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Testing the transferability of a coarse-grained model to intrinsically disordered proteins

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Rutter, Gil, Brown, Aaron H., Quigley, David, Walsh, Tiffany R. and Allen, M. P. (2015) Testing the transferability of a coarse-grained model to intrinsically disordered proteins. Physical Chemistry Chemical Physics, 17 (47). pp. 31741-31749. doi:10.1039/c5cp05652g ISSN 1463-9076.

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Official URL: http://dx.doi.org/10.1039/C5CP05652G

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Abstract

The intermediate-resolution coarse-grained protein model PLUM [T. Bereau and M. Deserno, J. Chem. Phys., 2009, 130, 235106] is used to simulate small systems of intrinsically disordered proteins involved in biomineralisation. With minor adjustments to reduce bias toward stable secondary structure, the model generates conformational ensembles conforming to structural predictions from atomistic simulation. Without additional structural information as input, the model distinguishes regions of the chain by predicted degree of disorder, manifestation of structure, and involvement in chain dimerisation. The model is also able to distinguish dimerisation behaviour between one intrinsically disordered peptide and a closely related mutant. We contrast this against the poor ability of PLUM to model the S1 quartz-binding peptide.

Item Type: Journal Article
Subjects: Q Science > QD Chemistry
Q Science > QH Natural history
Q Science > QP Physiology
Divisions: Faculty of Science, Engineering and Medicine > Science > Physics
Faculty of Science, Engineering and Medicine > Science > Centre for Scientific Computing
Library of Congress Subject Headings (LCSH): Biomineralization, Protein binding, Peptides
Journal or Publication Title: Physical Chemistry Chemical Physics
Publisher: Royal Society of Chemistry
ISSN: 1463-9076
Official Date: 5 November 2015
Dates:
DateEvent
5 November 2015Available
29 October 2015Accepted
21 September 2015Submitted
Volume: 17
Number: 47
Page Range: pp. 31741-31749
DOI: 10.1039/c5cp05652g
Status: Peer Reviewed
Publication Status: Published
Access rights to Published version: Open Access (Creative Commons)
Date of first compliant deposit: 2 September 2016
Date of first compliant Open Access: 2 September 2016
Funder: Engineering and Physical Sciences Research Council (EPSRC), United States. Air Force. Office of Scientific Research (AFOSR), Australian Academy of Science
Grant number: EP/I001514/1 (EPSR), FA9550-12-1-0226 (AFOSR)

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