Understanding the Mannose Transfer Mechanism of Mycobacterial Phosphatidyl-myo-inositol Mannosyltransferase A from Molecular Dynamics Simulations

Abstract

Glycolipids like phosphatidylinositol hexamannosides (PIM 6 ) and lipoglycans, such as lipomannan (LM) and lipoarabinomannan (LAM), play crucial roles in virulence, survival, and antibiotic resistance of various mycobacterial species. Phosphatidyl-myo-inositol mannosyltransferase A (PimA) catalyzes the transfer of the mannose moiety (M) from GDP-mannose (GDPM) to phosphatidyl-myo-inositol (PI) to synthesize GDP and phosphatidyl-myo-inositol monomannoside (PIM). This PIM is mannosylated, acylated, and further modified to give rise to the higher PIMs, LM, and LAM. It is yet to be known how PI, PIM, PI-GDPM, and PIM-GDP interact with PimA. Here, we report the docked structures of PI and PIM to understand how the substrates and the products interact with PimA. Using molecular dynamics (MD) simulations for 300 ns, we have investigated how various ligand-bound conformations change the dynamics of PimA. Our studies demonstrated the “open to closed” motions of PimA. We observed that PimA is least dynamic when bound to both GDPM and PI. MD simulations indicated that the loop residues 59–70 and the α-helical residues 73–86 of PimA play important roles while interacting with both PI and PIM. MD analyses also suggested that the residues Y9, P59, R68, L69, N97, R196, R201, K202, and R228 of PimA play significant roles in the mannose transfer reaction. Overall, docking studies and MD simulations provide crucial insights to design future therapeutic drugs against mycobacterial PimA.

HDX-MS Reveals Substrate-Dependent, Localized EX1 Conformational Dynamics in the Retaining GT-B Glycosyltransferase, MshA

“…In CgMshA, this residue is a proline that does not interfere with the flexibility of F318 in the closed structure. Despite the lack of evidence from crystal structures, a recent molecular dynamics simulation of PimA in various liganded complexes supports several aspects of the proposed model . The donor substrate complex of PimA was shown to be slightly more destabilized compared with the nucleotide diphosphate product complex.…”

“…Despite the lack of evidence from crystal structures, a recent molecular dynamics simulation of PimA in various liganded complexes supports several aspects of the proposed model. 16 The donor substrate complex of PimA was shown to be slightly more destabilized compared with the nucleotide diphosphate product complex. The destabilization was proposed to arise from interactions with the donor hexose and the polar groups on the flexible β4/α5 loop (E316, S317-equivalents), rather than the phenylalanine residue.…”

“…GTs have been well-characterized via both molecular dynamics simulations and static crystal structures. ,,– However, experiments designed to report on in-solution dynamics, such as 19 F NMR spectroscopy for PimA, single-molecule Förster resonance energy transfer for Fut1, and intrinsic tryptophan fluorescence for HepI, , are less common. This gap in characterization may explain the difficulties faced in identifying potent inhibitors for this class of enzymes.…”

Designing a conjugate vaccine targeting Klebsiella pneumoniae ST258 and ST11

“…As a commonly used statistical technique, Principal component analysis (PCA) was used to simplify the complexity of kinetic data and extract the collective and associated motions of biomolecular atoms [ 54 ]. The position of the Cα atom in the simulation system was obtained by using the Gromacs 2021.3 software package.…”