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Integration of FIRST, FRODA and NMM in a coarse grained method to study Protein Disulphide Isomerase conformational change
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Jiménez Roldán, J. E. (José Emilio), Wells, Stephen A., Freedman, R. B. and Römer, Rudolf A. (2011) Integration of FIRST, FRODA and NMM in a coarse grained method to study Protein Disulphide Isomerase conformational change. Journal of Physics: Conference Series, Vol.286 (No.1). Article No. 012002. doi:10.1088/1742-6596/286/1/012002
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Official URL: http://dx.doi.org/10.1088/1742-6596/286/1/012002
Abstract
Our simulations of protein motion are based on a rigidity-based coarse graining criteria which is able to identify flexible and constraint regions and on Normal Modes of Motion (NMM) which map out the directions of motion for a given network. The NMM and rigidity constraints are integrated together by the FRODA module to identify large scale conformational changes at low computational cost. In this context we identify the limits for conformational change of a large multi domain protein -Protein Disulphide Isomerase, by re-assessing the principal NMM at intermediate points along a trajectory as the protein moves over the trajectory defined by the initial principal NMM.
| Item Type: | Journal Article | ||||
|---|---|---|---|---|---|
| Subjects: | Q Science > QA Mathematics > QA76 Electronic computers. Computer science. Computer software Q Science > QP Physiology |
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| Divisions: | Faculty of Science > Computer Science Faculty of Science > Physics |
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| Library of Congress Subject Headings (LCSH): | Proteins -- Conformation, Proteins -- Conformation -- Computer simulation, Molecular dynamics | ||||
| Journal or Publication Title: | Journal of Physics: Conference Series | ||||
| Publisher: | Institute of Physics Publishing Ltd. | ||||
| ISSN: | 1742-6596 | ||||
| Official Date: | 2011 | ||||
| Dates: |
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| Volume: | Vol.286 | ||||
| Number: | No.1 | ||||
| Page Range: | Article No. 012002 | ||||
| DOI: | 10.1088/1742-6596/286/1/012002 | ||||
| Status: | Peer Reviewed | ||||
| Publication Status: | Published | ||||
| Access rights to Published version: | Restricted or Subscription Access | ||||
| Funder: | Biotechnology and Biological Sciences Research Council (Great Britain) (BBSRC), Engineering and Physical Sciences Research Council (EPSRC) | ||||
| Version or Related Resource: | Paper presented at: Conference on Condensed Matter and Materials Physics CMMP10), University of Warwick, Coventry, Dec 14-16, 2010. |
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