Source: https://medicine.uiowa.edu/biochemistry/crystallography/biochemistry/bryce-plapp-phd
Timestamp: 2019-04-21 03:34:19+00:00

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Alcohol dehydrogenases are enzymes used in yeast for the production of ethanol by fermentation of glucose and by man for the metabolism of alcohols. The five human alcohol dehydrogenases differ in specificities for substrates; their roles in normal metabolism and the pathogenesis of alcoholism are yet to be discovered. We are using protein engineering, steady-state and transient kinetics, chemical modification and x-ray crystallography to investigate the structure and catalytic mechanism of the enzymes. The diagram below shows the active site of the horse liver enzyme, based on X-ray studies. Site-directed mutagenesis is being used to prepare variants of the liver and yeast enzymes for studies on the catalytic mechanism and conformational flexibility. The size of the substrate binding pocket is being varied in order to study determinants of specificity. The overall structure of the protein, the tertiary and quaternary arrangements, are being modified so as to make a minimal catalytic unit and to study the role of dynamics in catalysis. The variant enzymes are crystallized for the determination of the three-dimensional structures.
Such fundamental studies expand our knowledge of enzyme catalysis and provide a basis for the design of specific agents that can increase or decrease the activity of liver alcohol dehydrogenase in vivo. We have designed and synthesized specific inhibitors of the enzyme and have found some to be effective in inhibiting ethanol metabolism. These compounds have been patented for their potential use in treatment of humans poisoned by methanol or ethylene glycol. Our studies show that liver alcohol dehydrogenases are rate-limiting factors in metabolism of ethanol. We think that the rational design of therapeutic agents, based on the knowledge of the three-dimensional structure, chemistry, and mechanism of enzymes, will lead to more efficacious drugs for treatment of alcoholism and other diseases.
Download kinetics programs for PCs operating under DOS or Windows: Cleland’s programs for fitting and graphing steady-state enzyme kinetic data. Frieden’s KINSIM and FITSIM programs for simulating progress curves. Read the .DOC or .TXT files for information on uncompressing and installing the programs. Included are sample input files for these programs: e.g., .STD files for Cleland’s programs and .MEC, .SIM, .SAV, .RDF, and .FDT Frieden’s programs. Download Kin Dist [.zip format].
Yun Ho Kim, David S. Gogerty, and Bryce V. Plapp (2018) Substitutions of a buried glutamate residue hinder the conformational change in horse liver alcohol dehydrogenase and yield a surprising complex with endogenous 3′-Dephosphocoenzyme A, 653:97-106. DOI:10.1016/j.abb.2018.07.003.
Karthik K. Shanmugantham, Rachel S. Wallace, Ann Ting-I Lee, and Bryce V. Plapp (2017) Contribution of Distal Amino Acid Residues Horse Liver Alcohol Dehydrogenase to Structure and Catalysis, Protein Science, 27(3):750-768. DOI:10.1002/pro.3370.
Keehyuk Kim and Bryce V. Plapp (2017) Inversion of Substrate Stereoselectivity of Horse Liver Alcohol Dehydrogenase by Substitutions of Ser-48 and Phe-93, Chem. Biol. Interact. 276,77-87. DOI: 10.1016/j.cbi.2016.12.016.
Bryce V. Plapp, Baskar Raj Savarimuthu, Daniel J. Ferraro, Jon K. Rubach, Eric N. Brown, and S. Ramaswamy. (2017) Horse Liver Alcohol Dehydrogenase: Zinc Coordination and Catalysis. Biochemistry. 56, 3632-3646. DOI: 10.1021/acs.biochem.7b00446. PMID: 28640600.
Bryce V. Plapp, Henry A. Charlier Jr., S. Ramaswamy. (2016) Mechanistic implications from structures of yeast alcohol dehydrogenase complexed with coenzyme and an alcohol. Archives of Biochemistry and Biophysics. 591, 35-42.
Savarimuthu Baskar Raj, S. Ramaswamy, Bryce V. Plapp (2014) Yeast Alcohol Dehydrogenase Structure and Catalysis. Biochemistry 53, 5791-5803. DOI: 10.1021/bi5006442. PMID: 251574460.
Atsushi Yahashiri, Jon K. Rubach, and Bryce V. Plapp (2014) Effects of Cavities at the Nicotinamide Binding Site of Liver Alcohol Dehydrogenase on Structure, Dynamics and Catalysis. Biochemistry. 53, 881-894. DOI: 10.1021/bi401583f. PMID: 24437493.
Plapp, B.V. and Ramaswamy, S. (2012) Atomic-Resolution Structures of Horse Liver Alcohol Dehydrogenase with NAD+ and Fluoroalcohols Define Strained Michaelis Complexes. Biochemistry. 51(19):4035-48.
Herdendorf, T. J., Plapp, B.V. Origins of the high catalytic activity of human alcohol dehydrogenase 4 studied with horse liver A317C alcohol dehydrogenase. (2011) Chem Biol Interact 191: 42-47.
Plapp, B.V. Conformational changes and catalysis by alcohol dehydrogenase. (2010) Arch Biochem Biophys. Jan 1;493(1):3-12.
Pal, S., Park, D.H., and Plapp, B.V. (2009) Activity of yeast alcohol dehydrogenases on benzyl alcohols and benzaldehydes Characterization of ADH1 from Saccharomyces carlsbergensis and transition state analysis. Chem Biol Interact, Mar 16;178(1-3):16-23.
Kovaleva, E.G., and Plapp, B.V. (2005) Deprotonation of the horse liver alcohol dehydrogenase-NAD+ complex controls formation of the ternary complexes. Biochemistry, Sep 27;44(38):12797-12808.
Plapp, B.V. and Berst, K.B. (2006) Human alcohol dehydrogenase 4: Mechanism, specificity and effects of ethanol on retinoid metabolism in Enzymology and Molecular Biology of Carbonyl Metabolism - 12. Henry Weiner, Bryce V. Plapp, Ronald Lindahl, and Edmund Maser, Eds., University Press, West Lafayette, IN, pp. 190-199.
Plapp, B.V., and Berst, K.B. (2005) Human alcohol dehydrogenase 4: Mechanism, specificity, and effects of ethanol on retinoid metabolism, in H. Weiner (Ed.) Enzymology and Molecular Biology of Carbonyl Metabolism: Aldehyde Dehydrogenase, Aldo-Keto Reductase and Alcohol Dehydrogenase, Purdue University Press, pp. 187-196.
Catalysis by alcohol dehydrogenases. Bryce V. Plapp, in Isotope effects in chemistry and biology (Amnon Kohen and Hans-Heinrich Limbach, eds.), CRC Press 2005, pp. 811-835.
Collins, X.H., Harmon, S.D., Kaduce, T.L., Berst, K.B., Fang, X., Moore, S.A., Raju, T.V., Falck, J.R., Weintraub, N.L., Duester, G., Plapp, B.V., and Spector, A.A. (2005) w-Oxidation of 20-hydroxyeicosatetraenoic Acid (20-HETE) in cerebral microvascular smooth muscle and endothelium by alcohol dehydrogenase 4. J. Biol. Chem. 280:33157-33164.
LeBrun, L.A., Park, D.-H., Ramaswamy, S., and Plapp, B.V. (2004) Participation of histidine-51 in catalysis by horse liver alcohol dehydrogenase. Biochemistry 43: 3014-3026.
Strömberg, P., Svensson, S., Berst, K.B., Plapp, B.V., and Höög, J.-O. (2004) Enzymatic mechanism of low-activity mouse alcohol dehydrogenase 2. Biochemistry 43:1323-1328.
Venkataramaiah, T.H. and Plapp, B.V. (2003) Formamides mimic aldehydes and inhibit liver alcohol dehydrogenases and ethanol metabolism. J. Biol. Chem. 278:36699-36706.

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