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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.
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Structural and biochemical differences between non-catalytic and catalytic antibodies.

Taizo Uda1,2, Ryuichi Kato3, Yasuteru Shigeta4

  • 1Research Center for GLOBAL/LOCAL Infectious Diseases, Oita University, Oita-shi, Oita, Japan.

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|May 13, 2025
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Summary

Deleting Pro95 in antibody light chains creates catalytic antibodies. This engineered variant effectively cleaves amyloid-beta peptides, representing a significant advancement in antibody engineering.

Keywords:
Catalytic antibodyX-ray crystallographyamyloid-betamolecular dynamicspro95 residue deletiontau-protein

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Immunology

Background:

  • Conventional antibodies can be engineered into catalytic counterparts.
  • The deletion of Pro95 in the CDR-3 region of antibody light chains has been previously reported to confer catalytic activity.

Purpose of the Study:

  • To elucidate the structural basis for enzymatic function acquisition in catalytic antibodies engineered by Pro95 deletion.
  • To investigate the catalytic activity of a naturally occurring human antibody light chain (T99wt) and its engineered variant (T99-Pro95(-)) against synthetic peptides and amyloid-beta.

Main Methods:

  • X-ray crystallography was employed to determine the structural changes upon Pro95 deletion.
  • Molecular dynamics (MD) simulations were used to analyze the dynamic behavior and active site formation.

Main Results:

  • Pro95 deletion in T99wt significantly reduced the distance between key catalytic residues Asp1 and His93, facilitating active site formation.
  • The engineered T99-Pro95(-) variant exhibited enhanced catalytic activity, effectively cleaving both Arg-pNA and amyloid-beta peptides.
  • MD simulations revealed transient proximity of catalytic residues (Asp1, His93, Ser27a) upon Pro95 removal, enabling a functional catalytic triad.

Conclusions:

  • Pro95 deletion is a key modification for converting conventional antibodies into efficient catalytic antibodies.
  • This finding represents a significant technological advancement for generating catalytic antibodies from known sequences.