Selected Research Area: Protein Folding and Enzymology
The structure and function of proteins form the very heart of an amazing number of processes/reactions taking place in living cells. Much about proteins remains to be explained: how their structure is determined by amino acid sequence, how enzymes achieve their high specificity and catalytic activity, how proteins of many types are regulated by post-translational modifications. Faculty in Biological Chemistry and their colleagues throughout the Medical School and Homewood campus are working to achieve molecular explanations for these and other phenomenon displayed by this remarkable class of macromolecules.
Suite 371 MRBBaltimore, MD 21205
Office Phone: 410-614-7566
Lab Phone: 410-614-6968
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Watkin EE, Arbez N, Waldron-Roby E, O'Meally R, Ratovitski T, Cole RN, and Ross CA (2014) Phosphorylation of mutant huntingtin at serine 116 modulates neuronal toxicity. PLoS One 9: e88284.PubMed Reference
Herbrich SM, Cole RN, West KP, Jr., Schulze K, Yager JD, Groopman JD, Christian P, Wu L, O'Meally RN, May DH, McIntosh MW, and Ruczinski I (2013) Statistical Inference from Multiple iTRAQ Experiments without Using Common Reference Standards. Journal of Proteome Research 12: 594-604.PubMed Reference
Foster DB, Liu T, Rucker J, O'Meally RN, Devine LR, Cole RN, and O'Rourke B (2013) The cardiac acetyl-lysine proteome. PLoS One 8: e67513.PubMed Reference
Cole RN, Ruczinski I, Schulze K, Christian P, Herbrich S, Wu L, Devine LR, O'Meally RN, Shrestha S, Boronina TN, Yager JD, Groopman J, and West KP, Jr. (2013) The plasma proteome identifies expected and novel proteins correlated with micronutrient status in undernourished Nepalese children. Journal of Nutrition 143: 1540-1548.PubMed Reference
Mattis VB, Svendsen SP, Ebert A, Svendsen CN, King AR, Casale M, Winokur ST, Batugedara G, Vawter M, Donovan PJ, Lock LF, Thompson LM, Atwal RS, Zhu Y, Fossale E, Gillis T, Mysore J, Li JH, Seong I, Shen Y, Chen X, Wheeler VC, MacDonald ME, Gusella JF, Akimov S, Arbez N, Juopperi T, Ratovitski T, Chiang JH, Kim WR, Chighladze E, Watkin E, Zhong C, Makri G, Cole RN, Margolis RL, Song H, Ming G, Ross CA, Kaye JA, Daub A, Sharma P, Mason AR, Finkbeiner S, Rushton D, Brazier SP, Battersby AA, Redfern A, Tseng HE, Harrison AW, Kemp PJ, Allen ND, Castiglioni V, Onorati M, Cattaneo E, Yu J, Thomson JA, and Arjomand J (2012) Induced pluripotent stem cells from patients with Huntington's disease show CAG-repeat-expansion-associated phenotypes. Cell Stem Cell 11: 264-278.PubMed Reference
Murray CI, Uhrigshardt H, O'Meally RN, Cole RN, and Van Eyk JE (2012) Identification and quantification of S-nitrosylation by cysteine reactive tandem mass tag switch assay. Molecular and Cellular Proteomics 11: M111 013441.PubMed Reference
Ratovitski T, Chighladze E, Arbez N, Boronina T, Herbrich S, Cole RN, and Ross CA (2012) Huntingtin protein interactions altered by polyglutamine expansion as determined by quantitative proteomic analysis. Cell Cycle 11: 2006-2021.PubMed Reference
Zizak M, Chen T, Bartonicek D, Sarker R, Zachos NC, Cha B, Kovbasnjuk O, Korac J, Mohan S, Cole RN, Chen Y, Tse CM, and Donowitz M (2012) Calmodulin kinase II constitutively binds, phosphorylates, and inhibits brush border Na+/H+ exchanger 3 (NHE3) by a NHERF2 protein-dependent process. Journal of Biological Chemistry 287: 13442-13456.PubMed Reference
Cammarato A, Ahrens CH, Alayari NN, Qeli E, Rucker J, Reedy MC, Zmasek CM, Gucek M, Cole RN, Van Eyk JE, Bodmer R, O'Rourke B, Bernstein SI, and Foster DB (2011) A Mighty Small Heart: The Cardiac Proteome of Adult Drosophila melanogaster. PLoS One 6: e18497.PubMed Reference
Hartman IZ, Kim A, Cotter RJ, Walter K, Dalai SK, Boronina T, Griffith W, Lanar DE, Schwenk R, Krzych U, Cole RN, and Sadegh-Nasseri S (2010) A reductionist cell-free major histocompatibility complex class II antigen processing system identifies immunodominant epitopes. Nature Medicine 16: 1333-1340.PubMed Reference
Ratovitski T, Gucek M, Jiang H, Chighladze E, Waldron E, D'Ambola J, Hou Z, Liang Y, Poirer MA, Hirschhorn RR, Graham R, Hayden MR, Cole RN, and Ross CA (2009) Mutant Huntingtin N-terminal fragments of specific size mediate aggregation and toxicity in neuronal cells. Journal of Biological Chemistry 284: 10855-10867.PubMed ReferenceGuo Y, Singleton PA, Rowshan A, Gucek M, Cole RN, Graham DR, Van Eyk JE, and Garcia JG (2007) Quantitative proteomic analysis of human endothelial cell membrane rafts: Evidence of MARCKS and MRP regulation in the sphingosine 1-phosphate-induced barrier enhancement. Molecular and Cellular Proteomics 6: 689-696.PubMed Reference
Wells L, Vosseller K, Cole RN, Cronshaw JM, Matunis MJ, and Hart GW (2002) Mapping sites of O-GlcNAc modification using affinity tags for serine and threonine post-translational modifications. Molecular and Cellular Proteomics 1: 791-804.PubMed Reference
Dinkova-Kostova AT, Holtzclaw WD, Cole RN, Itoh K, Wakabayashi N, Katoh Y, Yamamoto M, and Talalay P (2002) Direct evidence that sulfhydryl groups of Keap1 are the sensors regulating induction of phase 2 enzymes that protect against carcinogens and oxidants. Proceedings of the National Academy of Sciences, USA 99: 11908-11013.PubMed Reference
Cole RN and Hart GW (2001) Cytosolic O-glycosylation is abundant in nerve terminals. Journal of Neurochemistry 79: 1080-1089.PubMed Reference
725 N. Wolfe St. 400 BiophysicsBaltimore, MD 21205
Office Phone: 410-614-1944
Lab Phone: 410-955-3167
In addition to studies focused on elucidating the structure, mechanism, and regulation of the mammalian mitochondrial ATP synthase, a major disease focus of the Pedersen lab for many years has been cancer because of its well known alterations in energy metabolism. More recently, we have entered also into a study of heart dysfunction as the heart with every beat is totally dependent on energy metabolism, with the mitochondrial ATP synthase being intimately involved. The laboratory uses chemistry, molecular biology, biophysics, immunology, tissue culture and animal models to better understand the energetics/energy metabolism of normal and pathological cells/tissues. A major focus is on the two 'power plants', the mitochondria and the glucose catabolic system (glycolysis), as well as on the interaction between these two systems. The following are active research projects. 1) The mechanism and regulation of ATP synthesis in mammalian mitochondria.This involves the study of the molecular properties of the ATP synthase complex that consists of two nano-motors both of which are necessary to make ATP. In a collaborative study we have obtained the 3-D structure of one of the motors and are now working on the structure of the whole complex that consists of 17 subunit types and over 30 total subunits. Recently, we discovered that the ATP synthase is in complex formation with the transport system (carrier) for phosphate and the transport system for adenine nucleotides (ADP and ATP). We have named this complex the ATP Synthasome and are now carrying out studies to obtain a 3-D structure of the whole complex. It is important to note that the ATP synthasome represents the terminal complex of oxidative phosphorylation in mitochondria and makes most of the ATP needed/day to supply our energy needs. In addition to the above mentioned work, we have also recently discovered that the ATP synthasome contains another key protein originally thought to be within the outer membrane as well as at contact sites between inner and outer membranes. This protein is likely critical for channeling ATP to the cytoplasm.
Work on the ATP synthasome is being vigorously studied.2) Cancer: Regulation and targeting genes and proteins responsible for the most common phenotype and developing a novel potent anticancer agent, 3-bromopyruvate (3BP).The most common metabolic phenotype of malignant cells & tumors including those derived from liver, breast, lung, brain, etc. is their capacity to utilize glucose at high rates even in the presence of oxygen. The pivotal enzyme involved is hexokinase 2 (HK-2) that is markedly elevated and bound at or very near the outer mitochondrial membrane protein named "VDAC" (voltage dependent anion channel). At this location, hexokinase 2 not only helps couple ATP formation in mitochondria to the phosphorylation of glucose to "jump start"glucose catabolism, it also represses this organelle's contribution to cell death. Therefore, hexokinase 2, in addition to its critical metabolic role, also promotes cancer by helping immortalize cancer cells. We are studying both the hexokinase 2 gene and developing novel strategies to target both the gene and the protein. We use both tumor cells growing in tissue culture and animal models, i.e., animals with cancer.
While working in my laboratory at the beginning of this century Dr. Young Ko discovered that the small molecule 3-bromopyruvate (3BP) is a potent anticancer agent. Several years later while working as a new faculty member in collaboration with my laboratory she would lead a team that showed 3BP's capacity to completely cure (eradicate) cancers in 19 out of 19 treated animals, i.e.,100%.
Currently, in collaboration with Dr. Ko, we are now involved in the further development of 3BP while searching for other effective anticancer agents. A limited number of studies conducted in humans with 3BP have proved very promising.
3) Heart Dysfunction: Regulation of the mitochondrial ATP synthase in the normal and ischemic heart. The heart can survive only short periods without oxygen. Conditions where oxygen is limiting can have grave consequences as the mitochondrial membrane potential will collapse and the mitochondrial ATP synthase will switch from synthesizing ATP to hydrolyzing ATP, thus depleting heart cells (cardiomyocytes) of the energy reserves they require for survival. Fortunately, the ATP synthase is well regulated in the heart so that the ATP hydrolytic event is minimized during short periods of ischemia (reduced oxygen). In fact, there are 3 known small peptide regulators of the ATP synthase, one which optimizes ATP synthesis and the other two that suppress ATP hydrolysis. In addition, the ATP synthase is subjected to regulatory signal transduction events that result either in its phosphorylation or dephosphorylation.
We are currently involved in a project designed to understand the relative importance of these and other regulatory events in protecting the heart during sudden ischemic insults. [The laboratory has published over 240 papers of which >150 describe original research while the others refer either to novel methods or represent reviews]
Majkowska-Skrobek G, Augustyniak D, Lis P, Bartkowiak A, Gonchar M, Ko YH, Pedersen PL, Goffeau A, Ułaszewski S. Killing multiple myeloma cells with the small molecule 3-bromopyruvate: implications for therapy. Anticancer Drugs. 2014 Jul;25(6):673-82.PubMed ReferenceDyląg M, Lis P, Niedźwiecka K, Ko YH, Pedersen PL, Goffeau A, Ułaszewski S. 3-Bromopyruvate: a novel antifungal agent against the human pathogen Cryptococcus neoformans. Biochem Biophys Res Commun. 2013PubMed ReferenceDarpolor MM, Kaplan DE, Pedersen PL, Glickson JD. Human Hepatocellular Carcinoma Metabolism: Imaging by Hyperpolarized 13C Magnetic Resonance Spectroscopy. J Liver Disease Transplant. 2012 Sep 1;1(1).PubMed ReferencePedersen PL. Mitochondria in relation to cancer metastasis: introduction to a mini-review series. J Bioenerg Biomembr. 2012 Dec;44(6):615-7.PubMed ReferencePedersen PL. 3-Bromopyruvate (3BP) a fast acting, promising, powerful, specific, and effective "small molecule" anti-cancer agent taken from labside to bedside: introduction to a special issue. J Bioenerg Biomembr. 2012 Feb;44(1):1-6.PubMed ReferenceLis P, Zarzycki M, Ko YH, Casal M, Pedersen PL, Goffeau A, Ułaszewski S. Transport and cytotoxicity of the anticancer drug 3-bromopyruvate in the yeast Saccharomyces cerevisiae. J Bioenerg Biomembr. 2012.PubMed Reference
Hunterian 502Baltimore, MD 21205
Office Phone: 410-955-5759
Lab Phone: 410-955-1410
A major effort in our laboratory is focused on understanding the biochemistry and chemistry underlying the molecular aspects involved in regulating lipid metabolizing signaling enzymes and the physiological roles of this regulation. Control of lipid metabolizing enzymes involves the modulation of two key parameters; their sub-cellular distribution and their intrinsic enzymatic activity. Our studies have concentrated on three families of lipid-metabolizing signaling enzymes: diacylglycerol kinases, phospholipases D, and phospholipases C.
Specific Areas of Interest
Interfacial Enzymology of Lipid Metabolizing Signaling Enzymes: We are particularly interested in identifying the critical modulating proteins, lipids, and post-translational modifications that alter the localization and/or activity of lipid metabolizing enzymes. In these studies we consider the fact that these enzymes act as interfacial enzymes and their regulation includes a number of interfacial-dependent parameters. Our recent studies have identified some of the diacylglycerol metabolizing enzyme DGK-θ (diacylglycerol kinase-theta) interfacial parameters that are altered upon neuronal depolarization. Further, our studies demonstrated that activation of DGK-θ requires a protein that contains a polybasic region. We have recently obtained evidence that identifies at least one, if not only, activator binding domain on DGK-θ.Enzyme Structure/Function Studies: We are also interested in the structural components of these enzymes that are critical for their distribution/re-distribution to specific sub-cellular compartments. Additionally, and to compliment the enzymology studies, we are interested in elucidating the catalytic mechanism(s) of these enzymes. These studies will be conducted partly in collaboration with Dr. Mario Amzel. Our long-term goal is to understand the biochemistry and chemistry of these enzymes and determine how changes in their sub-cellular localization and/or enzymatic activity affect their signaling functions.Physiological Functions of DGKs in Neurons: There is growing evidence that DGKs play physiological roles in mammalian neurons. This evidence includes cellular localization of specific isoforms, and the observations that likely modulate (a) susceptibility to epileptic seizures (DGK-), (b) neuronal spine density (DGK- and DGK-), and (c) pre-synaptic glutamate release during DHPG (3,5-dihydroxyphenylglycine)-induced long-term potentiation (DGK-). We are currently examining the role of DGK-θ in glutamatergic neurons. These studies have initially focused on identifying the physiologic regulator of DGK-θ, and test the hypothesis that this enzyme modulates induced glutamate release in these mammalian neurons. We discovered that DGK-θ modulates glutamate release from cortical and hippocampal neurons in part by modulating synaptic vesicle cycling. These studies are conducted in collaboration with Dr. Rick Huganier’s laboratory.
Tu-Sekine, B., Goldschmidt, H, Raben, D.M. (2015) Diacylglycerol, Phosphatidic Acid, and their Metabolizing Enzymes in Synaptic Vesicle Recycling. Adv. Biol. Reg. Jan;57:147-52.PubMed Reference
Petro E, and Raben DM. (2013) Bacterial expression strategies for several Sus scrofa diacylglycerol kinase alpha constructs: solubility challenges. Scientific Reports 2013;3:160.PubMed Reference
Ueda S, Tu-Sekine B, Yamanoue M, Raben DM, and Shirai Y. (2013) The expression of diacylglycerol kinase theta during the organogenesis of mouse embryos. BMC Developmental Biology 2013, 13:35.PubMed Reference
Bolduc D, Rahdar M, Tu-Sekine B, Sivakumaren SC, Raben DM, Amzel LM, Devreotes P, Gabelli SB, and Cole P. (2013) Phosphorylation-mediated PTEN conformational closure and deactivation revealed with protein semisynthesis. Elife 2013 Jul 9;2:e00691.PubMed Reference
Tu-Sekine B, Goldschmidt H, Petro E, and Raben DM. (2013) Diacylglycerol Kinase Theta: Regulation and Stability. Adv. Biol. Reg. Jan;53(1):118-26.PubMed Reference
Tu-Sekine B, and Raben DM. (2012) Dual Regulation of DGK-θ: Polybasic Proteins Promote Activation by Phospholipids and Increase Substrate Affinity. J. Biol. Chem. 287(50):41619-41627.PubMed Reference
Tu-Sekin, B, and Raben DM. (2011) Regulation and Roles of Neuronal Diacylglycerol Kinases: a Lipid Perspective. Crit. Rev. Biochem. Mol. Biol. Oct;46(5):353-64.PubMed Reference
Mohan S, Tse CM, Gabelli SB, Sarker R, Cha B, Fahie K, Nadella M, Zachos NC, Tu-Sekine B, Raben DM, Amzel LM, Donowitz M. (2010) NHE3 Activity Is Dependent on Direct Phosphoinositide Binding at the N Terminus of Its Intracellular Cytosolic Region. J. Biol. Chem. 285(45): 34566-78.PubMed Reference
Tu-Sekine, B. and Raben DM. (2010) Characterization of Cellular DGKΘ. Advances in Enzyme Reg. 50:81-94.PubMed Reference
Link TM, Park U, Vonakis BM, Raben DM, Soloski M.J., Caterina MJ. (2010) TRPV2 plays a pivotal role in macrophage particle binding and phagocytosis. Nature Immunology Mar;11(3):232-9. Epub 2010 Jan 31.PubMed Reference
Tu-Sekine and Raben DM. (2009) Regulation of DGK-Θ J. Cell Physiol. 220(3):548-52.PubMed Reference
Raben DM and Wattenberg BW. (2009) Signaling at the Membrane Interface by the DGK/SK Enzyme Family. J Lipid Res 50th Anniversary Edition: J. Lipid Res. April Supplement: S35-S39.PubMed Reference
Raben DM and Tu-Sekine B. (2008) Nuclear Localization Of Diacylglycerol Kinases: Regulation And Roles. Frontiers in Bioscience 13:590-597.PubMed Reference
Wattenberg BW and Raben DM. (2007) Diacylglycerol Kinases Put the Brakes on Immune Function. Science STKE (398) pe43.PubMed Reference
Tu-Sekine B, Ostroski M, and Raben DM. (2007) Modulation of DGKΘ Activity by α-Thrombin and Phospholipids. Biochemistry, 46(3): 924 -932.PubMed Reference
513 PhysiologyBaltimore, MD 21205
Office Phone: 410-955-5759
Lab Phone: 410-955-3424
Consequently, on the theoretical side, efforts to predict protein structure from sequence focus intensively on enforcing these local interactions in fragments built de novo, using short segments of chain taken from high resolution protein structures. Beginning with fragments of length 4 to 8 residues lacking side chain atoms beyond CG, larger fragments are assembled in a hierarchical fashion, using a variety of statistical potentials to enforce protein-like interactions between elements of secondary structure. In the final step, heavy atoms are added to form complete side chains, and several high resolution all atom potential, including one to quantify solvation, are used as fitness functions in a genetic algorithm-based conformational search.
The laboratory has participated in CASPâ€™s 4, 5, and 6 in the new fold category and in CASP 6 in homology modeling. The upcoming CASP 7 challenge (May through August 2006) will provide us an opportunity to evaluate our new explicit side chain methods.