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The dynamical mechanism of auto-inhibition of AMP-activated protein kinase.

Peng C, Head-Gordon T - PLoS Comput. Biol. (2011)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: MOE-Microsoft Key Laboratory for Intelligent Computing and Intelligent Systems, Department of Computer Science and Engineering, Shanghai Jiao Tong University, Shanghai, China.

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.

Show MeSH
Instantaneous normal mode similarities calculated from many 10 ns molecular dynamics simulation showing signatures of (a) the open state, (b) transition from the open to closed state, (c) the closed state, and (d) transition from the closed to open state.
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pcbi-1002082-g004: Instantaneous normal mode similarities calculated from many 10 ns molecular dynamics simulation showing signatures of (a) the open state, (b) transition from the open to closed state, (c) the closed state, and (d) transition from the closed to open state.

Mentions: Therefore, to further investigate the interlobe conformational transition, we launched 90 independent 10 ns simulations starting from the open state for wild-type KD-AID, mutant 1, mutant 2 and mutant 3, and 70 independent 10 ns simulations starting from the open state for the isolated KD fragment. For the wild-type KD-AID fragment and mutant 1, all 90 of the 10 ns trajectories stay close to the open state with no fluctuations consistent with the closed state (Figure 4a). Mutants 2 and 3 and the KD fragment all show a fraction of trajectories that transition from the open to the closed state (Figure 4b). We then performed another 70 independent 10 ns simulation trajectories, this time from the newly obtained closed state for each of mutant 2, mutant 3 and the KD fragment. While most trajectories still remain in closed state (Figure 4c), a fair fraction of them revert back to the open state (Figure 4d). The detailed transition number in each case is reported in Table 1.


The dynamical mechanism of auto-inhibition of AMP-activated protein kinase.

Peng C, Head-Gordon T - PLoS Comput. Biol. (2011)

Instantaneous normal mode similarities calculated from many 10 ns molecular dynamics simulation showing signatures of (a) the open state, (b) transition from the open to closed state, (c) the closed state, and (d) transition from the closed to open state.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3140967&req=5

pcbi-1002082-g004: Instantaneous normal mode similarities calculated from many 10 ns molecular dynamics simulation showing signatures of (a) the open state, (b) transition from the open to closed state, (c) the closed state, and (d) transition from the closed to open state.
Mentions: Therefore, to further investigate the interlobe conformational transition, we launched 90 independent 10 ns simulations starting from the open state for wild-type KD-AID, mutant 1, mutant 2 and mutant 3, and 70 independent 10 ns simulations starting from the open state for the isolated KD fragment. For the wild-type KD-AID fragment and mutant 1, all 90 of the 10 ns trajectories stay close to the open state with no fluctuations consistent with the closed state (Figure 4a). Mutants 2 and 3 and the KD fragment all show a fraction of trajectories that transition from the open to the closed state (Figure 4b). We then performed another 70 independent 10 ns simulation trajectories, this time from the newly obtained closed state for each of mutant 2, mutant 3 and the KD fragment. While most trajectories still remain in closed state (Figure 4c), a fair fraction of them revert back to the open state (Figure 4d). The detailed transition number in each case is reported in Table 1.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: MOE-Microsoft Key Laboratory for Intelligent Computing and Intelligent Systems, Department of Computer Science and Engineering, Shanghai Jiao Tong University, Shanghai, China.

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.

Show MeSH