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共5篇 平均IF=3.9 (2.8-42.5)更多分析
  • 1区Q1影响因子: 42.5
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    1. High-Throughput Mapping of B Cell Receptor Sequences to Antigen Specificity.
    作者:Setliff Ian , Shiakolas Andrea R , Pilewski Kelsey A , Murji Amyn A , Mapengo Rutendo E , Janowska Katarzyna , Richardson Simone , Oosthuysen Charissa , Raju Nagarajan , Ronsard Larance , Kanekiyo Masaru , Qin Juliana S , Kramer Kevin J , Greenplate Allison R , McDonnell Wyatt J , Graham Barney S , Connors Mark , Lingwood Daniel , Acharya Priyamvada , Morris Lynn , Georgiev Ivelin S
    期刊:Cell
    日期:2019-11-28
    DOI :10.1016/j.cell.2019.11.003
    B cell receptor (BCR) sequencing is a powerful tool for interrogating immune responses to infection and vaccination, but it provides limited information about the antigen specificity of the sequenced BCRs. Here, we present LIBRA-seq (linking B cell receptor to antigen specificity through sequencing), a technology for high-throughput mapping of paired heavy- and light-chain BCR sequences to their cognate antigen specificities. B cells are mixed with a panel of DNA-barcoded antigens so that both the antigen barcode(s) and BCR sequence are recovered via single-cell next-generation sequencing. Using LIBRA-seq, we mapped the antigen specificity of thousands of B cells from two HIV-infected subjects. The predicted specificities were confirmed for a number of HIV- and influenza-specific antibodies, including known and novel broadly neutralizing antibodies. LIBRA-seq will be an integral tool for antibody discovery and vaccine development efforts against a wide range of antigen targets.
  • 3区Q1影响因子: 3.9
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    2. The role of Antibody Vκ Framework 3 region towards Antigen binding: Effects on recombinant production and Protein L binding.
    作者:Su Chinh Tran-To , Ling Wei-Li , Lua Wai-Heng , Poh Jun-Jie , Gan Samuel Ken-En
    期刊:Scientific reports
    日期:2017-06-19
    DOI :10.1038/s41598-017-02756-3
    Antibody research has traditionally focused on heavy chains, often neglecting the important complementary role of light chains in antibody formation and secretion. In the light chain, the complementarity-determining region 3 (VL-CDR3) is specifically implicated in disease states. By modulating VL-CDR3 exposure on the scaffold through deletions in the framework region 3 (VL-FWR3), we further investigated the effects on secretion in recombinant production and antigen binding kinetics. Our random deletions of two residues in the VL-FWR3 of a Trastuzumab model showed that the single deletions could impact recombinant production without significant effect on Her2 binding. When both the selected residues were deleted, antibody secretion was additively decreased, and so was Her2 binding kinetics. Interestingly, we also found allosteric effects on the Protein L binding site at VL-FWR1 elicited by these deletions in VL- FWR3. Together, these findings demonstrate the importance of light chain FWR3 in antigen binding, recombinant production, and antibody purification using Protein L.
  • 4区Q3影响因子: 2.8
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    3. Improved Antibody-Specific Epitope Prediction Using AlphaFold and AbAdapt.
    期刊:Chembiochem : a European journal of chemical biology
    日期:2022-08-11
    DOI :10.1002/cbic.202200303
    Antibodies recognize their cognate antigens with high affinity and specificity, but the prediction of binding sites on the antigen (epitope) corresponding to a specific antibody remains a challenging problem. To address this problem, we developed AbAdapt, a pipeline that integrates antibody and antigen structural modeling with rigid docking in order to derive antibody-antigen specific features for epitope prediction. In this study, we systematically assessed the impact of integrating the state-of-the-art protein modeling method AlphaFold with the AbAdapt pipeline. By incorporating more accurate antibody models, we observed improvement in docking, paratope prediction, and prediction of antibody-specific epitopes. We further applied AbAdapt-AF in an anti-receptor binding domain (RBD) antibody complex benchmark and found AbAdapt-AF outperformed three alternative docking methods. Also, AbAdapt-AF demonstrated higher epitope prediction accuracy than other tested epitope prediction tools in the anti-RBD antibody complex benchmark. We anticipate that AbAdapt-AF will facilitate prediction of antigen-antibody interactions in a wide range of applications.
  • 3区Q1影响因子: 4.5
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    4. Toward real-world automated antibody design with combinatorial Bayesian optimization.
    期刊:Cell reports methods
    日期:2023-01-03
    DOI :10.1016/j.crmeth.2022.100374
    Antibodies are multimeric proteins capable of highly specific molecular recognition. The complementarity determining region 3 of the antibody variable heavy chain (CDRH3) often dominates antigen-binding specificity. Hence, it is a priority to design optimal antigen-specific CDRH3 to develop therapeutic antibodies. The combinatorial structure of CDRH3 sequences makes it impossible to query binding-affinity oracles exhaustively. Moreover, antibodies are expected to have high target specificity and developability. Here, we present AntBO, a combinatorial Bayesian optimization framework utilizing a CDRH3 trust region for an design of antibodies with favorable developability scores. The experiments on 159 antigens demonstrate that AntBO is a step toward practically viable antibody design. In under 200 calls to the oracle, AntBO suggests antibodies outperforming the best binding sequence from 6.9 million experimentally obtained CDRH3s. Additionally, AntBO finds very-high-affinity CDRH3 in only 38 protein designs while requiring no domain knowledge.
  • 4区Q2影响因子: 3
    5. Length of the antibody heavy chain complementarity determining region 3 as a specificity-determining factor.
    作者:Barrios Yvelise , Jirholt Pernilla , Ohlin Mats
    期刊:Journal of molecular recognition : JMR
    日期:2004 Jul-Aug
    DOI :10.1002/jmr.679
    The antigen binding site of an antibody is made up of residues residing in six hypervariable loops of the heavy and light chains. In most cases several or all of these loops are required for the establishment of the antigen-binding surface. Five of these loops display a limited diversity in length and sequence while the third complementarity determining region (CDR) of the heavy chain is highly different between antibodies not only with respect to sequence but also with respect to length. Its extensive diversity is a key component in the establishment of binding sites allowing for the recognition of essentially any antigen by humoral immunity. The relative importance of its sequence vs its length diversity in this context is however, not very well established. To investigate this matter further we have used an approach employing combinatorial antibody libraries and antigen-specific selection in the search for CDRH3 length and sequence diversity compatible with a given antigen specificity, the major antigenic determinant on the tumour-associated antigen mucin-1. In this way we have now defined heavy chain CDR3 length as a critical parameter in the creation of an antigen-specific binding site. We also propose that this may reflect a dependence of a particular structure of this hypervariable loop, the major carrier of diversity in the binding site, for establishment of a given specificity.
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