Perturbation of the Conformational Dynamics of an Active-Site Loop Alters Enzyme Activity

Structure. 2015 Dec 1;23(12):2256-2266. doi: 10.1016/j.str.2015.10.011. Epub 2015 Nov 19.


The role of internal dynamics in enzyme function is highly debated. Specifically, how small changes in structure far away from the reaction site alter protein dynamics and overall enzyme mechanisms is of wide interest in protein engineering. Using RNase A as a model, we demonstrate that elimination of a single methyl group located >10 Å away from the reaction site significantly alters conformational integrity and binding properties of the enzyme. This A109G mutation does not perturb structure or thermodynamic stability, both in the apo and ligand-bound states. However, significant enhancement in conformational dynamics was observed for the bound variant, as probed over nano- to millisecond timescales, resulting in major ligand repositioning. These results illustrate the large effects caused by small changes in structure on long-range conformational dynamics and ligand specificities within proteins, further supporting the importance of preserving wild-type dynamics in enzyme systems that rely on flexibility for function.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adenosine Monophosphate / metabolism
  • Amino Acid Sequence
  • Animals
  • Catalytic Domain*
  • Cattle
  • Molecular Dynamics Simulation*
  • Molecular Sequence Data
  • Mutation
  • Protein Binding
  • Ribonuclease, Pancreatic / chemistry*
  • Ribonuclease, Pancreatic / genetics
  • Ribonuclease, Pancreatic / metabolism
  • Uridine Monophosphate / metabolism


  • Adenosine Monophosphate
  • Uridine Monophosphate
  • Ribonuclease, Pancreatic