Efficient one-cycle affinity selection of binding proteins or peptides specific for a small-molecule using a T7 phage display pool

Takakusagi, Yoichi; Kuramochi, Kouji; Takagi, Manami; Kusayanagi, Tomoe; Manita, Daisuke; OZAWA, Hiroko; Iwakiri, Kanako; Takakusagi, Kaori; Miyano, Yuka; Nakazaki, Atsuo; Kobayashi, Susumu; Sugawara, Fumio; Sakaguchi, Kengo

doi:10.1016/j.bmc.2008.09.061

Cited by 23 publications

(21 citation statements)

References 20 publications

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“…Other groups have shown that peptides selected to bind to other types of proteins have utility in understanding and predicting binding to natural binding partners [9-11]. Even small molecule binding peptides provide insight on their binding to natural proteins [3,12]. …”

Section: Introductionmentioning

confidence: 99%

GuiTope: an application for mapping random-sequence peptides to protein sequences

et al. 2012

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BackgroundRandom-sequence peptide libraries are a commonly used tool to identify novel ligands for binding antibodies, other proteins, and small molecules. It is often of interest to compare the selected peptide sequences to the natural protein binding partners to infer the exact binding site or the importance of particular residues. The ability to search a set of sequences for similarity to a set of peptides may sometimes enable the prediction of an antibody epitope or a novel binding partner. We have developed a software application designed specifically for this task.ResultsGuiTope provides a graphical user interface for aligning peptide sequences to protein sequences. All alignment parameters are accessible to the user including the ability to specify the amino acid frequency in the peptide library; these frequencies often differ significantly from those assumed by popular alignment programs. It also includes a novel feature to align di-peptide inversions, which we have found improves the accuracy of antibody epitope prediction from peptide microarray data and shows utility in analyzing phage display datasets. Finally, GuiTope can randomly select peptides from a given library to estimate a null distribution of scores and calculate statistical significance.ConclusionsGuiTope provides a convenient method for comparing selected peptide sequences to protein sequences, including flexible alignment parameters, novel alignment features, ability to search a database, and statistical significance of results. The software is available as an executable (for PC) at http://www.immunosignature.com/software and ongoing updates and source code will be available at sourceforge.net.

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Section: Introductionmentioning

confidence: 99%

GuiTope: an application for mapping random-sequence peptides to protein sequences

et al. 2012

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“…1B). 3,4,11,13 Figure 4A shows a similarity plot between 34 Brz2001-selected random peptides and the DWARF4 amino-acid sequence (M1-L513). This plot was calculated by a modified BLOSAM62 amino-acid matrix within each window of five amino acids in length across the entire length of the protein sequence.…”

Section: Resultsmentioning

confidence: 99%

“…[8][9][10] The use of this platform in a T7 phage display enabled a rapid capture of small-molecule recognizing T7 phages on the gold by sub-minutes of monitoring the frequency decrease, with no need of repeated rounds of biopanning. 3,4 This also corresponds to the fact that the QCM-based selection eliminated hitherto inevitable problems associated with phage distribution bias during the amplification process on classical methods. Furthermore, subsequent use of a host Escherichia coli culture realized a rapid and direct recovery of DNA from the trace amount of bound T7 phage, without elute condition exploration.…”

Section: Introductionmentioning

confidence: 90%

“…1A). 3,4 In 2004, Rodi and Makowski and their coworkers launched the receptor-ligand contacts (RELIC) bioinformatics server, and they have since extensively studied the annotation of a small-molecule binding site on protein by a similarity search using affinity-selected random peptides. [11][12][13][14][15][16] According to their earlier studies, phagedisplayed short peptides, most of which are basically disordered, can mimic the disordered loops in naturally occurring proteins that are considered an essential portion in many small-molecule/protein interactions.…”

Section: Introductionmentioning

confidence: 99%

“…1 A biosensor-based screening of T7 phage-displayed random peptide is a useful strategy for detecting small-molecule/protein interactions, which could circumvent those technical limitations. [2][3][4][5][6] This approach employs a high-sensitivity quartz-crystal microbalance (QCM) biosensor that can monitor the decrease of alternating voltage-induced intrinsic crystal vibrations in real time, which indicates a mass increase in the gold electrode deposited on the crystal of the QCM sensor chip (Fig. 1A).…”

Section: Introductionmentioning

confidence: 99%

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Mapping a Disordered Portion of the Brz2001-Binding Site on a Plant Monooxygenase, DWARF4, Using a Quartz-Crystal Microbalance Biosensor-Based T7 Phage Display

Takakusagi

Manita

Kusayanagi

et al. 2013

ASSAY and Drug Development Technologies

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In small-molecule/protein interaction studies, technical difficulties such as low solubility of small molecules or low abundance of protein samples often restrict the progress of research. Here, we describe a quartz-crystal microbalance (QCM) biosensor-based T7 phage display in combination use with a receptor-ligand contacts (RELIC) bioinformatics server for application in a plant Brz2001/DWARF4 system. Brz2001 is a brassinosteroid biosynthesis inhibitor in the less-soluble triazole series of compounds that targets DWARF4, a cytochrome P450 (Cyp450) monooxygenase containing heme and iron. Using a Brz2001 derivative that has higher solubility in 70% EtOH and forms a self-assembled monolayer on gold electrode, we selected 34 Brz2001-recognizing peptides from a 15-mer T7 phage-displayed random peptide library using a total of four sets of one-cycle biopanning. The RELIC/MOTIF program revealed continuous and discontinuous short motifs conserved within the 34 Brz2001-selected 15-mer peptide sequences, indicating the increase of information content for Brz2001 recognition. Furthermore, an analysis of similarity between the 34 peptides and the amino-acid sequence of DWARF4 using the RELIC/MATCH program generated a similarity plot and a cluster diagram of the amino-acid sequence. Both of these data highlighted an internally located disordered portion of a catalytic site on DWARF4, indicating that this portion is essential for Brz2001 recognition. A similar trend was also noted by an analysis using another 26 Brz2001-selected peptides, and not observed using the 27 gold electrode-recognizing control peptides, demonstrating the reproducibility and specificity of this method. Thus, this affinity-based strategy enables high-throughput detection of the small-molecule-recognizing portion on the target protein, which overcomes technical difficulties such as sample solubility or preparation that occur when conventional methods are used.

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A survey of the 2006–2009 quartz crystal microbalance biosensor literature

Becker

Cooper

2011

J of Molecular Recognition

163

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Since the publication of the original review of piezoelectric acoustic sensors in this series there has been a consistent, gradual expansion in the number of published papers using 'quartz crystal microbalances' (QCM). Between 2001 and 2009, the number of QCM publications per annum has increased from 49 to 273, with a two-fold increase in papers per annum between 2004 and 2008. Within the field, comparing the time covered by the current to the previous review, there are trends towards increasing use of QCM in the study of protein adsorption to surfaces (93% increase), homeostasis (67% increase), protein-protein interactions (40% increase) and carbohydrates (43% increase). New commercial systems have been released that are driving the uptake of the technology for characterization of binding specificities, affinities, kinetics and conformational changes associated with a molecular recognition event. This paper highlights theoretical and practical aspects of the principles that underpin acoustic analysis, then reviews exemplary papers in key application areas involving small molecular weight ligands, carbohydrates, proteins, nucleic acids, viruses, bacteria, cells and membrane interfaces.

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Efficient one-cycle affinity selection of binding proteins or peptides specific for a small-molecule using a T7 phage display pool

Cited by 23 publications

References 20 publications

GuiTope: an application for mapping random-sequence peptides to protein sequences

GuiTope: an application for mapping random-sequence peptides to protein sequences

Mapping a Disordered Portion of the Brz2001-Binding Site on a Plant Monooxygenase, DWARF4, Using a Quartz-Crystal Microbalance Biosensor-Based T7 Phage Display

A survey of the 2006–2009 quartz crystal microbalance biosensor literature

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