Seminar: Prof. Gerhard Klebe

Perturbance of Enzyme Function by Blocking a Dimer Interface: Analysis of Homodimer Stability and Ligand Design Strategies

Date:
5 March 2014 00:00 hrs.
Location:
Figdor Lecture Theatre, 8th floor RIMLS Building, Geert Grooteplein 26-28, route 289
Title:
Perturbance of Enzyme Function by Blocking a Dimer Interface: Analysis of Homodimer Stability and Ligand Design Strategies
Speaker(s):

Prof. Gerhard Klebe, Institute of Pharmaceutical Chemistry, University of Marburg, Germany

Host(s):

Dr. Tina Ritschel, CDD Group, CMBI, Radboudumc

05-03-2014 00:00:00Europe/AmsterdamPerturbance of Enzyme Function by Blocking a Dimer Interface: Analysis of Homodimer Stability and Ligand Design Strategies  Figdor Lecture Theatre, 8th floor RIMLS Building, Geert Grooteplein 26-28, route 289Rimlsrimls@radboudumc.nl

Remarks / more information:

KlebeDrug research increasingly focuses on the interference with protein-protein interface formation as attractive opportunity for therapeutic intervention.  The tRNA-modifying enzyme Tgt, a putative drug target to fight Shigellosis, is only functionally active as a homodimer. To better understand the driving forces responsible for assembly and stability of the formed homodimer interface we embarked onto a computational and mutational analysis of the interface-forming residues. We also launched spiking ligands into the interface region to perturb contact formation. We controlled by non-degrading mass spectrometry the actual ratio of monomer-dimer equilibrium in solution and used crystal structure analysis to elucidate the geometrical changes resulting from the induced perturbance. A patch of four aromatic amino acids, embedded into a ring of hydrophobic residues and further stabilized by a network of H-bonds is essential for the dimer contact. Apart from the aromatic hot spot, the interface shows an extended loop-helix motif which exhibits remarkable flexibility. In the destabilized mutant variants and the complexes with the spiking ligands, the loop-helix motif adopts deviating conformations in the interface region. This motivated us to follow a strategy to raise small molecule binders against this motif to mould the loop geometry in a conformation incompatible with the interface formation. 

Key Publications:

  • An integrative approach combining noncovalent mass spectrometry, enzyme kinetics and Xray crystallography to decipher Tgt protein-protein and protein-RNA interaction J. Mol. Biol., 393 (2009) 833-847
  • Launching Spiking Ligands into a Protein-Protein Interface: A Promising Strategy to Destabilize and Break Interface Formation in a tRNA Modifying Enzyme ACS Chem Biol, 8 (6) (2013) 1163-1178

 



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