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Related Concept Videos

Cooperative Allosteric Transitions01:58

Cooperative Allosteric Transitions

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Cooperative allosteric transitions can occur in multimeric proteins, where each subunit of the protein has its own ligand-binding site. When a ligand binds to any of these subunits, it triggers a conformational change that affects the binding sites in the other subunits; this can change the affinity of the other sites for their respective ligands. The ability of the protein to change the shape of its binding site is attributed to the presence of a mix of flexible and stable segments in the...
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Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
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A stepwise docking molecular dynamics approach for simulating antibody recognition with substantial conformational

Yang Huang1,2, Zizhen Li1,2, Qiyang Hong1,2

  • 1State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, School of Public Health, Xiamen University, Xiamen 361102, China.

Computational and Structural Biotechnology Journal
|February 24, 2022
PubMed
Summary

Researchers developed a novel stepwise molecular dynamics (MD) method to accurately simulate complex antibody-antigen interactions. This approach successfully captured the conformational changes of the 13D4 antibody

Keywords:
Antibody recognitionConformational rearrangementH5 broad-neutralizing antibodyMolecular dynamicsStepwise docking

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Area of Science:

  • Structural biology
  • Computational biophysics
  • Immunology

Background:

  • Inter-biomolecular recognition involves conformational changes crucial for understanding allosteric mechanisms.
  • The H5 influenza virus antibody 13D4 exhibits significant heavy chain complementarity-determining region 3 (HCDR3) rearrangement upon binding hemagglutinin (HA).
  • Standard molecular dynamics (MD) and steered MD methods failed to accurately simulate this HCDR3 conformational change.

Purpose of the Study:

  • To develop and validate a new computational method for simulating challenging antibody-antigen conformational rearrangements.
  • To accurately model the HCDR3 loop's adaptation to the hemagglutinin receptor-binding site (RBS).
  • To gain insights into the allosteric mechanisms governing antibody-mediated viral recognition.

Main Methods:

  • Utilized a novel stepwise docking molecular dynamics (MD) approach.
  • Simulated the gradual docking of the antibody fragment (Fab) to the hemagglutinin (HA) antigen.
  • Compared simulation results with existing crystal structures of free and bound 13D4 Fab.

Main Results:

  • The stepwise docking MD method successfully recapitulated the bound conformation of the HCDR3 loop.
  • Achieved a root-mean-square deviation (RMSD) of 0.926 Å compared to the co-crystal structure.
  • Demonstrated the method's ability to approximate the experimentally determined bound shape.

Conclusions:

  • The developed stepwise docking MD strategy provides a flexible and accurate approach for simulating complex molecular recognition events.
  • This method enhances the understanding of allosteric mechanisms involved in antibody-antigen interactions.
  • Offers a valuable tool for studying challenging conformational changes in biomolecular recognition.