{"data":{"id":"10.6084/m9.figshare.c.2116772.v1","type":"dois","attributes":{"doi":"10.6084/m9.figshare.c.2116772.v1","prefix":"10.6084","suffix":"m9.figshare.c.2116772.v1","identifiers":[],"alternateIdentifiers":[],"creators":[{"name":"Chen, Lin","givenName":"Lin","familyName":"Chen","affiliation":[],"nameIdentifiers":[]},{"name":"Li, Xue","givenName":"Xue","familyName":"Li","affiliation":[],"nameIdentifiers":[]},{"name":"Yang, Wanli","givenName":"Wanli","familyName":"Yang","affiliation":[],"nameIdentifiers":[]},{"name":"Wang, Ruige","givenName":"Ruige","familyName":"Wang","affiliation":[],"nameIdentifiers":[]},{"name":"Fang, Fengqin","givenName":"Fengqin","familyName":"Fang","affiliation":[],"nameIdentifiers":[]},{"name":"Kan, Wei","givenName":"Wei","familyName":"Kan","affiliation":[],"nameIdentifiers":[]}],"titles":[{"title":"Thermal Stability and Unfolding Pathways of Hyperthermophilic and Mesophilic Periplasmic binding proteins studied by Molecular Dynamics Simulation"}],"publisher":"Taylor \u0026 Francis","container":{},"publicationYear":2015,"subjects":[{"subject":"Computational Biology"},{"subject":"Infectious Diseases"},{"subject":"FOS: Health sciences","schemeUri":"http://www.oecd.org/science/inno/38235147.pdf","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"Information and Computing Sciences"},{"subject":"Biological Sciences"},{"subject":"Immunology"},{"subject":"FOS: Clinical medicine","schemeUri":"http://www.oecd.org/science/inno/38235147.pdf","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"Chemistry"},{"subject":"Biotechnology"},{"subject":"Genetics"},{"subject":"FOS: Biological sciences","schemeUri":"http://www.oecd.org/science/inno/38235147.pdf","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"Cell Biology"},{"subject":"Microbiology"},{"subject":"Physics"},{"subject":"Biochemistry"},{"subject":"Biophysics"}],"contributors":[],"dates":[{"date":"2015-12-05","dateType":"Created"},{"date":"2019-08-19","dateType":"Updated"},{"date":"2015","dateType":"Issued"}],"language":null,"types":{"ris":"GEN","bibtex":"misc","citeproc":"article","schemaOrg":"Collection","resourceType":"Collection","resourceTypeGeneral":"Collection"},"relatedIdentifiers":[{"relationType":"IsIdenticalTo","relatedIdentifier":"10.6084/m9.figshare.c.2116772","relatedIdentifierType":"DOI"}],"relatedItems":[],"sizes":[],"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":"The ribose binding protein (RBP), a sugar-binding periplasmic protein, is involved in the transport and signaling processes in both prokaryotes and eukaryotes. Although several cellular and structural studies have been reported, a description of the thermostability of RBP at the molecular level remains elusive. Focused on the hyperthermophilic \u003ci\u003eThermoytoga maritima\u003c/i\u003e RBP (tmRBP) and mesophilic \u003ci\u003eEscherichia coli\u003c/i\u003e homolog (ecRBP), we applied molecular dynamics simulations at four different temperatures (300, 380, 450, and 500 K) to obtain a deeper insight into the structural features responsible for the reduced thermostability of the ecRBP. The simulations results indicate that there are distinct structural differences in the unfolding pathway between the two homologues and the ecRBP unfolds faster than the hyperthermophilic homologues at certain temperatures in accordance with the lower thermal stability found experimentally. Essential dynamics analysis uncovers that the essential subspaces of ecRBP and tmRBP are non-overlapping and these two proteins show different direction of motion within the simulations trajectories. Such an understanding is required for designing efficient proteins with characteristics for a particular application.","descriptionType":"Abstract"}],"geoLocations":[],"fundingReferences":[],"xml":"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