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Related Concept Videos

Antibody Structure01:10

Antibody Structure

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...
Antibody Structure01:10

Antibody Structure

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...
Antibody Structure and Classes01:25

Antibody Structure and Classes

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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Peptide Scanning-assisted Identification of a Monoclonal Antibody-recognized Linear B-cell Epitope
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An antibody loop replacement design feasibility study and a loop-swapped dimer structure.

Louis A Clark1, P Ann Boriack-Sjodin, Eric Day

  • 1Biogen Idec Inc., Cambridge, MA 02142, USA. louie@alumni.northwestern.edu

Protein Engineering, Design & Selection : PEDS
|December 17, 2008
PubMed
Summary
This summary is machine-generated.

Antibody engineering can replace complementarity determining region (CDR) loops to expand design possibilities. While initial loop replacement designs showed structural feasibility, affinity improvements were not achieved, necessitating further optimization.

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Area of Science:

  • Antibody engineering
  • Protein structure analysis
  • Rational drug design

Background:

  • Complementarity determining region (CDR) loops are key to antibody-antigen interactions.
  • Current antibody design strategies, like mutation-based approaches, have limitations in expanding conformational space.
  • Crystal structure diversity offers opportunities for structure-based antibody design targeting CDR loops.

Purpose of the Study:

  • To investigate the feasibility of replacing single CDR antibody loops as a rational antibody design strategy.
  • To explore if CDR loop replacement can expand conformational space beyond simple mutation strategies.
  • To analyze the structural and functional consequences of CDR loop replacement in an anti-VLA1 antibody.

Main Methods:

  • Computational design and structural analysis of CDR loop replacements.
  • X-ray crystallography to determine the structure of designed antibody variants.
  • Circular dichroism and tryptophan fluorescence spectroscopy to assess protein stability and unfolding.
  • Affinity measurements to evaluate the functional impact of designed modifications.

Main Results:

  • CDR loop replacement by design was confirmed as feasible, with designed loops adopting desired conformations.
  • Initial L1 loop replacement in the anti-VLA1 antibody did not improve binding affinity.
  • Structural analysis revealed unintended domain swapping in one design, linked to structural instability and affinity loss.
  • A second round of design successfully eliminated domain swapping through targeted mutation.

Conclusions:

  • Replacing single CDR loops is a viable strategy for antibody engineering, offering conformational control.
  • Structural instability and unintended oligomerization can arise from CDR loop modifications, impacting antibody function.
  • Iterative design and structural analysis are crucial for overcoming challenges and achieving desired antibody properties.