QM/MM Well-Tempered Metadynamics Study of the Mechanism of XBP1 mRNA Cleavage by Inositol Requiring Enzyme 1α RNase

Abstract

A range of in silico methodologies were herein employed to study the unconventional XBP1 mRNA cleavage mechanism performed by the unfolded protein response (UPR) mediator Inositol Requiring Enzyme 1α (IRE1). Using Protein–RNA molecular docking along with a series of extensive restrained/unrestrained atomistic molecular dynamics (MD) simulations, the dynamical behavior of the system was evaluated and a reliable model of the IRE1/XBP1 mRNA complex was constructed. From a series of well-converged quantum mechanics molecular mechanics well-tempered metadynamics (QM/MM WT-MetaD) simulations using the Grimme dispersion interaction corrected semiempirical parametrization method 6 level of theory (PM6-D3) and the AMBER14SB-OL3 force field, the free energy profile of the cleavage mechanism was determined, along with intermediates and transition state structures. The results show two distinct reaction paths based on general acid–general base type mechanisms, with different activation energies that perfectly match observations from experimental mutagenesis data. The study brings unique atomistic insights into the cleavage mechanism of XBP1 mRNA by IRE1 and clarifies the roles of the catalytic residues H910 and Y892. Increased understanding of the details in UPR signaling can assist in the development of new therapeutic agents for its modulation.

Multiscale In Silico Study of the Mechanism of Activation of the RtcB Ligase by the PTP1B Phosphatase

“…Since DFT-based QM/MM-MetaD simulation is very demanding, the limited number of atoms in the QM region (64 atoms here) could be considered a potential limitation in our methodology. One might opt to employ the semiempirical-based QM/MM-MetaD simulation methodology as an effective means to accommodate a larger number of QM atoms and expedite computational throughput . However, the utilization of either DFT-based or semiempirical-based computations represents a substantial trade-off, necessitating a rigorous and deliberate assessment between precision and computational efficiency.…”

“…One might opt to employ the semiempirical-based QM/MM-MetaD simulation methodology as an effective means to accommodate a larger number of QM atoms and expedite computational throughput. 20 However, the utilization of either DFT-based or semiempirical-based computations represents a substantial trade-off, necessitating a rigorous and deliberate assessment between precision and computational efficiency. The reasonable assumption of a “single initial reactant state”, where the most representative form of the reactant comes from the atomistic models of protein–protein docking, clustering, and relaxation, might affect the minimum energy pathway.…”

“…However, neither the 3D structure and binding mode of the RtcB-PTP1B complex nor the underlying atomistic mechanism of the first part of the dephosphorylation reaction (phosphoryl transfer from the substrate to the enzyme) of RtcB has been elucidated so far. Therefore, in the current study, we addressed these missing pieces of the UPRosome machinery using advanced in silico methods such as our recently developed protein–protein docking meta-approach, 19 quantum mechanics molecular mechanics well-tempered metadynamics (QM/MM WT-MetaD), 20 and classical molecular dynamics (MD) simulations.…”

Novel Insights into the Catalytic Mechanism of Collagenolysis by Zn(II)-Dependent Matrix Metalloproteinase-1

“…The development of enhanced sampling methods, such as QM/MM MetD, − allows the exploration of the free energy surface (FES) of (bio)chemical reactions with numerous minima, separated by barriers much higher than thermal energies. By implementing collective variables (CVs), this approach explores chemical changes at real temperatures, incorporating dynamical and entropic effects for the entire system. ,− Understanding the origin of enzyme catalytic power often involves comparing the enzyme-catalyzed reactions with their corresponding counterparts in a solution. This comparison dissects structural and energetic effects leading to TS stabilization and decreasing the activation energy of the catalyzed reaction in the enzyme, as well as the role of solvent molecules in catalysis. − The water solvent influences the structure, dynamics, and kinetics of the enzymes. − Quantifying the contributions of crucial enzyme residues and explicit water molecules to the kinetics of enzyme-catalyzed reactions is critical to understanding catalytic mechanisms and the origin of the enzyme catalytic effect properly. − An insertion of a water molecule into the active site can accelerate the reaction by influencing its dielectric properties .…”

Challenges in Protein QM/MM Simulations with Intra-Backbone Link Atoms

“…However, even more drastic effects may be expected over simulation time, as artifacts and quirks in trajectories arise. Recent development of QM/MM interfaces with fast and reasonably accurate semiempirical QM methods allow researchers to go beyond single-point calculations and study processes as they are, in dynamics. − These approaches are becoming more and more popular. − Coupling fast semiempirical QM potentials with machine learning corrections was shown to dramatically improve its accuracy making it comparable with more sophisticated density functional theory (DFT) methods . Thus, we speculate that a field will witness a rise in popularity of such approaches.…”