Mechanistic Insights on Human Phosphoglucomutase Revealed by Transition Path Sampling and Molecular Dynamics Calculations

Abstract

Human α-phosphoglucomutase 1 (α-PGM) catalyzes the isomerization of glucose-1-phosphate into glucose-6-phosphate (G6P) through two sequential phosphoryl transfer steps with a glucose-1,6-bisphosphate (G16P) intermediate. Given that the release of G6P in the gluconeogenesis raises the glucose output levels, α-PGM represents a tempting pharmacological target for type 2 diabetes. Here, we provide the first theoretical study of the catalytic mechanism of human α-PGM. We performed transition-path sampling simulations to unveil the atomic details of the two catalytic chemical steps, which could be key for developing transition state (TS) analogue molecules with inhibitory properties. Our calculations revealed that both steps proceed through a concerted S 2-like mechanism, with a loose metaphosphate-like TS. Even though experimental data suggests that the two steps are identical, we observed noticeable differences: 1) the transition state ensemble has a well-defined TS region and a late TS for the second step, and 2) larger coordinated protein motions are required to reach the TS of the second step. We have identified key residues (Arg23, Ser117, His118, Lys389), and the Mg ion that contribute in different ways to the reaction coordinate. Accelerated molecular dynamics simulations suggest that the G16P intermediate may reorient without leaving the enzymatic binding pocket, through significant conformational rearrangements of the G16P and of specific loop regions of the human α-PGM.

A Hotspot for Disease-Associated Variants of Human PGM1 Is Associated with Impaired Ligand Binding and Loop Dynamics

“…An analysis of the C α root mean square fluctuations (RMSF), relative to the energy-minimized starting structures, shows that the D4 loop (residues 505–511) is the most highly mobile region of the protein, even in the R503Q variant (Figures 4 and S4C–D). (A previous study of PGM1 mechanism by MD showed a similar result for WT enzyme (Bras et al, 2018)). We further examined the range of conformers of the D4 loop sampled during the MD simulation, and find that the conformers observed in the crystal structures of the missense variants and PGM1-G6P complex are encompassed within this range (Figure 4B).…”

Structural and dynamical description of the enzymatic reaction of a phosphohexomutase

“…Both binding orientations must occur during the catalytic cycle depending on whether the first or second phosphoryl transfer needs to or has already taken place, although only the first has been observed in crystal structures in the superfamily 16 . Other catalytically relevant states involving E deP :I, which are not characterizable by crystallography, include the two phosphoryl transfer steps, shown for a related enzyme to proceed through a concerted S N –2-like mechanism, with a loose, metaphosphate-like transition state 17 . Another is the dynamically reorienting G16P present in between phosphoryl transfer steps [Fig.…”

Anthocyanins as Antidiabetic Agents—In Vitro and In Silico Approaches of Preventive and Therapeutic Effects

“…GP catalyzes the rate-limiting step of glycogen breakdown, releasing glucose-1-phosphate. After this, phosphoglucomutase shifts the position of the phosphate in the sugar, making it suitable to fulfill the energetic requirements of the organism [ 155 ]. GP is an allosteric enzyme that changes between active (GPa) and tense (GPb) conformation states.…”