Article

Journal of Computer-Aided Molecular Design

, Volume 19, Issue 3, pp 165-187

First online:

Multiple ligand-binding modes in bacterial R67 dihydrofolate reductase

  • Hernán AlonsoAffiliated withComputational Proteomics Group, John Curtin School of Medical Research, The Australian National University
  • , Malcolm B. GilliesAffiliated withComputational Proteomics Group, John Curtin School of Medical Research, The Australian National University
  • , Peter L. CumminsAffiliated withComputational Proteomics Group, John Curtin School of Medical Research, The Australian National University
  • , Andrey A. BliznyukAffiliated withANU Supercomputer Facility, The Australian National University
  • , Jill E. GreadyAffiliated withComputational Proteomics Group, John Curtin School of Medical Research, The Australian National University Email author 

Rent the article at a discount

Rent now

* Final gross prices may vary according to local VAT.

Get Access

Summary

R67 dihydrofolate reductase (DHFR), a bacterial plasmid-encoded enzyme associated with resistance to the drug trimethoprim, shows neither sequence nor structural homology with the chromosomal DHFR. It presents a highly symmetrical toroidal structure, where four identical monomers contribute to the unique central active-site pore. Two reactants (dihydrofolate, DHF), two cofactors (NADPH) or one of each (R67•DHF•NADPH) can be found simultaneously within the active site, the last one being the reactive ternary complex. As the positioning of the ligands has proven elusive to empirical determination, we addressed the problem from a theoretical perspective. Several potential structures of the ternary complex were generated using the docking programs AutoDock and FlexX. The variability among the final poses, many of which conformed to experimental data, prompted us to perform a comparative scoring analysis and molecular dynamics simulations to assess the stability of the complexes. Analysis of ligand–ligand and ligand–protein interactions along the 4 ns trajectories of eight different structures allowed us to identify important inter-ligand contacts and key protein residues. Our results, combined with published empirical data, clearly suggest that multipe binding modes of the ligands are possible within R67 DHFR. While the pterin ring of DHF and the nicotinamide ring of NADPH assume a stacked endo-conformation at the centre of the pore, probably assisted by V66, Q67 and I68, the tails of the molecules extend towards opposite ends of the cavity, adopting multiple configurations in a solvent rich-environment where hydrogen-bond interactions with K32 and Y69 may play important roles.

Keywords

AutoDock consensus scoring docking FlexX GROMACS interligand cooperativity ligand mobility molecular dynamics reactive complex