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Rapid shape determination of tissue transglutaminase using high-throughput computing

Lammie, Donna, Osborne, James, Aeschlimann, Daniel and Wess, Timothy James 2007. Rapid shape determination of tissue transglutaminase using high-throughput computing. Acta Crystallographica Section D: Biological Crystallography 63 (9) , pp. 1022-1024. 10.1107/S0907444907032933

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Abstract

Small-angle X-ray scattering can be used to determine the molecular shape of macromolecules in solution which are otherwise refractory to conventional high-resolution studies. DAMMIN and GASBOR are applications that utilize ab initio methods to build models of proteins using simulated annealing; both DAMMIN and GASBOR have to be run numerous times on the same input data to generate the most likely protein shape. Condor is a specialized workload-management system for PC computation-intensive tasks. Using Condor, DAMMIN and GASBOR can be run a number of times simultaneously on the same input data, allowing the shape of proteins to be determined in a fraction of the time it would have taken to have run DAMMIN and GASBOR sequentially. The main advantage of this approach is that it allows quicker data processing; therefore, results are obtained promptly and without undue delay. Tissue transglutaminase is a multidomain enzyme that catalyses the formation of isopeptide bonds between polypeptide chains. This reaction requires the enzyme to undergo a series of conformational changes that are not well understood in order to allow the sequential interaction with the two substrate proteins and their subsequent release when cross-linked. Condor was applied to determine the solution shape of tissue transglutaminase in a rapid fashion. Eventually, the next step will be to move towards online analysis at synchrotron sources by developing a graphical user interface that will enable remote access, allowing users to submit jobs to Condor whilst at synchrotrons.

Item Type: Article
Date Type: Publication
Status: Published
Schools: Advanced Research Computing @ Cardiff (ARCCA)
Dentistry
Information Services
Optometry and Vision Sciences
Subjects: Q Science > Q Science (General)
Q Science > QA Mathematics > QA75 Electronic computers. Computer science
Uncontrolled Keywords: Condor; DAMMIN; GASBOR; small-angle X-ray scattering
Publisher: International Union of Crystallography
ISSN: 0907-4449
Last Modified: 04 Jun 2017 03:38
URI: http://orca.cf.ac.uk/id/eprint/23904

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