scholarly journals Surprisingly Fast Interface and Elbow Angle Dynamics of Antigen-Binding Fragments

2020 ◽  
Vol 7 ◽  
Author(s):  
Monica L. Fernández-Quintero ◽  
Katharina B. Kroell ◽  
Martin C. Heiss ◽  
Johannes R. Loeffler ◽  
Patrick K. Quoika ◽  
...  
Keyword(s):  
Light Chain ◽  
Variable Region ◽  
Affinity Maturation ◽  
Antigen Binding ◽  
Antigen Specificity ◽  
Antigen Binding Site ◽  
Elbow Angle ◽  
Distinct Distribution ◽  
Complementarity Determining Region

Fab consist of a heavy and light chain and can be subdivided into a variable (VH and VL) and a constant region (CH1 and CL). The variable region contains the complementarity-determining region (CDR), which is formed by six hypervariable loops, shaping the antigen binding site, the paratope. Apart from the CDR loops, both the elbow angle and the relative interdomain orientations of the VH–VL and the CH1–CL domains influence the shape of the paratope. Thus, characterization of the interface and elbow angle dynamics is essential to antigen specificity. We studied nine antigen-binding fragments (Fab) to investigate the influence of affinity maturation, antibody humanization, and different light-chain types on the interface and elbow angle dynamics. While the CDR loops reveal conformational transitions in the micro-to-millisecond timescale, both the interface and elbow angle dynamics occur on the low nanosecond timescale. Upon affinity maturation, we observe a substantial rigidification of the VH and VL interdomain and elbow-angle flexibility, reflected in a narrower and more distinct distribution. Antibody humanization describes the process of grafting non-human CDR loops onto a representative human framework. As the antibody framework changes upon humanization, we investigated if both the interface and the elbow angle distributions are changed or shifted. The results clearly showed a substantial shift in the relative VH–VL distributions upon antibody humanization, indicating that different frameworks favor distinct interface orientations. Additionally, the interface and elbow angle dynamics of five antibody fragments with different light-chain types are included, because of their strong differences in elbow angles. For these five examples, we clearly see a high variability and flexibility in both interface and elbow angle dynamics, highlighting the fact that Fab interface orientations and elbow angles interconvert between each other in the low nanosecond timescale. Understanding how the relative interdomain orientations and the elbow angle influence antigen specificity, affinity, and stability has broad implications in the field of antibody modeling and engineering.

scholarly journals The relationship between variable region determinants and antigen specificity on mitogen reactive B cell subsets.

1982 ◽  
Vol 156 (3) ◽  
pp. 924-929 ◽  
Author(s):  
D Primi ◽  
F Mami ◽  
C Le Guern ◽  
P A Cazenave
Keyword(s):  
B Cell ◽  
Variable Region ◽  
Antigen Specificity ◽  
Antigen Binding Site ◽  
V Region ◽  
Set Up ◽  
Cell Mitogen ◽  
B Cell Subsets ◽  
The Relationship ◽  
Beta Galactosidase

On the basis of previous frequency determinations we could set up large numbers of cultures, each containing less than one competent precursor B cell specific for beta-galactosidase or for each of three idiotopes previously found on a monoclonal anti-beta-galactosidase antibody. Cultures were polyclonally activated by either lipopolysaccharide or Nocardia-delipidated cell mitogen. Each culture supernatant was individually tested for hemagglutination activity against sheep erythrocytes coupled with beta-galactosidase or with each of the three purified monoclonal anti-idiotypic antibodies. The results showed that only a minority of those clones positive for only one or two idiotopes recognized antigen. However, all those clones simultaneously positive for the three V region determinants recognized beta-galactosidase. The implications of these results for our understanding of the relationship between the antigen-binding site and idiotope expression are discussed.

Biochemical characterization of amyloid derived from the variable region of thek light chain subgroup III

1990 ◽  
Vol 33 (6) ◽  
pp. 880-884 ◽  
Author(s):  
Maria M. Picken ◽  
Gloria R. Gallo ◽  
Waldemar Pruzanski ◽  
Blas Frangione
Keyword(s):  
Light Chain ◽  
Biochemical Characterization ◽  
Variable Region

scholarly journals Reprogramming the antigen specificity of B cells using genomeediting technologies

2018 ◽  
Author(s):  
James E. Voss ◽  
Alicia Gonzalez-Martin ◽  
Raiees Andrabi ◽  
Roberta P. Fuller ◽  
Ben Murrell ◽  
...  
Keyword(s):  
B Cells ◽  
B Cell ◽  
Cytidine Deaminase ◽  
Variable Region ◽  
Neutralizing Antibody ◽  
Surface Expression ◽  
Affinity Maturation ◽  
Cell Surface Expression ◽  
Human Antibody ◽  
Antigen Specificity

We have developed a method to introduce novel paratopes into the human antibody repertoire by modifying the immunoglobulin genes of mature B cells directly using genome editing technologies. We used CRISPR-Cas9 in a homology directed repair strategy, to replace the heavy chain (HC) variable region in B cell lines with that from an HIV broadly neutralizing antibody, PG9. Our strategy is designed to function in cells that have undergone VDJ recombination using any combination of variable (V), diversity (D) and joining (J) genes. The modified locus expresses PG9 HC which pairs with native light chains resulting in the cell surface expression of HIV specific B cell receptors (BCRs). Endogenous activation-induced cytidine deaminase (AID) in engineered cells allowed for Ig class switching and generated BCR variants with improved anti-HIV neutralizing activity. Thus, BCRs engineered in this way retain the genetic flexibility normally required for affinity maturation during adaptive immune responses.

scholarly journals Conformational selection of allergen-antibody complexes—surface plasticity of paratopes and epitopes

2019 ◽  
Vol 32 (11) ◽  
pp. 513-523
Author(s):  
Monica L Fernández-Quintero ◽  
Johannes R Loeffler ◽  
Franz Waibl ◽  
Anna S Kamenik ◽  
Florian Hofer ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Structural Information ◽  
High Surface ◽  
Epitope Prediction ◽  
Antigen Binding ◽  
Antigen Binding Site ◽  
Surface Plasticity ◽  
Structural Framework ◽  
Dynamics Simulations

Abstract Antibodies have the ability to bind various types of antigens and to recognize different antibody-binding sites (epitopes) of the same antigen with different binding affinities. Due to the conserved structural framework of antibodies, their specificity to antigens is mainly determined by their antigen-binding site (paratope). Therefore, characterization of epitopes in combination with describing the involved conformational changes of the paratope upon binding is crucial in understanding and predicting antibody-antigen binding. Using molecular dynamics simulations complemented with strong experimental structural information, we investigated the underlying binding mechanism and the resulting local and global surface plasticity in the binding interfaces of distinct antibody-antigen complexes. In all studied allergen-antibody complexes, we clearly observe that experimentally suggested epitopes reveal less plasticity, while non-epitope regions show high surface plasticity. Surprisingly, the paratope shows higher conformational diversity reflected in substantially higher surface plasticity, compared to the epitope. This work allows a visualization and characterization of antibody-antigen interfaces and might have strong implications for antibody-antigen docking and in the area of epitope prediction.

Insertion of atypical glycans into the tumor antigen-binding site identifies DLBCLs with distinct origin and behavior

Blood ◽  
2021 ◽  
Author(s):  
Giorgia Chiodin ◽  
Joel D. Allen ◽  
Dean Bryant ◽  
Philip Rock ◽  
Enrica Antonia Martino ◽  
...  
Keyword(s):  
Follicular Lymphoma ◽  
B Cell ◽  
Variable Region ◽  
Cell Receptor ◽  
Antigen Binding ◽  
Post Translational Modification ◽  
Antigen Binding Site ◽  
Lymphoma Cells ◽  
X Ray Crystallography ◽  
Significant Gene

Glycosylation of the surface immunoglobulin variable region is a remarkable follicular lymphoma-associated feature rarely seen in normal B cells. Here, we define a subset of diffuse large B-cell lymphomas (DLBCL) which acquire N-glycosylation sites selectively in the immunoglobulin (Ig) complementary-determining-regions (CDR) of the antigen-binding sites. Mass-spectrometry and X-ray crystallography demonstrate how the inserted glycans are stalled at oligomannose-type structures due to burial in the CDR loops. Acquisition of sites occurs in ~50% of germinal center B-cell-like DLBCL, mainly of the genetic EZB subtype, irrespective of IGHV-D-J use. This markedly contrasts with the activated B-cell-like DLBCL Ig, which rarely has sites in the CDR, and appears not to acquire oligomannose-type structures. Acquisition of CDR-located acceptor sites associates with mutations of epigenetic regulators and BCL2 translocations, indicating an origin shared with follicular lymphoma. Within the EZB subtype, these sites associate with more rapid disease progression and with significant gene-set enrichment of the B-cell receptor, PI3K/AKT/MTORC1, glucose metabolism, and MYC signaling pathways, particularly in the fraction devoid of MYC translocations. The oligomannose-type glycans on the lymphoma cells interact with the candidate lectin DC-SIGN, mediating low-level signals, and lectin-expressing cells form clusters with lymphoma cells. Both clustering and signaling are inhibited by antibodies specifically targeting the DC-SIGN carbohydrate-recognition-domain. Oligomannosylation of the tumor immunoglobulin is a post-translational modification that readily identifies a distinct GCB-DLBCL category with more aggressive clinical behavior, and could be a potential precise therapeutic target via antibody-mediated inhibition of the tumor Ig interaction with DC-SIGN-expressing M2-polarized macrophages.

scholarly journals Highly sensitive and unbiased approach for elucidating antibody repertoires

2016 ◽  
Vol 113 (28) ◽  
pp. 7846-7851 ◽  
Author(s):  
Sherry G. Lin ◽  
Zhaoqing Ba ◽  
Zhou Du ◽  
Yu Zhang ◽  
Jiazhi Hu ◽  
...  
Keyword(s):  
B Cells ◽  
B Cell ◽  
Germ Line ◽  
Variable Region ◽  
Cell Receptor ◽  
Affinity Maturation ◽  
Antigen Binding ◽  
Variable Regions ◽  
Antibody Repertoires ◽  
B Lineage

Developing B lymphocytes undergo V(D)J recombination to assemble germ-line V, D, and J gene segments into exons that encode the antigen-binding variable region of Ig heavy (H) and light (L) chains. IgH and IgL chains associate to form the B-cell receptor (BCR), which, upon antigen binding, activates B cells to secrete BCR as an antibody. Each of the huge number of clonally independent B cells expresses a unique set of IgH and IgL variable regions. The ability of V(D)J recombination to generate vast primary B-cell repertoires results from a combinatorial assortment of large numbers of different V, D, and J segments, coupled with diversification of the junctions between them to generate the complementary determining region 3 (CDR3) for antigen contact. Approaches to evaluate in depth the content of primary antibody repertoires and, ultimately, to study how they are further molded by secondary mutation and affinity maturation processes are of great importance to the B-cell development, vaccine, and antibody fields. We now describe an unbiased, sensitive, and readily accessible assay, referred to as high-throughput genome-wide translocation sequencing-adapted repertoire sequencing (HTGTS-Rep-seq), to quantify antibody repertoires. HTGTS-Rep-seq quantitatively identifies the vast majority of IgH and IgL V(D)J exons, including their unique CDR3 sequences, from progenitor and mature mouse B lineage cells via the use of specific J primers. HTGTS-Rep-seq also accurately quantifies DJH intermediates and V(D)J exons in either productive or nonproductive configurations. HTGTS-Rep-seq should be useful for studies of human samples, including clonal B-cell expansions, and also for following antibody affinity maturation processes.

scholarly journals Molecular composition of an antigen-specific, Ly-1 T suppressor inducer factor. One molecule binds antigen and is I-J-; another is I-J+, does not bind antigen, and imparts an Igh-variable region-linked restriction.

1982 ◽  
Vol 155 (3) ◽  
pp. 655-665 ◽  
Author(s):  
K Yamauchi ◽  
N Chao ◽  
D B Murphy ◽  
R K Gershon
Keyword(s):  
Biological Activity ◽  
Variable Region ◽  
The Other ◽  
Antigen Binding ◽  
Suppressive Activity ◽  
Antigen Specificity ◽  
Igh Locus ◽  
Binding Factor ◽  
Producer Cell ◽  
Inductive Signal

Immunized Ly-1+2-T cells (Ly-1 cells) make an antigen-specific soluble suppressor product (Lyl-1 TsiF) that will induce Ly-2+ cells to express suppressive activity but only if the Ly-2+ and the Ly-1 producer cell share genetic polymorphisms that are linked to the Igh locus and in particular that part where the Igh-V (or VH) is encoded. Ly-1 TsiF can be separated into entities, one binds antigen and does not express I-J determinants, and the other is I-J+ and does not bind antigen. Neither of these "subfactors" has biological activity, but a 50:50 mixture of them reconstitutes biological activity that expresses the antigen specificity of the antigen-binding molecule. Any of the three heterologous erythrocytes (antigens) studied can be used for immunization to produce the I-J+ nonantigen-binding factor, i.e., the I-J+ moiety makes no contribution to the factor's specificity. It does, however, determine the intact factor's Igh-V linked restriction. Thus, the antigen combining site of the factor is irrelevant to the factor's Igh-V restriction but crucial for its specificity. The I-J+ molecule does not bind antigen nor influence the factor's antigen specificity but expresses the Igh-V polymorphism (or anti-Igh-V polymorphism) that is required for the transmission of an inductive signal to the factor's Ly-2+ acceptor cell.

scholarly journals Isolation and characterization of a light chain variable region gene for human rheumatoid factors.

1987 ◽  
Vol 166 (6) ◽  
pp. 1900-1905 ◽  
Author(s):  
P P Chen ◽  
D L Robbins ◽  
F R Jirik ◽  
T J Kipps ◽  
D A Carson
Keyword(s):  
Light Chain ◽  
Human Placenta ◽  
Variable Region ◽  
Light Chains ◽  
Rheumatoid Factors ◽  
Region Gene ◽  
Isolation And Characterization ◽  
Variable Region Gene

Previously, we isolated a Vk gene (Humkv325) from a human placenta that encodes RF light chains bearing the PSL2 and PSL3 CRI markers. Here we report the isolation and characterization of a second human Vk gene (Humkv328) that can be used for RF synthesis. This Vk gene probably encodes at least two 6B6.6 CRI+ RF light chains (Les and Pom) from unrelated subjects, and thus may be related to the light chain-associated 6B6.6 CRI.

Role of antibody heavy and light chain interface residues in affinity maturation of binding to HIV envelope glycoprotein

2019 ◽  
Vol 4 (4) ◽  
pp. 737-746 ◽  
Author(s):  
Alberto Cisneros ◽  
Rachel Stecker Nargi ◽  
Erica Hammaker Parrish ◽  
Christian Marie Haliburton ◽  
Jens Meiler ◽  
...  
Keyword(s):  
Binding Affinity ◽  
Heavy Chain ◽  
Light Chain ◽  
Envelope Glycoprotein ◽  
Affinity Maturation ◽  
Antigen Binding ◽  
Glycoprotein P ◽  
Contact Residues ◽  
Hiv Envelope

Optimization of the heavy chain/light chain interface could serve as an important tool for maximizing antibody/antigen binding affinity without altering antigen contact residues.

Sign in / Sign up

Export Citation Format

Share Document