Please use this identifier to cite or link to this item: http://buratest.brunel.ac.uk/handle/2438/9779
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dc.contributor.authorPandini, A-
dc.contributor.authorBonati, L-
dc.date.accessioned2015-01-16T14:33:00Z-
dc.date.available2005-03-
dc.date.available2015-01-16T14:33:00Z-
dc.date.issued2005-
dc.identifier.citationProtein Engineering, Design and Selection, 18:3, pp. 127 - 137, 2005en_US
dc.identifier.issn1741-0126-
dc.identifier.urihttp://peds.oxfordjournals.org/content/18/3/127-
dc.identifier.urihttp://bura.brunel.ac.uk/handle/2438/9779-
dc.description.abstractThe PAS (Per-ARNT-Sim) superfamily is presented as a well-suited study case to demonstrate how comparison of functional motions among distant homologous proteins with conserved fold characteristics may give insight into their functional specialization. Based on the importance of structural flexibility of the receptive structures in anticipating the signal-induced conformational changes of these sensory systems, the dynamics of these structures were analysed. Molecular dynamics was proved to be an effective method to obtain a reliable picture of the dynamics of the crystal structures of HERG, phy3, PYP and FixL, provided that an extensive conformational space sampling is performed. Other reliable sources of dynamic information were the ensembles of NMR structures of hPASK, HIF-2α and PYP. Essential dynamics analysis was successfully employed to extract the relevant information from the sampled conformational spaces. Comparison of motion patterns in the essential subspaces, based on the structural alignment, allowed identification of the specialized region in each domain. This appears to be evolved in the superfamily by following a specific trend, that also suggests the presence of a limited number of general solutions adopted by the PAS domains to sense external signals. These findings may give insight into unknown mechanisms of PAS domains and guide further experimental studies. © The Author 2005. Published by Oxford University Press. All rights reserved.en_US
dc.languageeng-
dc.language.isoenen_US
dc.subjectEssential motionsen_US
dc.subjectMolecular dynamicsen_US
dc.subjectProtein structuresen_US
dc.titleConservation and specialization in PAS domain dynamicsen_US
dc.typeArticleen_US
dc.identifier.doihttp://dx.doi.org/10.1093/protein/gzi017-
dc.relation.isPartOfProtein Engineering, Design and Selection-
dc.relation.isPartOfProtein Engineering, Design and Selection-
pubs.organisational-data/Brunel-
pubs.organisational-data/Brunel/Brunel Staff by College/Department/Division-
pubs.organisational-data/Brunel/Brunel Staff by College/Department/Division/College of Engineering, Design and Physical Sciences-
pubs.organisational-data/Brunel/Brunel Staff by College/Department/Division/College of Engineering, Design and Physical Sciences/Dept of Computer Science-
pubs.organisational-data/Brunel/Brunel Staff by College/Department/Division/College of Engineering, Design and Physical Sciences/Dept of Computer Science/Computer Science-
Appears in Collections:Dept of Design Research Papers

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