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Rapid simulation of protein motion : merging flexibility, rigidity and normal mode analyses
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Jiménez Roldán, J. E. (José Emilio), Freedman, R. B., Römer, Rudolf A. and Wells, Stephen A. (2012) Rapid simulation of protein motion : merging flexibility, rigidity and normal mode analyses. Physical Biology, Vol.9 (No.1). 016008. doi:10.1088/1478-3975/9/1/016008 ISSN 1478-3967.
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Official URL: http://dx.doi.org/10.1088/1478-3975/9/1/016008
Abstract
Protein function frequently involves conformational changes with large amplitude on timescales which are difficult and computationally expensive to access using molecular dynamics. In this paper, we report on the combination of three computationally inexpensive simulation methods—normal mode analysis using the elastic network model, rigidity analysis using the pebble game algorithm, and geometric simulation of protein motion—to explore conformational change along normal mode eigenvectors. Using a combination of ElNemo and First/Froda software, large-amplitude motions in proteins with hundreds or thousands of residues can be rapidly explored within minutes using desktop computing resources. We apply the method to a representative set of six proteins covering a range of sizes and structural characteristics and show that the method identifies specific types of motion in each case and determines their amplitude limits.
Item Type: | Journal Article | ||||
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Subjects: | Q Science > QC Physics | ||||
Divisions: | Faculty of Science, Engineering and Medicine > Science > Physics | ||||
Journal or Publication Title: | Physical Biology | ||||
Publisher: | IOP Publishing | ||||
ISSN: | 1478-3967 | ||||
Official Date: | February 2012 | ||||
Dates: |
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Volume: | Vol.9 | ||||
Number: | No.1 | ||||
Page Range: | 016008 | ||||
DOI: | 10.1088/1478-3975/9/1/016008 | ||||
Status: | Peer Reviewed | ||||
Publication Status: | Published | ||||
Access rights to Published version: | Restricted or Subscription Access |
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