{"data":{"id":"10.6084/m9.figshare.3492149","type":"dois","attributes":{"doi":"10.6084/m9.figshare.3492149","prefix":"10.6084","suffix":"m9.figshare.3492149","identifiers":[],"alternateIdentifiers":[],"creators":[{"name":"Sarath Chandra Dantu","affiliation":[],"nameIdentifiers":[]},{"name":"Khavnekar, Sagar","nameType":"Personal","givenName":"Sagar","familyName":"Khavnekar","affiliation":[],"nameIdentifiers":[]},{"name":"Kale, Avinash","nameType":"Personal","givenName":"Avinash","familyName":"Kale","affiliation":[],"nameIdentifiers":[]}],"titles":[{"title":"Conformational dynamics of Peb4 exhibit “mother’s arms” chain model: a molecular dynamics study"}],"publisher":"Taylor \u0026 Francis","container":{},"publicationYear":2016,"subjects":[{"subject":"Biophysics"},{"subject":"Biochemistry"},{"subject":"29999 Physical Sciences not elsewhere classified","subjectScheme":"FOR"},{"subject":"FOS: Physical sciences","schemeUri":"http://www.oecd.org/science/inno/38235147.pdf","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"FOS: Physical sciences","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"Cell Biology"},{"subject":"39999 Chemical Sciences not elsewhere classified","subjectScheme":"FOR"},{"subject":"FOS: Chemical sciences","schemeUri":"http://www.oecd.org/science/inno/38235147.pdf","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"FOS: Chemical sciences","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"69999 Biological Sciences not elsewhere classified","subjectScheme":"FOR"},{"subject":"FOS: Biological sciences","schemeUri":"http://www.oecd.org/science/inno/38235147.pdf","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"FOS: Biological sciences","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"Cancer"},{"subject":"Computational Biology"}],"contributors":[],"dates":[{"date":"2016-07-19","dateType":"Created"},{"date":"2019-06-01","dateType":"Updated"},{"date":"2016","dateType":"Issued"}],"language":null,"types":{"ris":"DATA","bibtex":"misc","citeproc":"dataset","schemaOrg":"Dataset","resourceType":"Dataset","resourceTypeGeneral":"Dataset"},"relatedIdentifiers":[{"relationType":"IsSupplementTo","relatedIdentifier":"10.1080/07391102.2016.1209131","relatedIdentifierType":"DOI"}],"relatedItems":[],"sizes":["5607782 Bytes"],"formats":[],"version":null,"rightsList":[{"rights":"Creative Commons Attribution 4.0 International","rightsUri":"https://creativecommons.org/licenses/by/4.0/legalcode","schemeUri":"https://spdx.org/licenses/","rightsIdentifier":"cc-by-4.0","rightsIdentifierScheme":"SPDX"}],"descriptions":[{"description":"Peb4 from \u003ci\u003eCampylobacter jejuni\u003c/i\u003e is an intertwined dimeric, periplasmic holdase, which also exhibits peptidyl prolyl cis/trans isomerase (PPIase) activity. Peb4 gene deletion alters the outer membrane protein profile and impairs cellular adhesion and biofilm formation for \u003ci\u003eC. jejuni\u003c/i\u003e. Earlier crystallographic study has proposed that the PPIase domains are flexible and might form a cradle for holding the substrate and these aspects of Peb4 were explored using sub-microsecond molecular dynamics simulations in solution environment. Our simulations have revealed that PPIase domains are highly flexible and undergo a large structural change where they move apart from each other by 8 nm starting at .5 nm. Further, this large conformational change renders Peb4 as a compact protein with crossed-over conformation, forms a central cavity, which can “cradle” the target substrate. As reported for other chaperone proteins, flexibility of linker region connecting the chaperone and PPIase domains is key to forming the “crossed-over” conformation. The conformational transition of the Peb4 protein from the X-ray structure to the crossed-over conformation follows the “mother’s arms” chain model proposed for the FkpA chaperone protein. Our results offer insights into how Peb4 and similar chaperones can use the conformational heterogeneity at their disposal to perform its much-revered biological function.","descriptionType":"Abstract"}],"geoLocations":[],"fundingReferences":[],"xml":"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