BDB -BiopanningDataSet Details

Biopanning Data

BiopanningDataSet ID: 3580

Peptides:

Sequences

Affinity Values

DYHDPSLPTLRK(86.3%)
TAKYLPMRPGPL(7.8%)
QVNGLGERSQQM(0.9%)
RDYHPRDHTATW(0.7%)
GNNPLHVHHDKR(0.4%)
SPLRAVAFSGAQ(0.1%)
INIVPGPEKPVG(0.1%)
QGYKQEYTRWGE(0.1%)

[0.0321±0.0062]
[NT]
[NT]
[NT]
[NT]
[NT]
[NT]
[NT]

Sequences Features:

Motif:

Unique Sequence Number:

Experimental Method:

Phage display (common panning)

Sequencing Platform:

Illumina HiSeq2500 Genome Sequencer (San Diego, CA, USA)

Sequencing Method:

Next-generation sequencing

Rounds of Panning:

Reference:

PMID: 36861429

Target Name:

Surfaces of crystalline gypsum

Template Name:

Not determined.

Structure of Target-Template Complex:

Not determined.

Structure of Target-Peptide Complex:

Not determined.

Library Name:

Ph.D.-12 phage display library (X12)

Affinity Measurement Method:

Affinity Measurement Description:

The affinity of selected oligopeptides and synthesized copolymers to bind to the surface of gypsum and C-S-H particles was assessed in batch assays based on total organic carbon (TOC) analysis.

Brief Description:

For the selection phase, the following procedure was used: 10 µL of the original phage library solution was mixed with 990 µL saturated gypsum solution (to prevent the dissolution of the gypsum particles during the experiment) in standard Eppendorf vials. To this dilution, solid gypsum powder was added at a ratio of 0.1% (w/v) and the resulting suspension was incubated at room temperature for 30 min while shaking at 800 rpm. Afterward, the solid particles carrying the strongly adhering phages were separated by centrifugation for 30 s at 8000 rpm, while the non- and weakly bound phages remained in the supernatant, which was removed. The remaining solid material was washed ten times with 1 mL saturated gypsum solution by vortexing for 15 s and subsequent centrifugation, in order to further separate weakly from strongly binding phages. During the washing sequence, the Eppendorf vial was replaced three times to eliminate any potential influence of phages sticking to the polypropylene surface of the vials (i.e., to increase the selection pressure and remove peptide sequences with enhanced affinity for the vial surfaces prior to analysis). To isolate the strongly bound phages in the last step, the washed gypsum particles were dissolved in a mixture of 1 mL Tris/HCl and 100 µL Tris-buffered saline. Subsequently, the released phages were amplified in a 20 mL lysogeny broth (LB) medium containing 400 µL Escherichia Coli solution (strain ER2738, OD600 ≈ 0.5). After 4-5 hours of vigorous shaking at 37 °C, the phages were reprocessed according to the protocol of the supplier to prepare the selected library for another panning round.

BiopanningDataSet Comments:

Based on next-generation sequencing of phages enriched during the screening process, a triplet of amino acids, DYH, is identified as the main driver for adsorption on the mineral substrate. Furthermore, oligopeptides containing this motif prove to exert their influence in a strictly selective manner during the hydration of cement, where the sulfate reaction (initial setting) is strongly retarded while the silicate reaction (final hardening) remains unaffected. In the final step, these desired additive characteristics are successfully translated from the level of peptides to that of scalable synthetic copolymers.

Curator:

Bowen Li

Curation Date:

2023-10-13

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