Key Dynamic Residues in the Catalytic Activity of Human Cyclophilins Identified with a Dynamical Evolution Analysis

Abstract

Cyclophilins belong to peptidyl‐prolyl isomerases (PPIases), a group of enzymes catalyzing the interconversion of the peptide bond preceding a proline between the cis and trans isomer. Of the 17 unique human cyclophilins, five closely related homologues (CypA‐E) were the focus of this project. These five isoforms function in a variety of environments, and participate in diverse subcellular processes, yet all have highly conserved sequences, very similar structures, and the same core catalytic function. As dynamics are known to couple protein function, looking into the conserved dynamics can provide insights into the catalysis of peptidyl‐prolyl isomerization by cyclophilins. Functional dynamics were compared using multiple statistical analyses, including Cartesian and dihedral principal component analysis (PCA), root mean square fluctuation (RMSF), and angular variance analysis. A set of key dynamical residues, defined by the most dynamically conserved positions, were identified in the gatekeeper 2 region. The highly conserved glycine (GLY79) in this region was predicted to underlie the local flexibility. To test it, additional simulations were performed for CypE and CypA, where GLY79 was mutated to alanine. Mutation of GLY79 to ALA79 leads to decreased flexibility of CypE and CypA during substrate binding (free → cis) but increased flexibility during catalysis (cis → ts). Dynamical changes occur in the mutated region, as well as in a distal loop downstream of the mutation site in sequence. Allosteric effects on catalysis by the mutation were also examined. Both mutated CypE and CypA show shifted binding free energies of substrate under distinct substrate peptide cis‐trans conformations. The results suggest a reversal in the direction of catalysis in the mutated CypE and enhanced catalytic activity in the mutated CypA.Support or Funding InformationNSF‐REU program award no. 1757933, NSF grant (MCB‐1517617)