Insight into the Nucleotide Based Modulation of the Grp94 Molecular Chaperone Using Multiscale Dynamics

Area of Science:

• Molecular Biology
• Biochemistry
• Structural Biology

Background:

• Grp94 is an endoplasmic reticulum (ER)-localized molecular chaperone essential for folding and activating membrane and secretory proteins.
• Grp94's client activation mechanism involves nucleotide binding and conformational changes.
• Understanding the link between microscopic nucleotide hydrolysis events and macroscopic Grp94 conformational changes is critical.

Purpose of the Study:

• To elucidate how microscopic changes from nucleotide hydrolysis drive large-scale conformational alterations in Grp94.
• To investigate the role of different nucleotide-bound states on Grp94 dynamics and allosteric communication.

Main Methods:

• All-atom molecular dynamics (MD) simulations of the Grp94 dimer in four distinct nucleotide-bound states.
• Normal-mode analysis (NMA) using an elastic network model to study large-scale conformational dynamics.
• Stochastic perturbation (SPM) analysis to identify key residues involved in conformational signaling.

Main Results:

• Grp94 exhibited maximum rigidity in the ATP-bound state.
• ATP hydrolysis or nucleotide removal increased mobility in the N-terminal domain and ATP lid, reducing interdomain communication.
• An asymmetric conformation with one hydrolyzed nucleotide revealed a compact state, consistent with experimental data.
• A flexible linker was identified to potentially regulate Grp94 activity through electrostatic interactions with the M-domain helix.
• SPM analysis pinpointed functionally relevant residues in ATP coordination, catalysis, client binding, and BiP interaction sites.

Conclusions:

• ATP hydrolysis significantly alters the allosteric network within Grp94.
• These alterations facilitate essential large-scale conformational changes required for chaperone function.
• Findings provide insights into the regulatory mechanisms of Grp94 and its interactions.