Segment swapping aided the evolution of enzyme function: The case of uroporphyrinogen III synthase

Proteins. 2017 Jan;85(1):46-53. doi: 10.1002/prot.25190. Epub 2016 Nov 4.

Abstract

In an earlier study, we showed that two-domain segment-swapped proteins can evolve by domain swapping and fusion, resulting in a protein with two linkers connecting its domains. We proposed that a potential evolutionary advantage of this topology may be the restriction of interdomain motions, which may facilitate domain closure by a hinge-like movement, crucial for the function of many enzymes. Here, we test this hypothesis computationally on uroporphyrinogen III synthase, a two-domain segment-swapped enzyme essential in porphyrin metabolism. To compare the interdomain flexibility between the wild-type, segment-swapped enzyme (having two interdomain linkers) and circular permutants of the same enzyme having only one interdomain linker, we performed geometric and molecular dynamics simulations for these species in their ligand-free and ligand-bound forms. We find that in the ligand-free form, interdomain motions in the wild-type enzyme are significantly more restricted than they would be with only one interdomain linker, while the flexibility difference is negligible in the ligand-bound form. We also estimated the entropy costs of ligand binding associated with the interdomain motions, and find that the change in domain connectivity due to segment swapping results in a reduction of this entropy cost, corresponding to ∼20% of the total ligand binding free energy. In addition, the restriction of interdomain motions may also help the functional domain-closure motion required for catalysis. This suggests that the evolution of the segment-swapped topology facilitated the evolution of enzyme function for this protein by influencing its dynamic properties. Proteins 2016; 85:46-53. © 2016 Wiley Periodicals, Inc.

Keywords: conformational entropy; free energy; ligand binding; protein dynamics; protein evolution.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacterial Proteins / chemistry*
  • Biocatalysis
  • Entropy
  • Evolution, Molecular
  • Ligands
  • Molecular Dynamics Simulation
  • Motion
  • Protein Binding
  • Protein Domains
  • Protein Structure, Secondary
  • Thermus thermophilus / chemistry*
  • Thermus thermophilus / enzymology
  • Uroporphyrinogen III Synthetase / chemistry*
  • Uroporphyrinogens / chemistry*

Substances

  • Bacterial Proteins
  • Ligands
  • Uroporphyrinogens
  • hydroxymethylbilane
  • Uroporphyrinogen III Synthetase