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The flexibility and dynamics of protein disulphide-isomerase
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Römer, Rudolf A., Wells, Stephen A., Jiménez Roldán, J. E. (José Emilio), Bhattacharyya, Moitrayee, Vishweshwara, Saraswathi and Freedman, R. B. (2016) The flexibility and dynamics of protein disulphide-isomerase. Proteins : Structure, Function, and Bioinformatics, 84 (12). pp. 1776-1785. doi:10.1002/prot.25159 ISSN 0887-3585.
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Official URL: http://dx.doi.org/10.1002/prot.25159
Abstract
We have studied the mobility of the multi-domain folding catalyst, protein disulphide-isomerase (PDI), by a coarse-graining approach based on exibility. We analyse our simulations of yeast PDI
(yPDI) using measures of backbone movement, relative positions and orientations of domains, and distances between functional sites. We nd that there is interdomain exibility at every interdomain junction but these show very di erent characteristics. The extent of interdomain exibility is such that yPDI's two active sites can approach much more closely than is found in crystal structures | and indeed hinge motion to bring these sites into proximity is the lowest energy normal mode
of motion of the protein. The exibility predicted for yPDI (based on one structure) includes the other known conformation of yPDI and is consistent with (i) the mobility observed experimentally
for mammalian PDI and (ii) molecular dynamics. We also observe intradomain exibility and clear di erences between the domains in their propensity for internal motion. Our results suggest that
PDI exibility enables it to interact with many di erent partner molecules of widely di erent sizes and shapes, and highlights considerable similarities of yPDI and mammalian PDI.
Item Type: | Journal Article | ||||||||
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Subjects: | Q Science > QP Physiology | ||||||||
Divisions: | Faculty of Science, Engineering and Medicine > Science > Life Sciences (2010- ) Faculty of Science, Engineering and Medicine > Science > Physics |
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Library of Congress Subject Headings (LCSH): | Protein disulfide isomerase, Biomolecules, Computer simulation | ||||||||
Journal or Publication Title: | Proteins : Structure, Function, and Bioinformatics | ||||||||
Publisher: | John Wiley & Sons Ltd. | ||||||||
ISSN: | 0887-3585 | ||||||||
Official Date: | December 2016 | ||||||||
Dates: |
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Volume: | 84 | ||||||||
Number: | 12 | ||||||||
Page Range: | pp. 1776-1785 | ||||||||
DOI: | 10.1002/prot.25159 | ||||||||
Status: | Peer Reviewed | ||||||||
Publication Status: | Published | ||||||||
Access rights to Published version: | Open Access (Creative Commons) | ||||||||
Date of first compliant deposit: | 26 August 2016 | ||||||||
Date of first compliant Open Access: | 3 October 2016 | ||||||||
Funder: | Wellcome Trust (London, England) | ||||||||
Grant number: | Grant number 093125/Z/10/Z |
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