Abstract
We use a novel normal mode analysis of an elastic network model drawn from configurations generated during microsecond all-atom molecular dynamics simulations to analyze the mechanism of auto-inhibition of AMP-activated protein kinase (AMPK). A recent X-ray and mutagenesis experiment (Chen, et al Nature 2009, 459, 1146) of the AMPK homolog S. Pombe sucrose non-fermenting 1 (SNF1) has proposed a new conformational switch model involving the movement of the kinase domain (KD) between an inactive unphosphorylated open state and an active or semi-active phosphorylated closed state, mediated by the autoinhibitory domain (AID), and a similar mutagenesis study showed that rat AMPK has the same auto-inhibition mechanism. However, there is no direct dynamical evidence to support this model and it is not clear whether other functionally important local structural components are equally inhibited. By using the same SNF1 KD-AID fragment as that used in experiment, we show that AID inhibits the catalytic function by restraining the KD into an unproductive open conformation, thereby limiting local structural rearrangements, while mutations that disrupt the interactions between the KD and AID allow for both the local structural rearrangement and global interlobe conformational transition. Our calculations further show that the AID also greatly impacts the structuring and mobility of the activation loop.
Highlights
AMP-activated protein kinase (AMPK) is a highly conserved enzyme in eukaryotic cells that regulates cellular and whole-body energy homeostasis by phosphorylating a wide variety of substrates [1,2,3,4]
We report on a novel method that uses normal mode analysis of an elastic network model drawn from microsecond all-atom molecular dynamics simulations to analyze the activation mechanism of the AMPK homolog sucrose nonfermenting 1 (SNF1), which is believed to have the same mechanism as mammalian AMPK
We provide a dynamical analysis to show that autoinhibitory domain (AID) inhibits catalytic function by restraining kinase domain (KD) into an unproductive open conformation and limiting functional local structural rearrangement, and that mutations that disrupt the interactions between the KD and AID free the KD to undergo both the global interlobe conformational transition and functional local structural rearrangement
Summary
AMP-activated protein kinase (AMPK) is a highly conserved enzyme in eukaryotic cells that regulates cellular and whole-body energy homeostasis by phosphorylating a wide variety of substrates [1,2,3,4]. The binding of AMP to the Bateman domains can allosterically activate the catalytic function in the a-subunit, and instigates the phosphorylation of downstream proteins to mediate other biological pathways. This signaling progression requires the phosphorylation of a threonine residue in the activation loop of KD by an upstream kinase. Each of the subunits has multiple isoforms (a1, a2, b1, b2, c1, c2 and c3) [6], so there may be as many as 12 combinations, each with a different function
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