Structure and Dynamics of Stacking Interactions in an Antibody Binding Site

Area of Science:

• Protein dynamics
• Molecular recognition
• Spectroscopy

Background:

• Antibodies (Abs) are crucial for understanding protein structure in molecular recognition.
• Evolving Abs for specific chromophores reveals their potential as models for protein dynamics in molecular recognition.
• Previous studies showed the immune system produces Abs with varying flexibility.

Purpose of the Study:

• Characterize the complexes formed between two specific antibodies (5D11 and 10A6) and their chromophoric ligand, 8-methoxypyrene-1,3,6-trisulfonic acid (MPTS).
• Investigate the photophysics and dynamics of these antibody-ligand complexes using spectroscopic methods.
• Elucidate the structural basis for the unique binding interactions and their contribution to molecular recognition dynamics.

Main Methods:

• Three-pulse photon echo peak shift spectroscopy to assess protein flexibility.
• Various spectroscopic methods to probe photophysics and dynamics of antibody-MPTS complexes.
• Structural studies to determine the binding mode and interactions.

Main Results:

• Two antibodies, 5D11 and 10A6, evolved from a common precursor, recognize MPTS.
• The antibody-MPTS complexes exhibit similar photophysics and dynamics, distinct from previously characterized anti-MPTS Abs.
• Structural analysis revealed a unique binding mode where MPTS is sandwiched between PheH98 (T-stacking) and TrpL91 (parallel stacking).
• T-stacking mediates picosecond relaxation, while parallel stacking mediates ultrafast femtosecond relaxation.

Conclusions:

• These anti-MPTS antibodies showcase the simultaneous use of T-stacking and parallel stacking in molecular recognition.
• They provide a model system for studying the contribution of protein dynamics to molecular recognition.
• The identified stacking interactions and their dynamic roles are relevant to other proteins and protein complexes.