title: Identification of AMP-activated protein kinase targets by a consensus sequence search of the proteome.
abstract: BACKGROUND
  AMP-activated protein kinase (AMPK) is a heterotrimeric serine/threonine protein kinase that is activated by cellular perturbations associated with ATP depletion or stress. While AMPK modulates the activity of a variety of targets containing a specific phosphorylation consensus sequence, the number of AMPK targets and their influence over cellular processes is currently thought to be limited.
  
  
  RESULTS
  We queried the human and the mouse proteomes for proteins containing AMPK phosphorylation consensus sequences. Integration of this database into Gaggle software facilitated the construction of probable AMPK-regulated networks based on known and predicted molecular associations. In vitro kinase assays were conducted for preliminary validation of 12 novel AMPK targets across a variety of cellular functional categories, including transcription, translation, cell migration, protein transport, and energy homeostasis. Following initial validation, pathways that include NAD synthetase 1 (NADSYN1) and protein kinase B (AKT2) were hypothesized and experimentally tested to provide a mechanistic basis for AMPK regulation of cell migration and maintenance of cellular NAD(+) concentrations during catabolic processes.
  
  
  CONCLUSIONS
  This study delineates an approach that encompasses both in silico procedures and in vitro experiments to produce testable hypotheses for AMPK regulation of cellular processes.
authors.affiliation: Divisions of Biochemistry and Molecular Biology and Biomedical Sciences, University of California, Riverside, CA, 92521-0121, USA. tmarin@llu.edu.|Department of Cardiopulmonary Sciences and Anatomy, Schools of Allied Health and Medicine, Loma Linda University, Loma Linda, CA, 92350, USA. tmarin@llu.edu.
authors.forename: Traci L
authors.initials: TL
authors.lastname: Marin
authors.affiliation: Divisions of Biochemistry and Molecular Biology and Biomedical Sciences, University of California, Riverside, CA, 92521-0121, USA. brengong@gmail.com.|Department of Cardiopulmonary Sciences and Anatomy, Schools of Allied Health and Medicine, Loma Linda University, Loma Linda, CA, 92350, USA. brengong@gmail.com.
authors.forename: Brendan
authors.initials: B
authors.lastname: Gongol
authors.affiliation: Divisions of Biochemistry and Molecular Biology and Biomedical Sciences, University of California, Riverside, CA, 92521-0121, USA. mam085@ucsd.edu.|Division of Cardiology, Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA. mam085@ucsd.edu.
authors.forename: Marcy
authors.initials: M
authors.lastname: Martin
authors.affiliation: Divisions of Biochemistry and Molecular Biology and Biomedical Sciences, University of California, Riverside, CA, 92521-0121, USA. sking009@ucr.edu.
authors.forename: Stephanie J
authors.initials: SJ
authors.lastname: King
authors.affiliation: Divisions of Biochemistry and Molecular Biology and Biomedical Sciences, University of California, Riverside, CA, 92521-0121, USA. lsmit004@ucr.edu.
authors.forename: Lemar
authors.initials: L
authors.lastname: Smith
authors.affiliation: Divisions of Biochemistry and Molecular Biology and Biomedical Sciences, University of California, Riverside, CA, 92521-0121, USA. david.johnson@ucr.edu.
authors.forename: David A
authors.initials: DA
authors.lastname: Johnson
authors.affiliation: Division of Physiology, Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA. shankar@ucsd.edu.
authors.forename: Shankar
authors.initials: S
authors.lastname: Subramaniam
authors.affiliation: Division of Physiology, Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA. shuchien@ucsd.edu.|Department of Bioengineering and Institute of Engineering in Medicine, University of California, San Diego La Jolla, CA, 92093, USA. shuchien@ucsd.edu.
authors.forename: Shu
authors.initials: S
authors.lastname: Chien
authors.affiliation: Divisions of Biochemistry and Molecular Biology and Biomedical Sciences, University of California, Riverside, CA, 92521-0121, USA. jshyy@ucsd.edu.|Division of Cardiology, Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA. jshyy@ucsd.edu.
authors.forename: John Y-J
authors.initials: JY
authors.lastname: Shyy
mesh_terms: D055372:AMP-Activated Protein Kinases / Q000378:metabolism*; D000818:Animals; D001692:Biological Transport; D002118:Calcium / Q000378:metabolism; D002453:Cell Cycle; D002843:Chromatin / Q000378:metabolism; D002940:Circadian Rhythm; D016384:Consensus Sequence; D059865:Endoplasmic Reticulum Stress; D004789:Enzyme Activation; D044127:Epigenesis, Genetic; D005947:Glucose / Q000378:metabolism; D006706:Homeostasis; D006801:Humans; D007328:Insulin / Q000378:metabolism; D051379:Mice; D001678:Organelle Biogenesis; D010766:Phosphorylation; D011485:Protein Binding; D017510:Protein Folding; D040901:Proteomics; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D012270:Ribosomes / Q000378:metabolism; D015398:Signal Transduction; D012984:Software; D049490:Systems Biology; D015533:Transcriptional Activation
chemical_list: D002843:Chromatin; D007328:Insulin; D012333:RNA, Messenger; D055372:AMP-Activated Protein Kinases; D005947:Glucose; D002118:Calcium