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Nature Biotechnology Jun 2011A peptide library representing the entire human proteome is applied to the discovery of autoantigens.
A peptide library representing the entire human proteome is applied to the discovery of autoantigens.
Topics: Autoantigens; Female; Humans; Peptide Library; Proteome; Proteomics
PubMed: 21654669
DOI: 10.1038/nbt.1888 -
Scientific Reports May 2020The alpha-2,8-linked form of the polysaccharide polysialic acid (PSA) has widespread implications in physiological and pathological processes, ranging from neurological...
The alpha-2,8-linked form of the polysaccharide polysialic acid (PSA) has widespread implications in physiological and pathological processes, ranging from neurological development to disease progression. Though the high electronegativity and excluded volume of PSA often promotes interference of biomolecular interactions, PSA-binding ligands have important implications for both biological processes and biotechnological applications. As such, the design, identification, and characterisation of novel ligands towards PSA is critical for expanding knowledge of PSA interactions and achieving selective glycan targeting. Here, we report on a rational approach for the identification of alpha-2,8-PSA-binding peptides, involving design from the endogenous ligand Siglec-11 and multi-platform characterisation of peptide binding. Microarray-based examination of peptides revealed charge and sequence characteristics influencing peptide affinity to PSA, and carbohydrate-peptide binding was further quantified with a novel fluorescence anisotropy assay. PSA-binding peptides exhibited specific binding to polymeric SA, as well as different degrees of selective binding in various conditions, including competition with PSA of alternating 2,8/9-linkages and screening with PSA-expressing cells. A computational study of Siglec-11 and Siglec-11-derived peptides offered synergistic insight into ligand binding. These results demonstrate the potential of PSA-binding peptides for selective targeting and highlight the importance of the approaches described herein for the study of carbohydrate interactions.
Topics: Amino Acid Sequence; Binding Sites; Humans; Ligands; Peptide Library; Peptides; Protein Binding; Sialic Acids
PubMed: 32376914
DOI: 10.1038/s41598-020-64088-z -
Biological Chemistry Apr 2022Current biomedical research and diagnostics critically depend on detection agents for specific recognition and quantification of protein molecules. Monoclonal antibodies... (Review)
Review
Current biomedical research and diagnostics critically depend on detection agents for specific recognition and quantification of protein molecules. Monoclonal antibodies have been used for this purpose over decades and facilitated numerous biological and biomedical investigations. Recently, however, it has become apparent that many commercial reagent antibodies lack specificity or do not recognize their target at all. Thus, synthetic alternatives are needed whose complex designs are facilitated by multidisciplinary approaches incorporating experimental protein engineering with computational modeling. Here, we review the status of such an engineering endeavor based on the modular armadillo repeat protein scaffold and discuss challenges in its implementation.
Topics: Armadillo Domain Proteins; Indicators and Reagents; Models, Molecular; Peptide Library; Peptides; Protein Engineering; Proteins; Technology
PubMed: 35089661
DOI: 10.1515/hsz-2021-0384 -
Analytical Chemistry Dec 2021Despite advancements of data-independent acquisition mass spectrometry (DIA-MS) to provide comprehensive and reproducible proteome profiling, its utility in very...
Despite advancements of data-independent acquisition mass spectrometry (DIA-MS) to provide comprehensive and reproducible proteome profiling, its utility in very low-input samples is limited. Due to different proteome complexities and corresponding peptide ion abundances, the conventional LC-MS/MS acquisition and widely used large-scale DIA libraries may not be suitable for the micro-nanogram samples. In this study, we report a sample size-comparable library-based DIA approach to enhance the proteome coverage of low-input nanoscale samples (i.e., nanogram cells, ∼5-50 cells). By constructing sample size-comparable libraries, 2380 and 3586 protein groups were identified from as low as 0.75 (∼5 cells) and 1.5 ng (∼10 cells), respectively, highlighting one of the highest proteome coverage with good reproducibility (86%-99% in triplicate results). For the 0.75 ng sample (∼5 cells), significantly superior identification (2380 proteins) was achieved by small-size library-based DIA, compared to 1908, 1749, and 107 proteins identified from medium-size and large-size libraries and a lung cancer resource spectral library, respectively. A similar trend was observed using a different instrument and data analysis pipeline, indicating the generalized conclusion of the approach. Furthermore, the small-size library uniquely identified 518 (22%) proteins in the low-abundant region and spans over a 5-order dynamic range. Spectral similarity analysis revealed that the fragmentation ion pattern in the DIA-MS/MS spectra of the dataset and spectral library play crucial roles for mapping low abundant proteins. With these spectral libraries made freely available, the optimized library-based DIA strategy and DIA digital map will advance quantitative proteomics applications for mass-limited samples.
Topics: Chromatography, Liquid; Peptide Library; Proteome; Reproducibility of Results; Sample Size; Tandem Mass Spectrometry
PubMed: 34904835
DOI: 10.1021/acs.analchem.1c03477 -
International Journal of Molecular... Aug 2022For the treatment of inflammatory illnesses such as rheumatoid arthritis and carditis, as well as cancer, several anti-inflammatory medications have been created over... (Review)
Review
For the treatment of inflammatory illnesses such as rheumatoid arthritis and carditis, as well as cancer, several anti-inflammatory medications have been created over the years to lower the concentrations of inflammatory mediators in the body. Peptides are a class of medication with the advantages of weak immunogenicity and strong activity, and the phage display technique is an effective method for screening various therapeutic peptides, with a high affinity and selectivity, including anti-inflammation peptides. It enables the selection of high-affinity target-binding peptides from a complex pool of billions of peptides displayed on phages in a combinatorial library. In this review, we will discuss the regular process of using phage display technology to screen therapeutic peptides, and the peptides screened for anti-inflammation properties in recent years according to the target. We will describe how these peptides were screened and how they worked in vitro and in vivo. We will also discuss the current challenges and future outlook of using phage display to obtain anti-inflammatory therapeutic peptides.
Topics: Anti-Inflammatory Agents; Bacteriophages; Cell Surface Display Techniques; Peptide Library; Peptides; Protein Binding; Technology
PubMed: 35955688
DOI: 10.3390/ijms23158554 -
Proceedings of the National Academy of... Jul 2018T cell receptors (TCRs) bind to peptide-major histocompatibility complex (pMHC) with low affinity ( ∼ μM), which is generally assumed to facilitate cross-reactive TCR...
T cell receptors (TCRs) bind to peptide-major histocompatibility complex (pMHC) with low affinity ( ∼ μM), which is generally assumed to facilitate cross-reactive TCR "scanning" of ligands. To understand the relationship between TCR/pMHC affinity and cross-reactivity, we sought to engineer an additional weak interaction, termed "velcro," between the TCR and pMHC to probe the specificities of TCRs at relatively low and high affinities. This additional interaction was generated through an eight-amino acid peptide library covalently linked to the N terminus of the MHC-bound peptide. Velcro was selected through an affinity-based isolation and was subsequently shown to enhance the cognate TCR/pMHC affinity in a peptide-dependent manner by ∼10-fold. This was sufficient to convert a nonstimulatory ultra-low-affinity ligand into a stimulatory ligand. An X-ray crystallographic structure revealed how velcro interacts with the TCR. To probe TCR cross-reactivity, we screened TCRs against yeast-displayed pMHC libraries with and without velcro, and found that the peptide cross-reactivity profiles of low-affinity ( > 100 μM) and high-affinity ( ∼ μM) TCR/pMHC interactions are remarkably similar. The conservation of recognition of the TCR for pMHC across affinities reveals the nature of low-affinity ligands for which there are important biological functions and has implications for understanding the specificities of affinity-matured TCRs.
Topics: Cross Reactions; Humans; Major Histocompatibility Complex; Oligopeptides; Peptide Library; Protein Engineering; Receptors, Antigen, T-Cell
PubMed: 30021852
DOI: 10.1073/pnas.1802746115 -
BioTechniques Nov 2018
Topics: Biocatalysis; Biofuels; Humans; Immunotherapy; Neoplasms; Nobel Prize; Optical Tweezers; Peptide Library
PubMed: 30394126
DOI: 10.2144/btn-2018-0155 -
Current Issues in Molecular Biology 2011Filamentous bacteriophage, long and thin filaments that are secreted from the host cells without killing them, have been an antithesis to the standard view of... (Review)
Review
Filamentous bacteriophage, long and thin filaments that are secreted from the host cells without killing them, have been an antithesis to the standard view of head-and-tail bacterial killing machines. Episomally replicating filamentous phage Ff of Escherichia coli provide the majority of information about the principles and mechanisms of filamentous phage infection, episomal replication and assembly. Chromosomally- integrated "temperate" filamentous phage have complex replication and integration, which are currently under active investigation. The latter are directly or indirectly implicated in diseases caused by bacterial pathogens Vibrio cholerae, Pseudomonas aeruginosa and Neisseria meningitidis. In the first half of the review, both the Ff and temperate phage are described and compared. A large section of the review is devoted to an overview of phage display technology and its applications in nanotechnology.
Topics: Host-Pathogen Interactions; Inovirus; Nanotechnology; Peptide Library; Virion
PubMed: 21502666
DOI: No ID Found -
Molecules (Basel, Switzerland) Dec 2021Mycotoxins, the small size secondary metabolites of fungi, have posed a threat to the safety of medicine, food and public health. Therefore, it is essential to create... (Review)
Review
Mycotoxins, the small size secondary metabolites of fungi, have posed a threat to the safety of medicine, food and public health. Therefore, it is essential to create sensitive and effective determination of mycotoxins. Based on the special affinity between antibody and antigen, immunoassay has been proved to be a powerful technology for the detection of small analytes. However, the tedious preparation and instability of conventional antibodies restrict its application on easy and fast mycotoxins detection. By virtue of simplicity, ease of use, and lower cost, phage display library provides novel choices for antibodies or hapten conjugates, and lead random peptide or recombinant antibody to becoming the promising and environmental friendly immune-reagents in the next generation of immunoassays. This review briefly describes the latest developments on mycotoxins detection using M13 phage display, mainly focusing on the recent applications of phage display technology employed in mycotoxins detection, including the introduction of phage and phage display, the types of phage displayed peptide/recombinant antibody library, random peptides/recombinant antibodies-based immunoassays, as well as simultaneous determination of multiple mycotoxins.
Topics: Antigens; Cell Surface Display Techniques; Humans; Immunoassay; Mycotoxins; Peptide Library; Single-Domain Antibodies
PubMed: 34946736
DOI: 10.3390/molecules26247652 -
Viruses Dec 2020Peptides with specific affinities for various materials have been identified in the past three decades and utilized in materials science and engineering. A peptide's...
Peptides with specific affinities for various materials have been identified in the past three decades and utilized in materials science and engineering. A peptide's capability to specifically interact with materials is not naturally derived but screened from a biologically constructed peptide library displayed on phages or cells. To date, due to limitations in the screening procedure, the function of screened peptides has been primarily limited to the affinity for target materials. Herein, we demonstrated the screening of surfactant-like peptides from a phage-displayed peptide library. A screened phage clone displaying a peptide showed high activity for accumulating at emulsion surfaces with certain assembled structures, resulting in stable emulsions. The surface tension for the solution of the chemically synthesized peptide decreased with increasing peptide concentration, demonstrating certain surface activity, which corresponded to the ability to decrease the surface tension of liquids (e.g., water), owing to the accumulation of molecules at the air-liquid or liquid-liquid interface. Peptides with a randomized sequence did not lower the surface tension, indicating the essential role of amino acid sequences in surface activity. Our strategy for identifying novel functional peptides from a phage-displayed peptide library can be used to expand the applicability of peptidyl materials and biosurfactants.
Topics: Amino Acid Sequence; Cell Surface Display Techniques; Drug Discovery; Microscopy, Atomic Force; Peptide Library; Peptides; Surface Tension; Surface-Active Agents
PubMed: 33333956
DOI: 10.3390/v12121442