Bioinformatics Resources and Tools for Phage Display

Huang, Jian; Ru, Beibei; Dai, Peng

doi:10.3390/molecules16010694

Cited by 49 publications

(38 citation statements)

References 74 publications

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“…Amino acid sequences were deduced according to the nucleotide sequences and analyzed using DNA2PRO2 software from Relic Program [17], [41]. The similarity of selected peptides with A. marginale MSP1a was performed using BLAST search followed by sequence alignment with ClustalW2 software (http://www.ebi.ac.uk/Tools/msa/clustalw2/).…”

Section: Methodsmentioning

confidence: 99%

Functional Epitope Core Motif of the Anaplasma marginale Major Surface Protein 1a and Its Incorporation onto Bioelectrodes for Antibody Detection

et al. 2012

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Anaplasmosis, a persistent intraerythrocytic infection of cattle by Anaplasma marginale , causes severe anemia and a higher rate of abortion, resulting in significant loss to both dairy and beef industries. Clinical diagnosis is based on symptoms and confirmatory laboratory tests are required. Currently, all the diagnostic assays have been developed with whole antigens with indirect ELISA based on multiple epitopes. In a pioneer investigation we demonstrated the use of critical motifs of an epitope as biomarkers for immunosensor applications. Mimotopes of the MSP1a protein functional epitope were obtained through Phage Display after three cycles of selection of a 12-mer random peptide library against the neutralizing monoclonal antibody 15D2. Thirty-nine clones were randomly selected, sequenced, translated and aligned with the native sequence. The consensus sequence SxSSQSEASTSSQLGA was obtained, which is located in C-terminal end of the 28-aa repetitive motif of the MSP1a protein, but the alignment and sequences' variation among mimotopes allowed us to map the critical motif STSSxL within the consensus sequence. Based on these results, two peptides were chemically synthesized: one based on the critical motif (STSSQL, Am1) and the other based on the consensus sequence aligned with the native epitope (SEASTSSQLGA, Am2). Sera from 24 infected and 52 healthy animals were tested by ELISA for reactivity against Am1 and Am2, which presented sensitivities of 96% and 100%, respectively. The Am1 peptide was incorporated onto a biolectrode (graphite modified with poly-3-hydroxyphenylacetic acid) and direct serum detection was demonstrated by impedance, differential pulse voltammetry, and atomic force microscopy. The electrochemical sensor system proved to be highly effective in discriminating sera from positive and negative animals. These immunosensors were highly sensitive and selective for positive IgG, contaminants did not affect measurements, and were based on a simple, fast and reproducible electrochemical system.

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Section: Methodsmentioning

confidence: 99%

Functional Epitope Core Motif of the Anaplasma marginale Major Surface Protein 1a and Its Incorporation onto Bioelectrodes for Antibody Detection

et al. 2012

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“…In these counter selections, the phages that interact with the background are removed from the phage library. Besides this a specific binding TUP (Target Unrelated peptides), there are also propagation related TUP, which are selected because of there increased infectivity [30]. It is important to exclute this TUP from the selected peptide population, therefore special bioinformatic tools are available, like SAROTUP [31], MimoPRO [32], MimoDB [33].…”

Section: Peptide Phage Displaymentioning

confidence: 99%

“…Recently also several other bioinformatic tools are available or will become available in the near future leading to more complete insights in the peptides based on computational information. An overview of different bioinformatic tools and resources for analysing peptides selected with phage display is given in a recent review of Huang et al [30].…”

Section: Peptide Phage Displaymentioning

confidence: 99%

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

Dorst

Mehta

Rouah-Martin

et al. 2012

Methods

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“…All of these can help to characterise the binding. Moreover, structures of free and the receptor-bound mimetics can be compared experimentally, or with application of computational docking (Huang et al, 2011). As a result, lead compounds can be identified, and further developed to replace natural antigens in diagnostic assays, and in therapy (Deroo & Muller, 2001).…”

Section: Molecular Mimicry Phenomenonmentioning

confidence: 99%