},{"key":"10.1016\/j.jbc.2024.107851_bib34","doi-asserted-by":"crossref","first-page":"1078","DOI":"10.1038\/nature06232","article-title":"Open-to-closed transition in apo maltose-binding protein observed by paramagnetic NMR","volume":"449","author":"Tang","year":"2007","journal-title":"Nature"},{"key":"10.1016\/j.jbc.2024.107851_bib35","doi-asserted-by":"crossref","first-page":"32848","DOI":"10.1074\/jbc.M806021200","article-title":"Crystal structures of the choline\/acetylcholine substrate-binding protein ChoX from Sinorhizobium meliloti in the liganded and unliganded-closed states","volume":"283","author":"Oswald","year":"2008","journal-title":"J.\u00a0Biol. Chem."},{"key":"10.1016\/j.jbc.2024.107851_bib36","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1016\/j.bpj.2016.12.010","article-title":"PELDOR spectroscopy reveals two defined states of a sialic acid TRAP transporter SBP in solution","volume":"112","author":"Glaenzer","year":"2017","journal-title":"Biophys. J."},{"key":"10.1016\/j.jbc.2024.107851_bib37","article-title":"Triggering closure of a sialic acid TRAP transporter substrate binding protein through binding of natural or artificial substrates","volume":"433","author":"Peter","year":"2020","journal-title":"J.\u00a0Mol. Biol."},{"key":"10.1016\/j.jbc.2024.107851_bib38","doi-asserted-by":"crossref","first-page":"359","DOI":"10.1016\/j.str.2018.10.013","article-title":"Structural characterization of biomolecules through atomistic simulations guided by DEER Measurements","volume":"27","author":"Marinelli","year":"2019","journal-title":"Structure"},{"key":"10.1016\/j.jbc.2024.107851_bib39","doi-asserted-by":"crossref","first-page":"122","DOI":"10.1111\/j.1600-0757.1999.tb00160.x","article-title":"Actinobacillus actinomycetemcomitans and Porphyromonas gingivalis in nonoral infections","volume":"20","author":"Winkelhoff","year":"1999","journal-title":"Periodontol. 2000"},{"key":"10.1016\/j.jbc.2024.107851_bib40","doi-asserted-by":"crossref","first-page":"303","DOI":"10.1016\/j.micpath.2017.11.001","article-title":"Oral pathogenesis of Aggregatibacter actinomycetemcomitans","volume":"113","author":"Gholizadeh","year":"2017","journal-title":"Microb. Pathog."},{"key":"10.1016\/j.jbc.2024.107851_bib41","doi-asserted-by":"crossref","first-page":"188","DOI":"10.1016\/0006-291X(68)90728-6","article-title":"A\u00a0new method for the determination of N-terminus of peptides chain with fluorescein-isothiocyanate","volume":"31","author":"Maeda","year":"1968","journal-title":"Biochem. Biophys. Res. Commun."},{"key":"10.1016\/j.jbc.2024.107851_bib42","doi-asserted-by":"crossref","first-page":"293","DOI":"10.1002\/pro.3330","article-title":"MolProbity: more and better reference data for improved all-atom structure validation","volume":"27","author":"Williams","year":"2018","journal-title":"Protein Sci."},{"key":"10.1016\/j.jbc.2024.107851_bib43","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1107\/S0907444909042073","article-title":"MolProbity: all-atom structure validation for macromolecular crystallography","volume":"66","author":"Chen","year":"2010","journal-title":"Acta Crystallogr. D Biol. Crystallogr."},{"key":"10.1016\/j.jbc.2024.107851_bib44","doi-asserted-by":"crossref","first-page":"774","DOI":"10.1016\/j.jmb.2007.05.022","article-title":"Inference of macromolecular assemblies from crystalline state","volume":"372","author":"Krissinel","year":"2007","journal-title":"J.\u00a0Mol. Biol."},{"key":"10.1016\/j.jbc.2024.107851_bib45","unstructured":"Hopkins, A. P. (2010) Molecular and Biochemical Characterisation of SiaP as a Sialic Acid Binding Protein Component of a TRAP Transporter of Sialic Acid. Ph.D. thesis, The University of York."},{"key":"10.1016\/j.jbc.2024.107851_bib46","doi-asserted-by":"crossref","first-page":"1727","DOI":"10.1038\/nprot.2014.116","article-title":"Synchrotron-based small-angle X-ray scattering of proteins in solution","volume":"9","author":"Skou","year":"2014","journal-title":"Nat. Protoc."},{"key":"10.1016\/j.jbc.2024.107851_bib47","article-title":"Conformational and dynamic plasticity in substrate-binding proteins underlies selective transport in ABC importers","volume":"8","author":"Boer","year":"2019","journal-title":"eLife"},{"key":"10.1016\/j.jbc.2024.107851_bib48","doi-asserted-by":"crossref","first-page":"449","DOI":"10.1002\/jcc.26075","article-title":"Direct derivation of free energies of membrane deformation and other solvent density variations from enhanced sampling molecular dynamics","volume":"41","author":"Fiorin","year":"2019","journal-title":"J.\u00a0Comput. Chem."},{"key":"10.1016\/j.jbc.2024.107851_bib49","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1038\/s41467-023-44327-3","article-title":"Conformational coupling of the sialic acid TRAP transporter HiSiaQM with its substrate binding protein HiSiaP","volume":"15","author":"Peter","year":"2024","journal-title":"Nat. Commun."},{"key":"10.1016\/j.jbc.2024.107851_bib50","doi-asserted-by":"crossref","first-page":"515","DOI":"10.1038\/nature06264","article-title":"Crystal structure of a catalytic intermediate of the maltose transporter","volume":"450","author":"Oldham","year":"2007","journal-title":"Nature"},{"key":"10.1016\/j.jbc.2024.107851_bib51","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1038\/nsmb.2929","article-title":"Conformational dynamics in substrate-binding domains influences transport in the ABC importer GlnPQ","volume":"22","author":"Gouridis","year":"2014","journal-title":"Nat. Struct. Mol. Biol."},{"key":"10.1016\/j.jbc.2024.107851_bib52","doi-asserted-by":"crossref","first-page":"W636","DOI":"10.1093\/nar\/gkz268","article-title":"The EMBL-EBI search and sequence analysis tools APIs in 2019","volume":"47","author":"Madeira","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.jbc.2024.107851_bib53","doi-asserted-by":"crossref","first-page":"320","DOI":"10.1093\/nar\/gku316","article-title":"Deciphering key features in protein structures with the new ENDscript server","volume":"42","author":"Robert","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.jbc.2024.107851_bib54","doi-asserted-by":"crossref","first-page":"420","DOI":"10.1038\/s41587-019-0036-z","article-title":"SignalP 5.0 improves signal peptide predictions using deep neural networks","volume":"37","author":"Armenteros","year":"2019","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.jbc.2024.107851_bib55","article-title":"Determination of protein-ligand interactions using differential scanning fluorimetry","volume":"91","author":"Vivoli","year":"2014","journal-title":"J.\u00a0Vis. Exp."},{"key":"10.1016\/j.jbc.2024.107851_bib56","doi-asserted-by":"crossref","first-page":"7.13.1","DOI":"10.1002\/0471140864.ps0713s60","article-title":"Methods for the design and analysis of sedimentation velocity and sedimentation equilibrium experiments with proteins","volume":"60","author":"Demeler","year":"2010","journal-title":"Curr. Protoc. Protein Sci."},{"key":"10.1016\/j.jbc.2024.107851_bib57","series-title":"Modern Analytical Ultracentrifugation: Techniques and Methods","first-page":"210","article-title":"UltraScan - a comprehensive data analysis software package for analytical ultracentrifugation experiments","author":"Demeler","year":"2005"},{"key":"10.1016\/j.jbc.2024.107851_bib58","doi-asserted-by":"crossref","first-page":"405","DOI":"10.1007\/s00249-009-0413-5","article-title":"A\u00a0two-dimensional spectrum analysis for sedimentation velocity experiments of mixtures with heterogeneity in molecular weight and shape","volume":"39","author":"Brookes","year":"2010","journal-title":"Eur. Biophys. J."},{"key":"10.1016\/j.jbc.2024.107851_bib59","series-title":"Proceedings of the 9th Annual Conference on Genetic and Evolutionary Computation","first-page":"361","article-title":"Parsimonious regularization using genetic algorithms applied to the analysis of analytical ultracentrifugation experiments","author":"Brookes","year":"2007"},{"key":"10.1016\/j.jbc.2024.107851_bib60","doi-asserted-by":"crossref","first-page":"856","DOI":"10.1016\/j.bpj.2018.01.002","article-title":"HullRad: fast calculations of folded and disordered protein and nucleic acid hydrodynamic properties","volume":"114","author":"Fleming","year":"2018","journal-title":"Biophys. J."},{"key":"10.1016\/j.jbc.2024.107851_bib61","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1107\/S0907444909047337","article-title":"Xds","volume":"66","author":"Kabsch","year":"2010","journal-title":"Acta Crystallogr. D Biol. Crystallogr."},{"key":"10.1016\/j.jbc.2024.107851_bib62","doi-asserted-by":"crossref","first-page":"68","DOI":"10.1107\/S2059798317016035","article-title":"CCP4i2: the new graphical user interface to the CCP4 program suite","volume":"74","author":"Potterton","year":"2018","journal-title":"Acta Crystallogr. D Biol. Crystallogr."},{"key":"10.1016\/j.jbc.2024.107851_bib63","doi-asserted-by":"crossref","first-page":"658","DOI":"10.1107\/S0021889807021206","article-title":"Phaser crystallographic software","volume":"40","author":"McCoy","year":"2007","journal-title":"J.\u00a0Appl. Crystallogr."},{"key":"10.1016\/j.jbc.2024.107851_bib64","doi-asserted-by":"crossref","first-page":"2126","DOI":"10.1107\/S0907444904019158","article-title":"Coot: model-building tools for molecular graphics","volume":"60","author":"Emsley","year":"2004","journal-title":"Acta Crystallogr. D Biol. Crystallogr."},{"key":"10.1016\/j.jbc.2024.107851_bib65","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.jbc.2024.107851_bib66","doi-asserted-by":"crossref","first-page":"355","DOI":"10.1107\/S0907444911001314","article-title":"REFMAC5 for the refinement of macromolecular crystal structures","volume":"67","author":"Murshudov","year":"2011","journal-title":"Acta Crystallogr. D Biol. Crystallogr."},{"key":"10.1016\/j.jbc.2024.107851_bib67","doi-asserted-by":"crossref","first-page":"861","DOI":"10.1107\/S2059798319011471","article-title":"Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix","volume":"75","author":"Liebschner","year":"2019","journal-title":"Acta Crystallogr. D Biol. Crystallogr."},{"key":"10.1016\/j.jbc.2024.107851_bib68","doi-asserted-by":"crossref","first-page":"486","DOI":"10.1107\/S0907444910007493","article-title":"Features and development of Coot","volume":"66","author":"Emsley","year":"2010","journal-title":"Acta Crystallogr. D Biol. Crystallogr."},{"key":"10.1016\/j.jbc.2024.107851_bib69","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1107\/S1600576717017101","article-title":"An optimized SEC-SAXS system enabling high X-ray dose for rapid SAXS assessment with correlated UV measurements for biomolecular structure analysis","volume":"51","author":"Ryan","year":"2018","journal-title":"J.\u00a0Appl. Crystallogr."},{"key":"10.1016\/j.jbc.2024.107851_bib70","doi-asserted-by":"crossref","first-page":"1212","DOI":"10.1107\/S1600576717007786","article-title":"ATSAS 2.8: a comprehensive data analysis suite for small-angle scattering from macromolecular solutions","volume":"50","author":"Franke","year":"2017","journal-title":"J.\u00a0Appl. Crystallogr."},{"key":"10.1016\/j.jbc.2024.107851_bib71","doi-asserted-by":"crossref","first-page":"768","DOI":"10.1107\/S0021889895007047","article-title":"CRYSOL \u2013 a program to evaluate X-ray solution scattering of biological macromolecules from atomic coordinates","volume":"28","author":"Svergun","year":"1995","journal-title":"J.\u00a0Appl. Crystallogr."},{"key":"10.1016\/j.jbc.2024.107851_bib72","doi-asserted-by":"crossref","first-page":"1051","DOI":"10.1107\/S1399004715002576","article-title":"Ambiguity assessment of small-angle scattering curves from monodisperse systems","volume":"71","author":"Petoukhov","year":"2015","journal-title":"Acta Crystallogr. D Biol. Crystallogr."},{"key":"10.1016\/j.jbc.2024.107851_bib73","doi-asserted-by":"crossref","first-page":"2946","DOI":"10.1016\/S0006-3495(01)76260-1","article-title":"Determination of domain structure of proteins from X-ray solution scattering","volume":"80","author":"Svergun","year":"2001","journal-title":"Biophys. J."},{"key":"10.1016\/j.jbc.2024.107851_bib74","doi-asserted-by":"crossref","first-page":"860","DOI":"10.1107\/S0021889803000268","article-title":"Uniqueness of ab initio shape determination in small-angle scattering","volume":"36","author":"Volkov","year":"2003","journal-title":"J.\u00a0Appl. Crystallogr."},{"key":"10.1016\/j.jbc.2024.107851_bib75","doi-asserted-by":"crossref","first-page":"5707","DOI":"10.1039\/C5CP04540A","article-title":"Deciphering conformational transitions of proteins by small angle X-ray scattering and normal mode analysis","volume":"18","author":"Panjkovich","year":"2016","journal-title":"Phys. Chem. Chem. Phys."},{"key":"10.1016\/j.jbc.2024.107851_bib76","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1016\/j.softx.2015.06.001","article-title":"GROMACS: high performance molecular simulations through multi-level parallelism from laptops to supercomputers","volume":"1\u20132","author":"Abraham","year":"2015","journal-title":"SoftwareX"},{"key":"10.1016\/j.jbc.2024.107851_bib77","doi-asserted-by":"crossref","first-page":"2135","DOI":"10.1002\/jcc.23354","article-title":"CHARMM36 all-atom additive protein force field: validation based on comparison to NMR data","volume":"34","author":"Huang","year":"2013","journal-title":"J.\u00a0Comput. Chem."},{"key":"10.1016\/j.jbc.2024.107851_bib78","doi-asserted-by":"crossref","first-page":"10089","DOI":"10.1063\/1.464397","article-title":"Particle mesh Ewald: an N\u22c5log(N) method for Ewald sums in large systems","volume":"98","author":"Darden","year":"1993","journal-title":"J.\u00a0Chem. Phys."},{"key":"10.1016\/j.jbc.2024.107851_bib79","doi-asserted-by":"crossref","first-page":"98","DOI":"10.1103\/PhysRev.159.98","article-title":"Computer \u201cexperiments\u201d on classical fluids. I. Thermodynamical properties of Lennard-Jones molecules","volume":"159","author":"Verlet","year":"1967","journal-title":"Phys. Rev."},{"key":"10.1016\/j.jbc.2024.107851_bib80","doi-asserted-by":"crossref","first-page":"1463","DOI":"10.1002\/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H","article-title":"LINCS: a linear constraint solver for molecular simulations","volume":"18","author":"Hess","year":"1997","journal-title":"J.\u00a0Comput. Chem."},{"key":"10.1016\/j.jbc.2024.107851_bib81","article-title":"Canonical sampling through velocity rescaling","volume":"126","author":"Bussi","year":"2007","journal-title":"J.\u00a0Chem. Phys."},{"key":"10.1016\/j.jbc.2024.107851_bib82","doi-asserted-by":"crossref","first-page":"3684","DOI":"10.1063\/1.448118","article-title":"Molecular dynamics with coupling to an external bath","volume":"81","author":"Berendsen","year":"1984","journal-title":"J.\u00a0Chem. Phys."},{"key":"10.1016\/j.jbc.2024.107851_bib83","doi-asserted-by":"crossref","first-page":"1196","DOI":"10.1103\/PhysRevLett.45.1196","article-title":"Crystal structure and pair potentials: a molecular-dynamics study","volume":"45","author":"Parrinello","year":"1980","journal-title":"Phys. Rev. Lett."},{"key":"10.1016\/j.jbc.2024.107851_bib84","doi-asserted-by":"crossref","first-page":"926","DOI":"10.1063\/1.445869","article-title":"Comparison of simple potential functions for simulating liquid water","volume":"79","author":"Jorgensen","year":"1983","journal-title":"J.\u00a0Chem. Phys."},{"key":"10.1016\/j.jbc.2024.107851_bib85","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1016\/0263-7855(96)00018-5","article-title":"VMD: Visual molecular dynamics","volume":"14","author":"Humphrey","year":"1996","journal-title":"J.\u00a0Mol. Graph."},{"key":"10.1016\/j.jbc.2024.107851_bib86","series-title":"R: A Language and Environment for Statistical Computing","year":"2021"}],"container-title":["Journal of Biological Chemistry"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0021925824023536?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0021925824023536?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2024,11,28]],"date-time":"2024-11-28T15:52:33Z","timestamp":1732809153000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0021925824023536"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,11]]},"references-count":86,"journal-issue":{"issue":"11","published-print":{"date-parts":[[2024,11]]}},"alternative-id":["S0021925824023536"],"URL":"https:\/\/doi.org\/10.1016\/j.jbc.2024.107851","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2024.04.30.591957","asserted-by":"object"}]},"ISSN":["0021-9258"],"issn-type":[{"value":"0021-9258","type":"print"}],"subject":[],"published":{"date-parts":[[2024,11]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"On the function of TRAP substrate-binding proteins: Conformational variation of the sialic acid binding protein\u00a0SiaP","name":"articletitle","label":"Article Title"},{"value":"Journal of Biological Chemistry","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.jbc.2024.107851","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2024 The Authors. Published by Elsevier Inc on behalf of American Society for Biochemistry and Molecular Biology.","name":"copyright","label":"Copyright"}],"article-number":"107851"}}