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Related Concept Videos

Antibody Structure01:10

Antibody Structure

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Antibody Structure01:10

Antibody Structure

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Overview
Antibodies, also known as immunoglobulins (Ig), are essential players of the adaptive immune system. These antigen-binding proteins are produced by B cells and make up 20 percent of the total blood plasma by weight. In mammals, antibodies fall into five different classes, which each elicits a different biological response upon antigen binding.
The Y-Shaped Structure of Antibodies Consists of Four Polypeptide Chains
Antibodies consist of four polypeptide chains: two identical heavy...
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Conserved Binding Sites01:49

Conserved Binding Sites

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Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
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Antibody Structure and Classes01:25

Antibody Structure and Classes

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Antibodies, also known as immunoglobulins, are produced by B cells in response to foreign substances, such as bacteria and viruses. These proteins are critical for recognizing and neutralizing these substances, protecting the body from potential harm.
The basic structure of an antibody consists of four protein chains: two identical heavy chains and two identical light chains. These chains are held together by disulfide bonds and other non-covalent interactions, forming a Y-shaped structure.
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Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

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Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...
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Related Experiment Video

Updated: May 2, 2026

Assessment of Immunologically Relevant Dynamic Tertiary Structural Features of the HIV-1 V3 Loop Crown R2 Sequence by ab initio Folding
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Hypervariable loop profiling decodes sequence determinants of antibody stability.

Yue Wan1, Jiahao Liang1, Yile Dai1

  • 1Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA.

Nature Structural & Molecular Biology
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Summary
This summary is machine-generated.

Antibody folding stability is key for therapeutics. New deep loop profiling reveals complementarity-determining region sequences that control folding, enabling engineering of more stable antibodies.

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Last Updated: May 2, 2026

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VDJ-Seq: Deep Sequencing Analysis of Rearranged Immunoglobulin Heavy Chain Gene to Reveal Clonal Evolution Patterns of B Cell Lymphoma
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Area of Science:

  • Biophysics
  • Immunology
  • Protein Engineering

Background:

  • Antibody folding and aggregation present significant hurdles in developing therapeutic and reagent antibodies.
  • The diversity of complementarity-determining regions (CDRs), essential for antigen binding, often compromises antibody folding stability.
  • Understanding the relationship between CDR sequences and antibody folding is limited due to sequence diversity and data scarcity.

Purpose of the Study:

  • To develop a high-throughput method for quantifying the folding fitness of diverse CDR sequences.
  • To identify sequence-level rules governing CDR folding propensity.
  • To engineer more stable antibody scaffolds using folding insights.

Main Methods:

  • Development of a high-throughput 'deep loop profiling' technique.
  • Training machine learning models on large-scale CDR folding data.
  • Utilizing sequence-based predictions to guide protein engineering.

Main Results:

  • Quantification of folding fitness across millions of CDRs.
  • Identification of CDR1 and CDR2 as critical determinants of antibody folding.
  • Successful rescue of unstable nanobodies, including a SARS-CoV-2 binder and a GPCR-targeting intrabody.
  • Creation of next-generation synthetic antibody libraries with enhanced biophysical properties.

Conclusions:

  • Deep loop profiling offers a scalable framework for understanding antibody folding.
  • Sequence-based rules can predict and improve antibody folding competence.
  • This approach facilitates the engineering of stable, functional antibody-based therapeutics and reagents.