Antibody

Summary

An antibody (Ab), also known as an immunoglobulin (Ig), is a large, Y-shaped protein used by the immune system to identify and neutralize foreign objects such as pathogenic bacteria and viruses. The antibody recognizes a unique molecule of the pathogen, called an antigen. Each tip of the "Y" of an antibody contains a paratope (analogous to a lock) that is specific for one particular epitope (analogous to a key) on an antigen, allowing these two structures to bind together with precision. Using this binding mechanism, an antibody can tag a microbe or an infected cell for attack by other parts of the immune system, or can neutralize it directly (for example, by blocking a part of a virus that is essential for its invasion). To allow the immune system to recognize millions of different antigens, the antigen-binding sites at both tips of the antibody come in an equally wide variety. In contrast, the remainder of the antibody is relatively constant. In mammals, antibodies occur in a few

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Novel bee venom polypeptide and method of use thereof

PROBLEM TO BE SOLVED: To provide a novel polypeptide derived from bee venom and a method of use thereof, and also to provide a pharmaceutical composition useful for modulating bee immune responses to pollens. ;SOLUTION: The invention provides a substantially pure polypeptide comprising an amino acid sequence at least 70% identical, and more preferably at least 90% identical, to the amino acid sequence of an Api m 6 polypeptide. The invention further provides an antibody binding to an Api m 6 protein, and a composition comprising polypeptide fragments of the Api m 6 protein. ;COPYRIGHT: (C)2011,JPO&INPIT

2011

Structural differences of amyloid-beta fibrils revealed by antibodies from phage display

Patrick Droste, Hilal Lashuel

Background: Beside neurofibrillary tangles, amyloid plaques are the major histological hallmarks of Alzheimer's disease (AD) being composed of aggregated fibrils of beta-amyloid (A beta). During the underlying fibrillogenic pathway, starting from a surplus of soluble A beta and leading to mature fibrils, multiple conformations of this peptide appear, including oligomers of various shapes and sizes. To further investigate the fibrillization of beta-amyloid and to have tools at hand to monitor the distribution of aggregates in the brain or even act as disease modulators, it is essential to develop highly sensitive antibodies that can discriminate between diverse aggregates of A beta. Results: Here we report the generation and characterization of a variety of amyloid-beta specific human and human-like antibodies. Distinct fractions of monomers and oligomers of various sizes were separated by size exclusion chromatography (SEC) from A beta 42 peptides. These antigens were used for the generation of two A beta 42 specific immune scFv phage display libraries from macaque (Macaca fascicularis). Screening of these libraries as well as two naive human phage display libraries resulted in multiple unique binders specific for amyloid-beta. Three of the obtained antibodies target the N-terminal part of A beta 42 although with varying epitopes, while another scFv binds to the a-helical central region of the peptide. The affinities of the antibodies to various A beta 42 aggregates as well as their ability to interfere with fibril formation and disaggregation of preformed fibrils were determined. Most significantly, one of the scFv is fibril-specific and can discriminate between two different fibril forms resulting from variations in the acidity of the milieu during fibrillogenesis. Conclusion: We demonstrated that the approach of animal immunization and subsequent phage display based antibody selection is applicable to generate highly specific anti beta-amyloid scFvs that are capable of accurately discriminating between minute conformational differences.

Biomed Central Ltd2015

Transcription factor binding to a single binding site on DNA and its functional consequence in a promoter context are beginning to be relatively well understood. However, binding to clusters of sites has yet to be characterized in depth, and the functional relevance of binding site clusters remains uncertain. We employed a high-throughput biochemical method to characterize transcription factor binding to clusters varying across a range of affinities and configurations. We found that transcription factors can bind concurrently to overlapping sites, challenging the notion of binding exclusivity. Furthermore, compared to an individual high-affinity binding site, small clusters with binding sites an order of magnitude lower in affinity give rise to higher mean occupancies at physiologically-relevant transcription factor concentrations in vitro. To assess whether the observed in vitro occupancies translate to transcriptional activation in vivo, we tested low-affinity binding site clusters by inserting them into a synthetic minimal CYC1 and the native PHO5 S. cerevisiae promoter. In the minCYC1 promoter, clusters of low-affinity binding sites can generate transcriptional output comparable to a promoter containing three consensus binding sites. In the PHO5 promoter, replacing the native Pho4 binding sites with clusters of low-affinity binding sites recovered activation of these promoters as well. This systematic characterization demonstrates that clusters of low-affinity binding sites achieve substantial occupancies, and that this occupancy can drive expression in eukaryotic promoters. In the antibody discovery phase, before advancing a particular antibody sequence to clinical trials, a large number of candidates are characterized for properties of therapeutic interest. Above all, this includes their ability to bind to the target antigen. Standard processes currently in use to characterize antibody binding are either only semi-quantitative (ELISA), or low-throughput (SPR). We developed an experimental process to first retrieve DNA encoding promising synthetic antibody variants directly from the output pools of phage and ribosome display methods, followed by expressing these variants on a microfluidic chip for characterization in a fluorescence-based binding assay. We applied our method to characterize the binding of retrieved Sybody variants against the Spike trimer and RBD domain of the SARS-CoV-2 variant. After an initial proof-of-concept, we improved our method by removing bottlenecks, reducing costs, and incorporating a large degree of process automation to enable measuring binding affinities at scale.

EPFL2022

Structural differences of amyloid-beta fibrils revealed by antibodies from phage display

Patrick Droste, Hilal Lashuel

Biomed Central Ltd2015