Research Data Leeds Repository

Citation

Sandei, Ilaria, Gaule, Thembaninkosi, Batchelor, Matthew, Paci, Emanuele, Kim, Yi-Yeoun, Kulak, Alexander N., Tomlinson, Darren and Meldrum, Fiona C. (2025) Dataset for "Phage Display Identifies Affimer Proteins that Direct Calcium Carbonate Polymorph". University of Leeds. [Dataset] https://doi.org/10.5518/1374

Dataset description

Dataset supporting a study in which a phage display approach is used to identify proteins – rather than the short peptides typically identified using this method – that can direct calcium carbonate formation. A 1.3 X 1010 library of Affimer proteins was displayed on modified M13 phage, where Affimer is a 3 kDa protein scaffold that displays two variable regions of 9–13 residues. The phage displaying the Affimer library were then screened in binding assays against calcite and aragonite at pH 7.4, and four different strongly-binding proteins were identified. The two aragonite-binding proteins generated aragonite when calcium and magnesium ions were present at a 1:1 ratio, while the calcite-binding proteins produce magnesium-calcite under the same conditions. Calcite alone formed in the presence of all four proteins in the absence of magnesium ions. In combination with molecular dynamics simulations to evaluate the conformations of the proteins in solution, this work demonstrates the importance of conformation in polymorph control, and highlights the importance of magnesium ions, which are abundant in seawater, to reduce the energetic barriers associated with aragonite formation.

Keywords:	calcium carbonate, phage display, aragonite, calcite
Subjects:	F000 - Physical sciences > F100 - Chemistry F000 - Physical sciences > F100 - Chemistry > F120 - Inorganic chemistry F000 - Physical sciences > F100 - Chemistry > F160 - Organic chemistry > F165 - Biomolecular chemistry C000 - Biological sciences > C700 - Molecular biology, biophysics & biochemistry
Divisions:	Faculty of Engineering and Physical Sciences > School of Chemistry
Related resources:	Location Type https://doi.org/10.1039/D4BM00165F Publication https://eprints.whiterose.ac.uk/id/eprint/215138/ Publication https://doi.org/10.1021/acs.cgd.5c00205 Publication https://eprints.whiterose.ac.uk/id/eprint/227661/ Publication
License:	Creative Commons Attribution 4.0 International (CC BY 4.0)
Date deposited:	24 Oct 2025 16:56
URI:	https://archive.researchdata.leeds.ac.uk/id/eprint/1476
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 Sandei, Ilaria https://orcid.org/0000-0002-8542-2696 University of Leeds https://ror.org/024mrxd33 ror Gaule, Thembaninkosi https://orcid.org/0000-0003-2859-4093 University of Leeds https://ror.org/024mrxd33 ror Batchelor, Matthew https://orcid.org/0000-0001-6338-5698 University of Leeds https://ror.org/024mrxd33 ror Paci, Emanuele https://orcid.org/0000-0002-4891-2768 University of Leeds https://ror.org/024mrxd33 ror Kim, Yi-Yeoun https://orcid.org/0000-0002-8503-4554 University of Leeds https://ror.org/024mrxd33 ror Kulak, Alexander N. https://orcid.org/0000-0002-2798-9301 University of Leeds https://ror.org/024mrxd33 ror Tomlinson, Darren https://orcid.org/0000-0003-4134-7484 University of Leeds https://ror.org/024mrxd33 ror Meldrum, Fiona C. https://orcid.org/0000-0001-9243-8517 University of Leeds https://ror.org/024mrxd33 ror Type of data: Dataset Research funders: European Research Council, EPSRC Grant numbers: 788968, EP/T006331/1 Publication date: 2025 Resource language: English Metadata language: English Publisher: University of Leeds Contact email: chmfme@leeds.ac.uk Last Modified: 27 Oct 2025 09:54

Files

Documentation

Supplementary Information [1MB] Supplementary Information [1MB] Supplementary Information [1MB] Security: Anyone File name: Supplementary_Information.pdf Content type: Documentation Description: Supplementary Information published with main article Mime-Type: application/pdf License: Creative Commons Attribution 4.0 International (CC BY 4.0) File size: 1MB

README Meldrum 2025 [3kB] README Meldrum 2025 [3kB] README Meldrum 2025 [3kB] Security: Anyone File name: README_Meldrum_2025.txt Content type: Documentation Mime-Type: text/plain License: Creative Commons Attribution 4.0 International (CC BY 4.0) File size: 3kB

Data

IR [29kB] IR [29kB] IR [29kB] Security: Anyone File name: IR.zip Content type: Data Description: Raw IR data of calcite and aragonite crystals Mime-Type: application/zip License: Creative Commons Attribution 4.0 International (CC BY 4.0) File size: 29kB

MD Simulations [1GB] MD Simulations [1GB] MD Simulations [1GB] Security: Anyone File name: MD_simulations.zip Content type: Data Description: Data supporting simulations described in the main article Mime-Type: application/zip License: Creative Commons Attribution 4.0 International (CC BY 4.0) File size: 1GB

Phage Display [15MB] Phage Display [15MB] Phage Display [15MB] Security: Anyone File name: Phage_display.zip Content type: Data Description: Sequences of Affimer proteins raised against calcite and aragonite Mime-Type: application/zip License: Creative Commons Attribution 4.0 International (CC BY 4.0) File size: 15MB

Raman [3MB] Raman [3MB] Raman [3MB] Security: Anyone File name: Raman.zip Content type: Data Description: Raman data of crystals produced in the absence of additives, with proteins and with magnesium Mime-Type: application/zip License: Creative Commons Attribution 4.0 International (CC BY 4.0) File size: 3MB

SEM Affimer + Mg [58MB] SEM Affimer + Mg [58MB] SEM Affimer + Mg [58MB] Security: Anyone File name: SEM_Affimer_Plus_Mg.zip Content type: Data Description: SEM images of crystals produced in the presence of the different affimer proteins and Mg Mime-Type: application/zip License: Creative Commons Attribution 4.0 International (CC BY 4.0) File size: 58MB

SEM Affimer no Mg [56MB] SEM Affimer no Mg [56MB] SEM Affimer no Mg [56MB] Security: Anyone File name: SEM_Affimer_No_Mg.zip Content type: Data Description: SEM images of crystals produced in the presence of the different affimer proteins Mime-Type: application/zip License: Creative Commons Attribution 4.0 International (CC BY 4.0) File size: 56MB

Subcloning [7MB] Subcloning [7MB] Subcloning [7MB] Security: Anyone File name: Subcloning.zip Content type: Data Description: Subcloning data of Affimer proteins binding to calcite (CBA proteins) and aragonite (ABA proteins) Mime-Type: application/zip License: Creative Commons Attribution 4.0 International (CC BY 4.0) File size: 7MB

XRD [6MB] XRD [6MB] XRD [6MB] Security: Anyone File name: XRD.zip Content type: Data Description: Raw XRD data of calcite and aragonite crystals Mime-Type: application/zip License: Creative Commons Attribution 4.0 International (CC BY 4.0) File size: 6MB