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CDR-H3 loop ensemble in solution - conformational selection upon antibody binding.

Monica L Fernández-Quintero¹, Johannes Kraml¹, Guy Georges²

¹a Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck , Innsbruck , Austria.

|June 1, 2019

Summary

This summary is machine-generated.

Antibody complementarity-determining region (CDR)-H3 loops are flexible and exist as a conformational ensemble in solution. This study shows antibodies utilize pre-existing conformations for antigen binding, a phenomenon termed conformation selection.

Keywords:

CDR-H3 loop Markov-state models conformational ensemble conformational selection crystal structure dominant solution structure molecular dynamics

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Published on: September 15, 2010

Area of Science:

Immunology
Structural Biology
Computational Biology

Background:

Antibody complementarity-determining region (CDR)-H3 loops are crucial for antigen recognition.
The conformational flexibility of CDR-H3 loops and its role in antigen binding are not fully understood.
Previous studies often analyze antibody structures without considering dynamic conformational states.

Purpose of the Study:

To investigate the conformational landscape of CDR-H3 loops in solution.
To determine if antibodies utilize pre-existing conformations for antigen binding.
To assess the implications of CDR-H3 loop flexibility for structural studies of antibody-antigen interactions.

Main Methods:

Molecular dynamics simulations were employed to generate diverse conformational ensembles of CDR-H3 loops.
Analysis focused on protein-binding, peptide-binding, and hapten-binding antibodies.
Comparison of solution conformations with experimentally determined crystal structures.

Main Results:

CDR-H3 loops exhibit inherent flexibility and exist as a diverse conformational ensemble in solution.
The binding-competent conformation of the CDR-H3 loop was observed within the pre-existing ensemble, even without antigen present.
Antibody crystal structures without antigen often represent conformations selected for binding.

Conclusions:

Antibody CDR-H3 loops should be characterized as conformational ensembles rather than static structures.
The conformation selection mechanism explains how antibodies bind antigens using pre-existing states.
Caution is advised when interpreting antibody crystal structures, considering the potential for pre-existing conformations.