Phage display as a method for discovering cellular targets of small molecules

Dorst, Bieke Van; Mehta, Jaytry; Rouah-Martin, Elsa; Blust, Ronny; Robbens, Johan

doi:10.1016/j.ymeth.2012.07.011

Cited by 8 publications

(5 citation statements)

References 50 publications

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“…A random-peptide library is used to search for high affinity interactions to the target protein sequence. 47,48 Eventually the phage DNA can be extracted and encoded to be grown recombinantly in bacteria. 48,49 With phage display, the potential for discovering new biorecognition elements is growing, but it can be limited similarly to other natural biorecognition element paradigms.…”

Section: Biorecognition Elementsmentioning

confidence: 99%

“…In addition to aptamers, many researchers use protein-based phage display as a pseudonatural modality to identify protein–protein interactions. − Phage display inserts a DNA fragment that encodes the desired protein target into a phage coat protein gene. A random-peptide library is used to search for high affinity interactions to the target protein sequence. , Eventually the phage DNA can be extracted and encoded to be grown recombinantly in bacteria. , With phage display, the potential for discovering new biorecognition elements is growing, but it can be limited similarly to other natural biorecognition element paradigms.…”

Section: Biorecognition Elementsmentioning

confidence: 99%

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Guide to Selecting a Biorecognition Element for Biosensors

2018

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Biosensors are powerful diagnostic tools defined as having a biorecognition element for analyte specificity and a transducer for a quantifiable signal. There are a variety of different biorecognition elements, each with unique characteristics. Understanding the advantages and disadvantages of each biorecognition element and their influence on overall biosensor performance is crucial in the planning stages to promote the success of novel biosensor development. Therefore, this review will focus on selecting the optimal biorecognition element in the preliminary design phase for novel biosensors. Included is a review of the typical characteristics and binding mechanisms of various biorecognition elements, and how they relate to biosensor performance characteristics, specifically sensitivity, selectivity, reproducibility, and reusability. The goal is to point toward language needed to improve the design and development of biosensors toward clinical success.

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Section: Biorecognition Elementsmentioning

confidence: 99%

Section: Biorecognition Elementsmentioning

confidence: 99%

Guide to Selecting a Biorecognition Element for Biosensors

2018

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“…Site 2 is composed of hydrophobic and charged residues of Pro18, Arg26 and Arg30, in which the Arg30 is in close contact with the carboxyl group of GenX (Figure 6). Phage display can be applied to discover de novo binding partners for small molecules [14], and short peptides have been screened to target active bioengineered materials with high specificity [15]. In this paper, we screened short peptides (7mer) that recognize GenX, using in vitro phage display to identify amino-acid sequences bound to GenX and analyze the binding affinity with NMR.…”

Section: Resultsmentioning

confidence: 99%

Screening Peptide-Binding Partners for GenX via Phage Display

Burton,

Ghadami,

Dellinger

et al. 2024

IJMS

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Per- and poly-fluoroalkyl substances (PFAS), such as GenX, are a class of highly stable synthetic compounds that have recently become the focus of environmental remediation endeavors due to their toxicity. While considerable strides have been made in PFAS remediation, the diversity of these compounds, and the costs associated with approaches such as ion exchange resins and advanced oxidation technologies, remain challenging for widespread application. In addition, little is known about the potential binding and impacts of GenX on human proteins. To address these issues, we applied phage display and screened short peptides that bind specifically to GenX, with the ultimate goal of identifying human proteins that bind with GenX. In this study we identified the amino acids that contribute to the binding and measured the binding affinities of the two discovered peptides with NMR. A human protein, ankyrin-repeat-domain-containing protein 36B, with matching sequences of one of the peptides, was identified, and the binding positions were predicted by docking and molecular dynamics simulation. This study created a platform to screen peptides that bind with toxic chemical compounds, which ultimately helped us identify biologically relevant molecules that could be inhibited by the GenX, and also provided information that will contribute to future bioengineered GenX-binding device design.

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“…In phage display, very large libraries can be generated and selected and since the genotype and phenotype are physically linked, target identification is achieved by sequencing which is rapid and cheap compared to the mass spectrometry and large-scale protein production which are required for chemical proteomics and protein microarray approaches, respectively. Since the early successful identification of cellular proteins that bind the small molecule drugs taxol and doxorubicin [16, 17], a large number of small molecule-interacting cellular proteins have been identified by affinity-based selection from phage cDNA and peptide display libraries [18–31]. Nevertheless, despite these successes, the recovery of some interactions may be limited by potential expression bias against eukaryotic proteins expressed in a prokaryotic host, which could lead to a high rate of both false positive and negative results and the low number of fusion proteins displayed on each phage particle.…”

Section: Methods For Identifying Small Molecule-interacting Cellulamentioning

confidence: 99%

Utilizing Yeast Surface Human Proteome Display Libraries to Identify Small Molecule-Protein Interactions

Bidlingmaier

Liu

2015

Methods in Molecular Biology

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The identification of proteins that interact with small bioactive molecules is a critical but often difficult and time-consuming step in understanding cellular signaling pathways or molecular mechanisms of drug action. Numerous methods for identifying small molecule-interacting proteins have been developed and utilized, including affinity-based purification followed by mass spectrometry analysis, protein microarrays, phage display, and three-hybrid approaches. Although all these methods have been used successfully, there remains a need for additional techniques for analyzing small molecule-protein interactions. A promising method for identifying small molecule-protein interactions is affinity-based selection of yeast surface-displayed human proteome libraries. Large and diverse libraries displaying human protein fragments on the surface of yeast cells have been constructed and subjected to FACS-based enrichment followed by comprehensive exon microarray-based output analysis to identify protein fragments with affinity for small molecule ligands. In a recent example, a proteome-wide search has been successfully carried out to identify cellular proteins binding to the signaling lipids PtdIns(4,5)P2 and PtdIns(3,4,5)P3. Known phosphatidylinositide-binding proteins such as pleckstrin homology domains were identified, as well as many novel interactions. Intriguingly, many novel nuclear phosphatidylinositide-binding proteins were discovered. Although the existence of an independent pool of nuclear phosphatidylinositides has been known about for some time, their functions and mechanism of action remain obscure. Thus, the identification and subsequent study of nuclear phosphatidylinositide-binding proteins is expected to bring new insights to this important biological question. Based on the success with phosphatidylinositides, it is expected that the screening of yeast surface-displayed human proteome libraries will be of general use for the discovery of novel small molecule-protein interactions, thus facilitating the study of cellular signaling pathways and mechanisms of drug action or toxicity.

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Phage display as a method for discovering cellular targets of small molecules

Cited by 8 publications

References 50 publications

Guide to Selecting a Biorecognition Element for Biosensors

Guide to Selecting a Biorecognition Element for Biosensors

Screening Peptide-Binding Partners for GenX via Phage Display

Utilizing Yeast Surface Human Proteome Display Libraries to Identify Small Molecule-Protein Interactions

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