Rutter, Gil (2017) Data for Emergence of order in self-assembly of the intrinsically disordered biomineralisation peptide n16N. [Dataset]

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Abstract

We present the results of an aggregation study on the intrinsically disordered biomineralisation peptide n16N, which selects the aragonite polymorph of calcium carbonate and is expected to have aggregation-dependent structure and function. The peptide is a sub-sequence of the in vivo protein n16, with putative framework and polymorph selection roles in the nacre layer of pearl oyster (Pinctada fucata). Employing the intermediate-resolution coarse-grained protein model PLUM*, which has previously been validated with respect to n16N, we simulate assemblies of these peptide units for system sizes inaccessible to atomistic models. We use extensive conformational sampling to show that the configurational ensemble explored by n16N aggregates contains a significant proportion of ordered beta-structure, within which arrangement of monomers is consistent with a previous hypothesis on functionally distinct subdomains of n16N. We also study an n16N mutant which fails to aggregate in experimental studies and obtain very similar behaviour, the consequences of which are discussed.

Item Type:	Dataset
Subjects:	Q Science > QD Chemistry
Divisions:	Faculty of Science, Engineering and Medicine > Science > Physics
Type of Data:	Molecular structure and structure analysis data
Library of Congress Subject Headings (LCSH):	Self-assembly (Chemistry), Biomineralization, Peptides
Publisher:	University of Warwick, Department of Physics
Official Date:	19 July 2017
Dates:	Date Event 19 July 2017 Created
Collection date:	Date from Date to October 2014 July 2017
Status:	Not Peer Reviewed
Publication Status:	Published
Media of Output (format):	.pickle, .ARG, .NUMPY, .PDB and .VMD files
Access rights to Published version:	Open Access (Creative Commons)
Copyright Holders:	University of Warwick
Description:	The dataset is composed of .pickle files (PYTHON), .agr files (open with xmgrace. This is a standard (free and open source) Unix/Linux plotting tool https://en.wikipedia.org/wiki/Grace_(plotting_tool)), .numpy files (a standard format for reading arrays into numerical Python using the numpy.fromfile function) and .pdb files (Protein DataBank files, a standard open format for representing molecular structures. They can be opened in a number of programs. One of these is VMD (Visual Molecular Dynamics) and the .vmd files are input scripts for that software which will read and render the molecular structures. https://en.wikipedia.org/wiki/Visual_Molecular_Dynamics )
Date of first compliant deposit:	7 November 2017
Date of first compliant Open Access:	7 November 2017
RIOXX Funder/Project Grant:	Project/Grant ID RIOXX Funder Name Funder ID EP/I001514/1 Engineering and Physical Sciences Research Council http://dx.doi.org/10.13039/501100000266 FA9550-12-1-0226 Air Force Office of Scientific Research http://dx.doi.org/10.13039/100000181
Related URLs:	Related item in WRAP
Contributors:	Contribution Name Contributor ID Author Rutter, Gil 48182 Author Brown, Aaron Hugh 39009 Author Quigley, David 15132 Author Walsh, Tiffany R. 1006 Author Allen, M. P. 619

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