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Revisiting antibody modeling assessment for CDR-H3 loop.

Hiroshi Nishigami1,2, Narutoshi Kamiya1,3,4, Haruki Nakamura1

  • 1Institute for Protein Research, Osaka University, 3-2, Yamadaoka, Suita, Osaka 565-0871, Japan.

Protein Engineering, Design & Selection : PEDS
|August 13, 2016
PubMed
Summary

Antibody CDR-H3 loops are highly variable and difficult to model. Enhanced sampling methods reveal that crystal structures of these loops may not be stable in solution, suggesting crystal packing effects are crucial.

Keywords:
CDR-H3 loopantibodycrystal packingfree energy landscapemulticanonical molecular dynamics simulation

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Area of Science:

  • Structural biology
  • Immunology
  • Computational chemistry

Background:

  • Antibody antigen-binding sites, specifically complementarity-determining regions (CDRs), exhibit significant sequence variability.
  • The heavy chain's third CDR loop (CDR-H3) is particularly diverse in sequence, length, and conformation, posing challenges for accurate structural modeling.
  • Previous antibody modeling assessments highlighted difficulties in predicting CDR-H3 structures.

Purpose of the Study:

  • To refine structural models of a long CDR-H3 loop (13 residues, A52 antibody) using advanced computational methods.
  • To investigate the stability of CDR-H3 loop conformations in solution compared to crystal structures.

Main Methods:

  • Utilized enhanced conformational sampling with an explicit water model for CDR-H3 loop rebuilding.
  • Generated free energy landscapes at 300 K to identify stable molecular conformations.
  • Compared computational models with existing X-ray crystal structures.

Main Results:

  • Developed stable models of the CDR-H3 loop that resemble X-ray crystal structures.
  • The free energy landscape analysis indicated that crystal-observed CDR-H3 loop structures are not inherently stable in solution.
  • Crystal packing effects appear to stabilize these CDR-H3 loop conformations.

Conclusions:

  • Advanced sampling techniques improve the accuracy of CDR-H3 loop modeling.
  • CDR-H3 loop structures observed in crystals may be artifacts of the crystallization environment.
  • Understanding solution stability is critical for accurate antibody structure prediction and function analysis.