Mutated form (G52E) of inactive diphtheria toxin CRM197: molecular simulations clearly display effect of the mutation to NAD binding

J Biomol Struct Dyn. 2016 Nov;34(11):2462-8. doi: 10.1080/07391102.2015.1119060. Epub 2016 Feb 2.


Mutated form (G52E) of diphtheria toxin (DT) CRM197 is an inactive and nontoxic enzyme. Here, we provided a molecular insight using comparative molecular dynamics (MD) simulations to clarify the influence of a single point mutation on overall protein and active-site loop. Post-processing MD analysis (i.e. stability, principal component analysis, hydrogen-bond occupancy, etc.) is carried out on both wild and mutated targets to investigate and to better understand the mechanistic differences of structural and dynamical properties on an atomic scale especially at nicotinamide adenine dinucleotide (NAD) binding site when a single mutation (G52E) happens at the DT. In addition, a docking simulation is performed for wild and mutated forms. The docking scoring analysis and docking poses results revealed that mutant form is not able to properly accommodate the NAD molecule.

Keywords: CRM197; MD simulations; binding interactions analysis; diphtheria toxin.

MeSH terms

  • Bacterial Proteins / chemistry*
  • Bacterial Proteins / genetics
  • Bacterial Proteins / metabolism
  • Binding Sites
  • Catalytic Domain
  • Hydrogen Bonding
  • Ligands
  • Molecular Conformation
  • Molecular Docking Simulation
  • Molecular Dynamics Simulation*
  • Mutation
  • NAD / chemistry
  • NAD / metabolism
  • Protein Binding
  • Structure-Activity Relationship


  • Bacterial Proteins
  • Ligands
  • CRM197 (non-toxic variant of diphtheria toxin)
  • NAD