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Local and Global Rigidification Upon Antibody Affinity Maturation.

Monica L Fernández-Quintero1, Johannes R Loeffler1, Lisa M Bacher1

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Summary

The immune system refines antibodies through affinity maturation, a process involving somatic hypermutations. This study reveals that antibody maturation leads to reduced flexibility and plasticity, enhancing specificity.

Keywords:
CDR-H3 loopMarkov-state modelsaffinity maturationantibodieskineticslocalizing plasticityrigidification

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Area of Science:

  • Immunology
  • Structural Biology
  • Computational Biology

Background:

  • Affinity maturation enhances antibody specificity and activity via somatic hypermutations.
  • Understanding this process is crucial for immunity and biotherapeutic development.

Purpose of the Study:

  • To investigate changes in antibody flexibility and plasticity during affinity maturation.
  • To analyze differences in CDR-H3 loop dynamics and global plasticity.
  • To develop methods for defining and localizing surface plasticity post-maturation.

Main Methods:

  • Analysis of 10 antibody fragment pairs at different affinity maturation stages.
  • Utilized metadynamics and molecular dynamics (MD) simulations.
  • Employed Markov-state models to reconstruct CDR-H3 loop dynamics.

Main Results:

  • Observed significant rigidification in flexibility and plasticity across antibody pairs.
  • Noted a substantial decrease in conformational diversity upon maturation.
  • Successfully visualized and characterized these dynamic changes.

Conclusions:

  • Antibody affinity maturation leads to a more rigid structure with reduced conformational diversity.
  • The study provides novel methods for analyzing antibody dynamics and plasticity.
  • Findings contribute to a deeper understanding of immune response and biotherapeutic design.