Epitope-directed antibody selection by site-specific photocrosslinking

Chen, Longxin; C, Zhu; Guo, Hui; Zhao, Yuanli; Zhang, Limeng; Xing, Zhenzhen; Song, Yue; Zhang, Zihan; Wang, Fuping; Liu, Xiaofeng; Zhang, Yuhan; Runlin, Z.; Wang, Feng

doi:10.1126/sciadv.aaz7825

Cited by 21 publications

(19 citation statements)

References 44 publications

(58 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Amino acid residues of an antibody directly involved in binding epitope is called paratope [2]. The accurate recognition of paratope on a given antibody would greatly improve antibody affinity maturation [3]- [5] and de novo design [6]- [8].…”

Section: Introductionmentioning

confidence: 99%

Leveraging Sequential and Spatial Neighbors Information by Using CNNs Linked With GCNs for Paratope Prediction

Lü

Wang

et al. 2022

IEEE/ACM Trans. Comput. Biol. and Bioinf.

View full text Add to dashboard Cite

Antibodies consisting of variable and constant regions, are a special type of proteins playing a vital role in immune system of the vertebrate. They have the remarkable ability to bind a large range of diverse antigens with extraordinary affinity and specificity. This malleability of binding makes antibodies an important class of biological drugs and biomarkers. In this article, we propose a method to identify which amino acid residues of an antibody directly interact with its associated antigen based on the features from sequence and structure. Our algorithm uses convolution neural networks (CNNs) linked with graph convolution networks (GCNs) to make use of information from both sequential and spatial neighbors to understand more about the local environment of target amino acid residue. Furthermore, we process the antigen partner of an antibody by employing an attention layer. Our method improves on the state-of-the-art methodology.

show abstract

Section: Introductionmentioning

confidence: 99%

Leveraging Sequential and Spatial Neighbors Information by Using CNNs Linked With GCNs for Paratope Prediction

Lü

Wang

et al. 2022

IEEE/ACM Trans. Comput. Biol. and Bioinf.

View full text Add to dashboard Cite

show abstract

“…Additionally, a carbene formed from diazirine upon UV irradiation shows an equivalent crosslinking reactivity to all proteinogenic amino acids, avoiding biased estimation in the following mass spetrometric analyses. An unnatural amino acid containing a photo-activated residue (UAA) can be genetically and sitespecifically inserted into a protein or a photo-activated moiety can be synthetically incorporated into a peptide or a small molecule (Chen et al, 2020;Pham et al, 2013;. Alternatively, a natural amino acid residue such as amine or thiol in a protein is derivatized with N-hydroxysuccinimide (NHS) ester in a heterobifunctional linker that also contains a photo-activated group for a subsequent crosslinking reaction to a binding partner.…”

Section: Mapping Biological Interfaces By Clmsmentioning

confidence: 99%

Unveiling the biological interface of protein complexes by mass spectrometry-coupled methods

Lim

2022

Preprint

View full text Add to dashboard Cite

Most biomolecules become functional and bioactive by forming protein complexes through interaction with ligands that are diverse in size, shape, and physicochemical properties. In the complex biological milieu, the interaction is ligand-specific, driven by molecular sensing and recognition of a binding interface localized within a protein structure. Mapping interfaces of protein complexes is a highly sought area of research as it delivers fundamental insights into proteomes and pathology and hence strategies for therapeutics. While X-ray crystallography and electron microscopy still serve as a gold standard for structural elucidation of protein complexes, artificial and static analytic nature thereof often results in a non-native interface that otherwise might be negligible or non-existent in biological environment. In recent years, the mass spectrometry-coupled approaches, chemical crosslinking (CLMS) and hydrogen-deuterium exchange (HDMS), have become valuable analytic complements to traditional techniques. These methods explicitly identify hot residues and motifs embedded in binding interfaces, in particular, for which the interaction is predominantly dynamic, transient, and/or caused by an intrinsically disordered domain. Here we review the principal role of CLMS and HDMS in protein structural biology with a particular emphasis on the contribution of recent examples to exploring biological interfaces. In addition, we describe recent studies that utilized these methods to expand our understanding of protein complex formation and related biological processes and to increase probability of structure-based drug design.

show abstract

“…One recent approach to solving this issue involves the incorporation of noncanonical amino acids (ncAAs) into epitopes of interest in the antigen used for panning phage display libraries. 68 The advantage that ncAAs such as p -benzoyl-L-phenylalanine and p -azido-L-phenylalanine confer is their propensity to covalently cross-link proteins in the vicinity when exposed to UV light. Upon panning of phage, the photocrosslinker that forms between the epitope-specific ncAA and reactive antibody on the surface of phage after UV exposure enables the selection of antibodies specific to the target epitope containing the ncAA, regardless of affinity.…”

Section: Domain-specific Targeting For Elisa Antibodies To Prevent Interferencementioning

confidence: 99%

Challenges in Detection of Serum Oncoprotein: Relevance to Breast Cancer Diagnostics

Lengfeld¹,

Zhang²,

Stoesz³

et al. 2021

BCTT

View full text Add to dashboard Cite

Breast cancer is a highly prevalent malignancy that shows improved outcomes with earlier diagnosis. Current screening and monitoring methods have improved survival rates, but the limitations of these approaches have led to the investigation of biomarker evaluation to improve early diagnosis and treatment monitoring. The enzyme-linked immunosorbent assay (ELISA) is a specific and robust technique ideally suited for the quantification of protein biomarkers from blood or its constituents. The continued clinical relevancy of this assay format will require overcoming specific technical challenges, including the ultra-sensitive detection of trace biomarkers and the circumventing of potential assay interference due to the expanding use of monoclonal antibody (mAb) therapeutics. Approaches to increasing the sensitivity of ELISA have been numerous and include employing more sensitive substrates, combining ELISA with the polymerase chain reaction (PCR), and incorporating nanoparticles as shuttles for detection antibodies and enzymes. These modifications have resulted in substantial boosts in the ability to detect extremely low levels of protein biomarkers, with some systems reliably detecting antigen at sub-femtomolar concentrations. Extensive utilization of mAb therapies in oncology has presented an additional contemporary challenge for ELISA, particularly when both therapeutic and assay antibodies target the same protein antigen. Resolution of issues such as epitope overlap and steric hindrance requires a rational approach to the design of diagnostic antibodies that takes advantage of modern antibody generation pipelines, epitope binning techniques and computational methods to strategically target biomarker epitopes. This review discusses technical strategies in ELISA implemented to date and their feasibility to address current constraints on sensitivity and problems with interference in the clinical setting. The impact of these recent advancements will depend upon their transformation from research laboratory protocols into facile, reliable detection systems that can ideally be replicated in point-of-care devices to maximize utilization and transform both the diagnostic and therapeutic monitoring landscape.

show abstract

Epitope-directed antibody selection by site-specific photocrosslinking

Cited by 21 publications

References 44 publications

Leveraging Sequential and Spatial Neighbors Information by Using CNNs Linked With GCNs for Paratope Prediction

Leveraging Sequential and Spatial Neighbors Information by Using CNNs Linked With GCNs for Paratope Prediction

Unveiling the biological interface of protein complexes by mass spectrometry-coupled methods

Challenges in Detection of Serum Oncoprotein: Relevance to Breast Cancer Diagnostics

Contact Info

Product

Resources

About