Research Data Leeds Repository

Citation

Laurent, Harrison and Hughes, Matt D. G. and Walko, Martin and Brockwell, David and Mahmoudi, Najet and Youngs, Tristan G. A. and Headen, Thomas F. and Dougan, Lorna (2023) All-atom visualisation of self-assembly and hydration of a β-hairpin through integrated small and wide-angle neutron scattering. University of Leeds. [Dataset] https://doi.org/10.5518/1345

Dataset description

This work studies the CLN025 peptide in concentrated aqueous solution to understand its self assembly and hydration structure. Using SANS we are able to predict that hairpin monomers self assemble into stacks whose long axes are perpendicular to the plane of the hairpin, and that on average these stacks consist of ~7 peptides. Using this we constrain emperical potential structural refinement analysis of the WANS data to build an atomisically resolved hydration structure of the hairpin stacks.

Keywords:	hairpin, CLN025, neutron, WANS, SANS, EPSR, self-assembly, hydration, peptide
Divisions:	Faculty of Engineering and Physical Sciences > School of Physics and Astronomy
Related resources:	Location Type https://doi.org/10.1021/acs.biomac.3c00583 Publication https://eprints.whiterose.ac.uk/204756/ Publication
License:	Creative Commons Attribution 4.0 International (CC BY 4.0)
Date deposited:	17 Feb 2025 15:44
URI:	https://archive.researchdata.leeds.ac.uk/id/eprint/1377
Additional details Additional details Creators or authors: Creators ORCID Other ID Email Primary affiliation Primary affiliation ID Primary affiliation ID type Secondary affiliation Secondary affiliation ID Secondary affiliation ID type Laurent, Harrison https://orcid.org/0000-0002-8925-4773 University of Leeds https://ror.org/024mrxd33 ror Hughes, Matt D. G. https://orcid.org/0000-0001-5838-7939 University of Leeds https://ror.org/024mrxd33 ror Walko, Martin https://orcid.org/0000-0002-7160-6136 University of Leeds https://ror.org/024mrxd33 ror Brockwell, David https://orcid.org/0000-0002-0802-5937 University of Leeds https://ror.org/024mrxd33 ror Mahmoudi, Najet https://orcid.org/0000-0003-4936-6911 Rutherford Appleton Laboratory https://ror.org/03gq8fr08 ror Youngs, Tristan G. A. https://orcid.org/0000-0003-3538-5572 Rutherford Appleton Laboratory https://ror.org/03gq8fr08 ror Headen, Thomas F. https://orcid.org/0000-0003-0095-5731 Rutherford Appleton Laboratory https://ror.org/03gq8fr08 ror Dougan, Lorna https://orcid.org/0000-0002-2620-5827 University of Leeds https://ror.org/024mrxd33 ror Type of data: Dataset Research funders: EPSRC Grant numbers: EP/P02288X/1 Publication date: 2023 Resource language: English Metadata language: English Publisher: University of Leeds Contact email: L.Dougan@leeds.ac.uk Last Modified: 17 Feb 2025 15:54

Files

Data

CLN025 atom key [5kB] CLN025 atom key [5kB] CLN025 atom key [5kB] Security: Anyone File name: CLN025_atom_key.csv Content type: Data Description: csv file describing the atom label (1-172), element, host amino acid, atom type (as described in SI), EPSR reference potential parameters (as described in SI), and charge for each of the 172 atoms in a CL025 monomer Mime-Type: text/csv License: Creative Commons Attribution 4.0 International (CC BY 4.0) File size: 5kB

Radial distribution functions generated from EPSR analysis [3MB] Radial distribution functions generated from EPSR analysis [3MB] Radial distribution functions generated from EPSR analysis [3MB] Security: Anyone File name: Radial_distribution_functions_generated_from_EPSR_analysis.zip Content type: Data Description: Radial distribution function between CLN025 atom 'a' and water atom 'b'. a is the atom label as described in CLN025_atom_key.csv. b is 1 for water oxygen and 2 for water hydrogen. File format compatable with microsoft excel Mime-Type: application/zip License: Creative Commons Attribution 4.0 International (CC BY 4.0) File size: 3MB

CLN025 surface atom hydration info [14kB] CLN025 surface atom hydration info [14kB] CLN025 surface atom hydration info [14kB] Security: Anyone File name: EPSR_results_05012023.csv Content type: Data Description: .csv file summarising the peak locations of the RDFs, their differences, and their normalisations to assign the reported delta value Mime-Type: text/csv License: Creative Commons Attribution 4.0 International (CC BY 4.0) File size: 14kB

CLN025 surface atom SES info [99kB] CLN025 surface atom SES info [99kB] CLN025 surface atom SES info [99kB] Security: Anyone File name: EPSR_results_05012023_SES_SAS.csv Content type: Data Description: .csv file summarising the solvent accessible surface area for each atom present on CLN025 as predicted using chimera software Mime-Type: text/csv License: Creative Commons Attribution 4.0 International (CC BY 4.0) File size: 99kB

CLN025 monomer .ato file [77kB] CLN025 monomer .ato file [77kB] CLN025 monomer .ato file [77kB] Security: Anyone File name: CLN025_1_1.ato Content type: Data Description: .ato file describing a single CLN025 molecule required to run the dimer optimisation code License: Creative Commons Attribution 4.0 International (CC BY 4.0) File size: 77kB

CLN025 monomer .xyz file [10kB] CLN025 monomer .xyz file [10kB] CLN025 monomer .xyz file [10kB] Security: Anyone File name: CLN025_stack_1.xyz Content type: Data Description: .xyz file describing a single CLN025 molecule required to run the dimer optimisation code Mime-Type: chemical/x-xyz License: Creative Commons Attribution 4.0 International (CC BY 4.0) File size: 10kB

Program

Dimer optimisation code [25kB] Dimer optimisation code [25kB] Dimer optimisation code [25kB] Security: Anyone File name: CLN025_dimer_optimisation_1_2.py Content type: Program Description: Monte Carlo simulation designed to find the lowest energy conformation of two CLN025 dimers separated by 8.5 angstroms File size: 25kB

Delta to hydrophobicity calculator [15kB] Delta to hydrophobicity calculator [15kB] Delta to hydrophobicity calculator [15kB] Security: Anyone File name: AA_delta.py Content type: Program Description: python script that uses calculated delta values and SAS data to calculate a single hydrophobicity value for each amino acid File size: 15kB