B cells encounter antigen over a wide affinity range, from K(A)=10(5) M(-1) to K(A)=10(10) M(-1). The strength of B cell antigen receptor (BCR) signaling in response to antigen increases with affinity, a process known as "affinity discrimination". In this work, we use a computational simulation of B cell surface dynamics and membrane-proximal signaling to show that affinity discrimination can arise from the formation of BCR oligomers. It is known that BCRs form oligomers upon encountering antigen, and that the size and rate of formation of these oligomers both increase with affinity. In our simulation, we have introduced a requirement that only BCR-antigen complexes that are part of an oligomer can engage cytoplasmic signaling molecules such as Src-family kinases. Our simulation shows that as affinity increases, BCR signaling activity increases in addition to the number of collected antigen. Our results are also consistent with the existence of an experimentally-observed threshold affinity of activation at K(A)=10(5)-10(6) M(-1) (no signaling activity below this affinity value) and affinity discrimination ceiling of K(A)=10(10) M(-1) (no affinity discrimination above this affinity value). Comparison with experiments shows that the time scale of BCR oligomer formation predicted by our model (less than 10 s) is well within the time scale of experimentally observed association of BCR with Src-family kinases (10-20 s).
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http://dx.doi.org/10.1016/j.jtbi.2012.05.008 | DOI Listing |
ACS Cent Sci
December 2024
Department of Chemistry, North Carolina State University, 2620 Yarbrough Dr., Raleigh, North Carolina 27695, United States.
Aptamers are oligonucleotide-based affinity reagents that are increasingly being used in various applications. Systematic evolution of ligands by exponential enrichment (SELEX) has been widely used to isolate aptamers for small-molecule targets, but it remains challenging to generate aptamers with high affinity and specificity for targets with few functional groups. To address this challenge, we have systematically evaluated strategies for optimizing the isolation of aptamers for (+)-methamphetamine, a target for which previously reported aptamers have weak or no binding affinity.
View Article and Find Full Text PDFTalanta
December 2024
College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao, 266580, China. Electronic address:
Glutathione (GSH) is a key biomarker closely associated with cancer, and its content varies greatly between normal cells and cancer cells. However, intracellular detection of GSH was challenging because existing probes not only have a long detection time but also have fluorescence in the blue-green region that overlaps with the biological matrix's spontaneous fluorescence, thus affecting the detection accuracy. Therefore, a new red fluorescent nano-probe was needed to rapidly and accurately detected GSH within the biological matrix.
View Article and Find Full Text PDFACS Nano
December 2024
Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, United States.
Two or more protein ligands may compete against each other to interact transiently with a protein receptor. While this is a ubiquitous phenomenon in cell signaling, existing technologies cannot identify its kinetic complexity because specific subpopulations of binding events of different ligands are hidden in the averaging process in an ensemble. In addition, the limited time resolution of prevailing methods makes detecting and discriminating binding events among diverse interacting partners challenging.
View Article and Find Full Text PDFAdv Healthc Mater
December 2024
State Key Laboratory of Organic-Inorganic Composites, International Joint Bioenergy Laboratory of Ministry of Education, National Energy Research and Development Center for Biorefinery, Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China.
Prostate-specific membrane antigen (PSMA) is overexpressed in prostate cancer cells and tumor vasculature, making it an important biomarker. However, conventional PSMA-targeting agents like antibodies and small molecules have limitations. Antibodies exhibit instability and complex production, while small molecules show lower specificity and higher toxicity.
View Article and Find Full Text PDFInt J Mol Sci
November 2024
School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China.
Identifying a small set of effective biomarkers from multi-omics data is important for the discrimination of different cell types and helpful for the early detection diagnosis of complex diseases. However, it is challenging to identify optimal biomarkers from the high throughput molecular data. Here, we present a method called protein-protein interaction affinity and co-expression network (PPIA-coExp), a linear programming model designed to discover context-specific biomarkers based on co-expressed networks and protein-protein interaction affinity (PPIA), which was used to estimate the concentrations of protein complexes based on the law of mass action.
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