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Abstract
AMP-activated protein kinase is a family of heterotrimeric serine/threonine protein kinases that come in twelve different flavors. They serve an essential function in all eukaryotes of conserving cellular energy levels. AMPK complexes are regulated by changes in cellular AMP:ATP or ADP:ATP ratios and by a number of neutraceuticals and some of the widely-used diabetes medications such as metformin and thiazolinonediones. Moreover, biochemical activities of AMPK are tightly regulated by phosphorylation or dephosphorylation by upstream kinases and phosphatases respectively. Efforts are underway in many pharmaceutical companies to discover direct AMPK activators for the treatment of cardiovascular and metabolic diseases such as diabetes, non-alcoholic steatohepatitis (NASH) and diabetic nephropathy. Many advances have been made in the AMPK structural biology arena over the last few years that are beginning to provide detailed molecular insights into the overall topology of these fascinating enzymes and how binding of small molecules elicit subtle conformational changes leading to their activation and protection from dephosphorylation. In the brief review below on AMPK structure and function, we have focused on the recent crystallographic results especially on specific molecular interactions of direct synthetic AMPK activators which lead to biased activation of a sub-family of AMPK isoforms.
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Affiliation(s)
- Ravi G Kurumbail
- Pfizer Worldwide Research and Development, Pfizer Inc, Eastern Point Road, Groton, CT, 06340, USA.
| | - Matthew F Calabrese
- Pfizer Worldwide Research and Development, Pfizer Inc, Eastern Point Road, Groton, CT, 06340, USA
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Novikova DS, Garabadzhiu AV, Melino G, Barlev NA, Tribulovich VG. AMP-activated protein kinase: structure, function, and role in pathological processes. BIOCHEMISTRY (MOSCOW) 2015; 80:127-44. [PMID: 25756529 DOI: 10.1134/s0006297915020017] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Recently, AMP-activated protein kinase (AMPK) has emerged as a key regulator of energy balance at cellular and whole-body levels. Due to the involvement in multiple signaling pathways, AMPK efficiently controls ATP-consuming/ATP-generating processes to maintain energy homeostasis under stress conditions. Loss of the kinase activity or attenuation of its expression leads to a variety of metabolic disorders and increases cancer risk. In this review, we discuss recent findings on the structure of AMPK, its activation mechanisms, as well as the consequences of its targets in regulation of metabolism. Particular attention is given to low-molecular-weight compounds that activate or inhibit AMPK; the perspective of therapeutic use of such modulators in treatment of several common diseases is discussed.
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Affiliation(s)
- D S Novikova
- Saint Petersburg State Technological Institute (Technical University), St. Petersburg, 190013, Russia.
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Jiao R, Postnikoff S, Harkness TA, Arnason TG. The SNF1 Kinase Ubiquitin-associated Domain Restrains Its Activation, Activity, and the Yeast Life Span. J Biol Chem 2015; 290:15393-15404. [PMID: 25869125 DOI: 10.1074/jbc.m115.647032] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Indexed: 02/04/2023] Open
Abstract
The enzyme family of heterotrimeric AMP-dependent protein kinases is activated upon low energy states, conferring a switch toward energy-conserving metabolic pathways through immediate kinase actions on enzyme targets and delayed alterations in gene expression through its nuclear relocalization. This family is evolutionarily conserved, including the presence of a ubiquitin-associated (UBA) motif in most catalytic subunits. The potential for the UBA domain to promote protein associations or direct subcellular location, as seen in other UBA-containing proteins, led us to query whether the UBA domain within the yeast AMP-dependent protein kinase ortholog, SNF1 kinase, was important in these aspects of its regulation. Here, we demonstrate that conserved UBA motif mutations significantly alter SNF1 kinase activation and biological activity, including enhanced allosteric subunit associations and increased oxidative stress resistance and life span. Significantly, the enhanced UBA-dependent longevity and oxidative stress response are at least partially dependent on the Fkh1 and Fkh2 stress response transcription factors, which in turn are shown to influence Snf1 gene expression.
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Affiliation(s)
- Rubin Jiao
- Departments of Anatomy and Cell Biology and University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada
| | - Spike Postnikoff
- Departments of Anatomy and Cell Biology and University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada
| | - Troy A Harkness
- Departments of Anatomy and Cell Biology and University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada
| | - Terra G Arnason
- Departments of Anatomy and Cell Biology and University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada; Medicine, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada.
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Landgraf RR, Goswami D, Rajamohan F, Harris MS, Calabrese MF, Hoth LR, Magyar R, Pascal BD, Chalmers MJ, Busby SA, Kurumbail RG, Griffin PR. Activation of AMP-activated protein kinase revealed by hydrogen/deuterium exchange mass spectrometry. Structure 2013; 21:1942-53. [PMID: 24076403 DOI: 10.1016/j.str.2013.08.023] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Revised: 08/13/2013] [Accepted: 08/23/2013] [Indexed: 12/25/2022]
Abstract
AMP-activated protein kinase (AMPK) monitors cellular energy, regulates genes involved in ATP synthesis and consumption, and is allosterically activated by nucleotides and synthetic ligands. Analysis of the intact enzyme with hydrogen/deuterium exchange mass spectrometry reveals conformational perturbations of AMPK in response to binding of nucleotides, cyclodextrin, and a synthetic small molecule activator, A769662. Results from this analysis clearly show that binding of AMP leads to conformational changes primarily in the γ subunit of AMPK and subtle changes in the α and β subunits. In contrast, A769662 causes profound conformational changes in the glycogen binding module of the β subunit and in the kinase domain of the α subunit, suggesting that the molecular binding site of the latter resides between the α and β subunits. The distinct short- and long-range perturbations induced upon binding of AMP and A769662 suggest fundamentally different molecular mechanisms for activation of AMPK by these two ligands.
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Affiliation(s)
- Rachelle R Landgraf
- Department of Molecular Therapeutics, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458, USA
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Peng C, Head-Gordon T. The dynamical mechanism of auto-inhibition of AMP-activated protein kinase. PLoS Comput Biol 2011; 7:e1002082. [PMID: 21814500 PMCID: PMC3140967 DOI: 10.1371/journal.pcbi.1002082] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2010] [Accepted: 04/20/2011] [Indexed: 11/19/2022] Open
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 Nature2009, 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. AMP-activated protein kinase (AMPK) maintains the balance between ATP production and energy consumption in eukaryotic cells by responding to the rise of intracellular AMP. 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 SNF1, which is believed to have the same mechanism as mammalian AMPK. There has been important new X-ray crystallographic and mutagenesis information on the self-regulation of AMPK based on its auto-inhibitory domain, although that view is primarily static. We provide a dynamical analysis to show that AID inhibits catalytic function by restraining 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. This suggests new ways in which drugs might be used to regulate this important molecular machine.
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Affiliation(s)
- Cheng Peng
- MOE-Microsoft Key Laboratory for Intelligent Computing and Intelligent Systems, Department of Computer Science and Engineering, Shanghai Jiao Tong University, Shanghai, China
- Department of Bioengineering, University of California, Berkeley, Berkeley, California, United States of America
| | - Teresa Head-Gordon
- Department of Bioengineering, University of California, Berkeley, Berkeley, California, United States of America
- * E-mail:
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Momcilovic M, Carlson M. Alterations at dispersed sites cause phosphorylation and activation of SNF1 protein kinase during growth on high glucose. J Biol Chem 2011; 286:23544-51. [PMID: 21561858 DOI: 10.1074/jbc.m111.244111] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The SNF1/AMP-activated protein kinases are central energy regulators in eukaryotes. SNF1 of Saccharomyces cerevisiae is inhibited during growth on high levels of glucose and is activated in response to glucose depletion and other stresses. Activation entails phosphorylation of Thr(210) on the activation loop of the catalytic subunit Snf1 by Snf1-activating kinases. We have used mutational analysis to identify Snf1 residues that are important for regulation. Alteration of Tyr(106) in the αC helix or Leu(198) adjacent to the Asp-Phe-Gly motif on the activation loop relieved glucose inhibition of phosphorylation, resulting in phosphorylation of Thr(210) during growth on high levels of glucose. Substitution of Arg for Gly(53), at the N terminus of the kinase domain, increased activation on both high and low glucose. Alteration of the ubiquitin-associated domain revealed a modest autoinhibitory effect. Previous studies identified alterations of the Gal83 (β) and Snf4 (γ) subunits that relieve glucose inhibition, and we have here identified a distinct set of Gal83 residues that are required. Together, these results indicate that alterations at dispersed sites within each subunit of SNF1 cause phosphorylation of the kinase during growth on high levels of glucose. These findings suggest that the conformation of the SNF1 complex is crucial to maintenance of the inactive state during growth on high glucose and that the default state for SNF1 is one in which Thr(210) is phosphorylated and the kinase is active.
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Affiliation(s)
- Milica Momcilovic
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA
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Handa N, Takagi T, Saijo S, Kishishita S, Takaya D, Toyama M, Terada T, Shirouzu M, Suzuki A, Lee S, Yamauchi T, Okada-Iwabu M, Iwabu M, Kadowaki T, Minokoshi Y, Yokoyama S. Structural basis for compound C inhibition of the human AMP-activated protein kinase α2 subunit kinase domain. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2011; 67:480-7. [PMID: 21543851 DOI: 10.1107/s0907444911010201] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2010] [Accepted: 03/17/2011] [Indexed: 11/11/2022]
Abstract
AMP-activated protein kinase (AMPK) is a serine/threonine kinase that functions as a sensor to maintain energy balance at both the cellular and the whole-body levels and is therefore a potential target for drug design against metabolic syndrome, obesity and type 2 diabetes. Here, the crystal structure of the phosphorylated-state mimic T172D mutant kinase domain from the human AMPK α2 subunit is reported in the apo form and in complex with a selective inhibitor, compound C. The AMPK α2 kinase domain exhibits a typical bilobal kinase fold and exists as a monomer in the crystal. Like the wild-type apo form, the T172D mutant apo form adopts the autoinhibited structure of the `DFG-out' conformation, with the Phe residue of the DFG motif anchored within the putative ATP-binding pocket. Compound C binding dramatically alters the conformation of the activation loop, which adopts an intermediate conformation between DFG-out and DFG-in. This induced fit forms a compound-C binding pocket composed of the N-lobe, the C-lobe and the hinge of the kinase domain. The pocket partially overlaps with the putative ATP-binding pocket. These three-dimensional structures will be useful to guide drug discovery.
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Affiliation(s)
- Noriko Handa
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
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