BDB -BiopanningDataSet Details

Biopanning Data

BiopanningDataSet ID: 3627

Peptides:

Sequences

Affinity Values

DYHDPSLPTLRK(4)
GNNPLHVHHDKR(2)
STVRPLLMMDKY(1)
HHLRIPYALDQT(1)
DSAPSYNYRPSY(1)
DYHDPSPPTLRK(1)
KVYFSIPWRVPM(1)
QVNGLGERSQQM(1)
HSNDPRLITMRK(1)
TCFAHTHNNFGH(1)
RDYHPRDHTATW(1)
IPGTAPPLARTG(1)
KDFLPSPQTATW(1)
VRAFSGEHSFVS(1)

[0.7929±0.1464, NT]
[0.6135±0.0746, NT]
[1.2004±0.2109, NT]
[0.5489±0.0904, NT]
[1.6395±0.1421, 520±7]
[0.6436±0.2095, NT]
[1.6281±0.198, 74±3]
[1.1559±0.1119, NT]
[0.3179±0.2239, n.d.]
[0.8001±0.3975, NT]
[0.3394±0.1579, NT]
[1.044±0.023, NT]
[1.5606±0.1277, 488±33]
[1.1746±0.023, NT]

Sequences Features:

Motif:

Unique Sequence Number:

Experimental Method:

Phage display (common panning)

Sequencing Platform:

Sequencing Method:

Sanger sequencing

Rounds of Panning:

Reference:

PMID: 35059169

Target Name:

9-fluorenylmethoxycarbonyl-phenylalanine-tyrosinephosphate (Fmoc-Fργ ) micellar aggregates

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:

ELISA

Affinity Measurement Description:

The absorbance at 405 nm was monitored in a SpectraMax i3 (Molecular Devices). Wild-type M13 phage has been used as a positive control of ELISA assay and as a negative control of Fmoc-FpY binding. In addition, NMR experiments were acquired in a Bruker Avance III 600 spectrometer equipped with a triple-resonance cryoprobe (TCI). Spectra were processed using software TOPSPIN (Bruker Biospin, Karlsruhe, Germany) and peaks assigned with Sparky (TD Goddard and DG Kneller, Sparky 3, University of California, San Francisco, USA). The dissociation constants KD (μM) were determined in the OriginPro9. The first column of affinity values is the absorbance405 value reproduced from Figure 1C, the second column is the KD (μM) determined by NMR experiments.

Brief Description:

BiopanningDataSet Comments:

The lead peptide, KVYFSIPWRVPM-NH2 (P7) was found to bind to the Fmoc-FpY ligand exclusively in its self-assembled state with KD =74 ± 3 μM. Circular dichroism, NMR and molecular dynamics simulations revealed that the peptide interacts with Fmoc-FpY through the KVYF terminus and this binding event disrupts the assembled structure. In absence of the target micellar aggregate, P7 was further found to dynamically alternate between multiple conformations, with a preferred hairpin-like conformation that was shown to contribute to supramolecular ligand binding. Three identified phages presented appreciable binding, and two showed to catalyze the hydrolysis of a model para-nitro phenol phosphate substrate, with P7 demonstrating conformation-dependent activity with a modest kcat/KM = 4 ± 0.3 * 10^(-4) M^(-1)s^(-1).

Curator:

Bowen Li

Curation Date:

2023-10-13

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