posted on 2022-12-19, 05:46authored byJacques Kumutima, Xin-Qiu Yao, Donald Hamelberg
Mitochondria are the powerhouse of a cell, whose disruption
due
to mitochondrial pore opening can cause cell death, leading to necrosis
and many other diseases. The peptidyl-prolyl cis–trans isomerase cyclophilin D (CypD) is a key player in the regulation
of the mitochondrial pore. The activity of CypD can be modulated by
the post-translational modification (PTM). However, the detailed mechanism
of this functional modulation is not well understood. Here, we investigate
the catalytic mechanism of unmodified and modified CypD by calculating
the reaction free energy profiles and characterizing the function-related
conformational dynamics using molecular dynamics simulations and associated
analyses. Our results show that unmodified and modified CypD considerably
lower the isomerization free energy barrier compared to a free peptide
substrate, supporting the catalytic activity of CypD in the simulation
systems. The unmodified CypD reduces the free energy difference between
the cis and trans states of the
peptide substrate, suggesting a stronger binding affinity of CypD
toward cis, consistent with experiments. In contrast,
phosphorylated CypD further stabilizes trans, leading
to a lower catalytic rate in the trans-to-cis direction. The differential catalytic activities of
the unmodified and phosphorylated CypD are due to a significant shift
of the conformational ensemble upon phosphorylation under different
functional states. Interestingly, the local flexibility is both reduced
and enhanced at distinct regions by phosphorylation, which is explained
by a “seesaw” model of flexibility modulation. The allosteric
pathway between the phosphorylation site and a distal site displaying
substantial conformational changes upon phosphorylation is also identified,
which is influenced by the presence of the substrate or the substrate
conformation. Similar conclusions are obtained for the acetylation
of CypD using the same peptide substrate and the influence of substrate
sequence is also examined. Our work may serve as the basis for the
understanding of other PTMs and PTM-initiated allosteric regulations
in CypD.