Enzyme Structure and Function
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Kohen Curriculum Vitae
Curriculum Vitae Amnon Kohen Department of Chemistry Tel: (319) 335-0234 University of Iowa FAX: (319) 335-1270 Iowa City, IA 52242 [email protected] EDUCATION AND PROFESSIONAL HISTORY Education D.Sc., Chemistry 1989-1994 Technion – Israel Institute of Technology, Haifa, Israel Advisor: Professor T. Baasov Topic: Mechanistic Studies of the Enzyme KDO8P Synthase B.Sc., Chemistry (with Honors) 1986-1989 Hebrew University, Jerusalem, Israel Positions Professor 2010-Present Department of Chemistry, University of Iowa, Iowa City, IA and Molecular and Cellular Biology Program, and MSTP faculty member Associate Professor 2005-2010 Department of Chemistry, University of Iowa, Iowa City, IA and Molecular and Cellular Biology Program Assistant Professor 1999-2005 Department of Chemistry, University of Iowa, Iowa City, IA Postgraduate Researcher 1997-1999 With Professor Judith Klinman Department of Chemistry, University of California, Berkeley Topic: Hydrogen Tunneling in Biology: Alcohol Dehydrogenases Postgraduate Fellow 1995-1997 With Professor Judith Klinman Department of Chemistry, University of California, Berkeley Topic: Hydrogen Tunneling in Biology: Glucose Oxidase Visiting Scholar Fall 1994 With Professor Karen S. Anderson Department of Pharmacology, Yale Medical School, New Haven, CT Kohen, A. Affiliations American Society for Biochemistry and Molecular Biology (ASBMB, 2013 - present) Center for Biocatalysis and Bioprocessing (CBB) University of Iowa (2000-Present) The Interdisciplinary Graduate Program in Molecular Biology, University of Iowa (2003- Present) American Association for the Advancement of Science (AAAS, 2011-present) American Chemical Society (1995-Present) Divisions: Organic Chemistry, Physical Chemistry, Biochemistry Sigma Xi (1997-Present) Protein Society (1996-1998) Honors and Awards • Career Development Award (University of Iowa- 2015-2016) • Graduate College Outstanding Faculty Mentor Award (2015). -
Revised Glossary for AQA GCSE Biology Student Book
Biology Glossary amino acids small molecules from which proteins are A built abiotic factor physical or non-living conditions amylase a digestive enzyme (carbohydrase) that that affect the distribution of a population in an breaks down starch ecosystem, such as light, temperature, soil pH anaerobic respiration respiration without using absorption the process by which soluble products oxygen of digestion move into the blood from the small intestine antibacterial chemicals chemicals produced by plants as a defence mechanism; the amount abstinence method of contraception whereby the produced will increase if the plant is under attack couple refrains from intercourse, particularly when an egg might be in the oviduct antibiotic e.g. penicillin; medicines that work inside the body to kill bacterial pathogens accommodation ability of the eyes to change focus antibody protein normally present in the body acid rain rain water which is made more acidic by or produced in response to an antigen, which it pollutant gases neutralises, thus producing an immune response active site the place on an enzyme where the antimicrobial resistance (AMR) an increasing substrate molecule binds problem in the twenty-first century whereby active transport in active transport, cells use energy bacteria have evolved to develop resistance against to transport substances through cell membranes antibiotics due to their overuse against a concentration gradient antiretroviral drugs drugs used to treat HIV adaptation features that organisms have to help infections; they -
NADPH-Dependent A-Oxidation of Unsaturated Fatty Acids With
Proc. Natl. Acad. Sci. USA Vol. 89, pp. 6673-6677, August 1992 Biochemistry NADPH-dependent a-oxidation of unsaturated fatty acids with double bonds extending from odd-numbered carbon atoms (5-enoyl-CoA/A3,A2-enoyl-CoA isomerase/A3',52'4-dienoyl-CoA isomerase/2,4-dienoyl-CoA reductase) TOR E. SMELAND*, MOHAMED NADA*, DEAN CUEBASt, AND HORST SCHULZ* *Department of Chemistry, City College of the City University of New York, New York, NY 10031; and tJoined Departments of Chemistry, Manhattan College/College of Mount Saint Vincent, Riverdale, NY 10471 Communicated by Salih J. Wakil, April 13, 1992 ABSTRACT The mitochondrial metabolism of 5-enoyl- a recent observation of Tserng and Jin (5) who reported that CoAs, which are formed during the (3-oxidation of unsaturated the mitochondrial -oxidation of 5-enoyl-CoAs is dependent fatty acids with double bonds extending from odd-numbered on NADPH. Their analysis of metabolites by gas chroma- carbon atoms, was studied with mitochondrial extracts and tography/mass spectrometry led them to propose that the purified enzymes of (3-oxidation. Metabolites were identified double bond of 5-enoyl-CoAs is reduced by NADPH to yield spectrophotometrically and by high performance liquid chro- the corresponding saturated fatty acyl-CoAs, which are then matography. 5-cis-Octenoyl-CoA, a putative metabolite of further degraded by P-oxidation. linolenic acid, was efficiently dehydrogenated by medium- This report addresses the question of how 5-enoyl-CoAs chain acyl-CoA dehydrogenase (EC 1.3.99.3) to 2-trans-5-cis- are chain-shortened by P-oxidation. We demonstrate that octadienoyl-CoA, which was isomerized to 3,5-octadienoyl- 5-enoyl-CoAs, after dehydrogenation to 2,5-dienoyl-CoAs, CoA either by mitochondrial A3,A2-enoyl-CoA isomerase (EC can be isomerized to 2,4-dienoyl-CoAs, which are reduced by 5.3.3.8) or by peroxisomal trifunctional enzyme. -
(Helianthus Annuus L.) Plastidial Lipoyl Synthases Genes Expression In
Impact of sunflower (Helianthus annuus L.) plastidial lipoyl synthases genes expression in glycerolipids composition of transgenic Arabidopsis plants Raquel Martins-Noguerol, Antonio Javier Moreno-Pérez, Acket Sebastien, Manuel Adrián Troncoso-Ponce, Rafael Garcés, Brigitte Thomasset, Joaquín Salas, Enrique Martínez-Force To cite this version: Raquel Martins-Noguerol, Antonio Javier Moreno-Pérez, Acket Sebastien, Manuel Adrián Troncoso- Ponce, Rafael Garcés, et al.. Impact of sunflower (Helianthus annuus L.) plastidial lipoyl synthases genes expression in glycerolipids composition of transgenic Arabidopsis plants. Scientific Reports, Nature Publishing Group, 2020, 10, pp.3749. 10.1038/s41598-020-60686-z. hal-02881038 HAL Id: hal-02881038 https://hal.archives-ouvertes.fr/hal-02881038 Submitted on 25 Jun 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. www.nature.com/scientificreports OPEN Impact of sunfower (Helianthus annuus L.) plastidial lipoyl synthases genes expression in glycerolipids composition of transgenic Arabidopsis plants Raquel Martins-Noguerol1,2, Antonio Javier Moreno-Pérez 1,2, Acket Sebastien2, Manuel Adrián Troncoso-Ponce2, Rafael Garcés1, Brigitte Thomasset2, Joaquín J. Salas1 & Enrique Martínez-Force 1* Lipoyl synthases are key enzymes in lipoic acid biosynthesis, a co-factor of several enzyme complexes involved in central metabolism. -
Chapter 7. "Coenzymes and Vitamins" Reading Assignment
Chapter 7. "Coenzymes and Vitamins" Reading Assignment: pp. 192-202, 207-208, 212-214 Problem Assignment: 3, 4, & 7 I. Introduction Many complex metabolic reactions cannot be carried out using only the chemical mechanisms available to the side-chains of the 20 standard amino acids. To perform these reactions, enzymes must rely on other chemical species known broadly as cofactors that bind to the active site and assist in the reaction mechanism. An enzyme lacking its cofactor is referred to as an apoenzyme whereas the enzyme with its cofactor is referred to as a holoenzyme. Cofactors are subdivided into essential ions and organic molecules known as coenzymes (Fig. 7.1). Essential ions, commonly metal ions, may participate in substrate binding or directly in the catalytic mechanism. Coenzymes typically act as group transfer agents, carrying electrons and chemical groups such as acyl groups, methyl groups, etc., depending on the coenzyme. Many of the coenzymes are derived from vitamins which are essential for metabolism, growth, and development. We will use this chapter to introduce all of the vitamins and coenzymes. In a few cases--NAD+, FAD, coenzyme A--the mechanisms of action will be covered. For the remainder of the water-soluble vitamins, discussion of function will be delayed until we encounter them in metabolism. We also will discuss the biochemistry of the fat-soluble vitamins here. II. Inorganic cation cofactors Many enzymes require metal cations for activity. Metal-activated enzymes require or are stimulated by cations such as K+, Ca2+, or Mg2+. Often the metal ion is not tightly bound and may even be carried into the active site attached to a substrate, as occurs in the case of kinases whose actual substrate is a magnesium-ATP complex. -
Curriculum Vitae Natalie G. Ahn
Natalie G. Ahn Curriculum Vitae Natalie G. Ahn ADDRESS: Department of Biochemistry Jennie Smoly Caruthers Biotechnology Building 3415 Colorado Avenue, 596 UCB University of Colorado at Boulder Boulder, CO 80309-0596 Phone: (303) 492-4799 (Phone) Email: [email protected] I. ACADEMICS EDUCATION Postdoctoral Fellow, 1988-1990, Department of Pharmacology, Univ. of Washington, Seattle Research advisor: Edwin G. Krebs Postdoctoral Fellow, 1985-1987, Department of Medicine, Univ of Washington, Seattle Research advisor: Christoph de Haën Ph.D.,1985, Department of Chemistry University of California, Berkeley Thesis advisor: Judith P. Klinman 1979-1981 Teaching Assistant, undergraduate chemistry, Dept. of Chemistry 1981-1985 Research Assistant, Dept. of Chemistry B.S., 1979, Department of Chemistry, University of Washington, Seattle Undergraduate senior thesis advisor: Lyle H. Jensen, Department of Biological Structure Undergraduate research advisor: David C. Teller, Department of Biochemistry APPOINTMENTS 2018-present Distinguished Professor, University of Colorado 2003-present Associate Director, BioFrontiers Institute, Univ. Colorado, Boulder 1994-2014 Investigator, Howard Hughes Medical Institute (1994-2002 Assistant Investigator; 2003-2004 Associate Investigator; 2005-2014 Investigator) 1993-present Member, UCHSC Cancer Center, Univ. Colorado Health Sciences Center, Denver 1992-2018 Professor, Department of Chemistry and Biochemistry, Univ. Colorado, Boulder (1992-1998 Assistant Professor; 1998-2003 Associate Professor; 2003-present Professor) 1990-1992 Research Assistant Professor, Department of Biochemistry, Univ. Washington, Seattle 3 Natalie G. Ahn II. HONORS 2018 Distinguished Professor, University of Colorado 2018 Member, National Academy of Sciences 2018 Member, American Academy of Arts and Sciences 2016-2018 President, American Society of Biochemistry and Molecular Biology 2012 Professor of Distinction, College of Arts & Sciences, U. -
Crystallographic Snapshots of Sulfur Insertion by Lipoyl Synthase
Crystallographic snapshots of sulfur insertion by lipoyl synthase Martin I. McLaughlina,b,1, Nicholas D. Lanzc, Peter J. Goldmana, Kyung-Hoon Leeb, Squire J. Bookerb,c,d, and Catherine L. Drennana,e,f,2 aDepartment of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139; bDepartment of Chemistry, The Pennsylvania State University, University Park, PA 16802; cDepartment of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802; dHoward Hughes Medical Institute, The Pennsylvania State University, University Park, PA 16802; eDepartment of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139; and fHoward Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139 Edited by Vern L. Schramm, Albert Einstein College of Medicine, Bronx, NY, and approved July 5, 2016 (received for review March 8, 2016) Lipoyl synthase (LipA) catalyzes the insertion of two sulfur atoms substrate and at an intermediate stage in the reaction, just after at the unactivated C6 and C8 positions of a protein-bound octanoyl insertion of the C6 sulfur atom but before sulfur insertion at C8. chain to produce the lipoyl cofactor. To activate its substrate for sulfur insertion, LipA uses a [4Fe-4S] cluster and S-adenosylmethio- Results nine (AdoMet) radical chemistry; the remainder of the reaction The crystal structure of LipA from M. tuberculosis was de- mechanism, especially the source of the sulfur, has been less clear. termined to 1.64-Å resolution by iron multiwavelength anoma- One controversial proposal involves the removal of sulfur from a lous dispersion phasing (Table S1). The overall fold of LipA consists second (auxiliary) [4Fe-4S] cluster on the enzyme, resulting in de- of a (β/α)6 partial barrel common to most AdoMet radical enzymes struction of the cluster during each round of catalysis. -
Anti-Inflammatory Role of Curcumin in LPS Treated A549 Cells at Global Proteome Level and on Mycobacterial Infection
Anti-inflammatory Role of Curcumin in LPS Treated A549 cells at Global Proteome level and on Mycobacterial infection. Suchita Singh1,+, Rakesh Arya2,3,+, Rhishikesh R Bargaje1, Mrinal Kumar Das2,4, Subia Akram2, Hossain Md. Faruquee2,5, Rajendra Kumar Behera3, Ranjan Kumar Nanda2,*, Anurag Agrawal1 1Center of Excellence for Translational Research in Asthma and Lung Disease, CSIR- Institute of Genomics and Integrative Biology, New Delhi, 110025, India. 2Translational Health Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India. 3School of Life Sciences, Sambalpur University, Jyoti Vihar, Sambalpur, Orissa, 768019, India. 4Department of Respiratory Sciences, #211, Maurice Shock Building, University of Leicester, LE1 9HN 5Department of Biotechnology and Genetic Engineering, Islamic University, Kushtia- 7003, Bangladesh. +Contributed equally for this work. S-1 70 G1 S 60 G2/M 50 40 30 % of cells 20 10 0 CURI LPSI LPSCUR Figure S1: Effect of curcumin and/or LPS treatment on A549 cell viability A549 cells were treated with curcumin (10 µM) and/or LPS or 1 µg/ml for the indicated times and after fixation were stained with propidium iodide and Annexin V-FITC. The DNA contents were determined by flow cytometry to calculate percentage of cells present in each phase of the cell cycle (G1, S and G2/M) using Flowing analysis software. S-2 Figure S2: Total proteins identified in all the three experiments and their distribution betwee curcumin and/or LPS treated conditions. The proteins showing differential expressions (log2 fold change≥2) in these experiments were presented in the venn diagram and certain number of proteins are common in all three experiments. -
Enzymes Main Concepts: •Proteins Are Polymers Made up of Amino Acids
Biology 102 Karen Bledsoe, Instructor Notes http://www.wou.edu/~bledsoek/ Chapter 6, section 4 Topic: Enzymes Main concepts: • Proteins are polymers made up of amino acids. Enzymes are a category of proteins. • Enzymes are catalysts. They speed up the rate of a chemical reaction by reducing the activation energy, which is the energy needed to carry out the reaction. An example of a catalyst: if you put a lit match to a sugar cube, it’s hard to make the sugar catch fire. But if you rub a corner of the sugar cube with ash or charcoal, it catches more easily. The ash or charcoal acts as a catalyst. • Many important chemical reactions in living cells can happen spontaneously, but these reactions happen too rarely and too slowly to sustain life. Enzymes make the reactions happen more quickly and more often. • Some reactions happen too violently to support life. Sugar, when burned, released a lot of energy, but the energy is mostly heat. A rapid reaction like that would overheat our cells. Enzyme-controlled reactions can release energy from sugar in a way that captures most of the energy and loses less of the energy as heat, so that the energy is useful to the cell and does not overheat the cell. • The structure of enzymes allows them to carry out reactions. Each enzyme is shaped to carry out only one specific reaction. This is known as enzyme specificity. Amylase, for example, is an enzyme that breaks down starch into glucose. Amylase only breaks down starch; it does not break down any other molecule, nor does it build starch out of glucose. -
Supplemental Methods
Supplemental Methods: Sample Collection Duplicate surface samples were collected from the Amazon River plume aboard the R/V Knorr in June 2010 (4 52.71’N, 51 21.59’W) during a period of high river discharge. The collection site (Station 10, 4° 52.71’N, 51° 21.59’W; S = 21.0; T = 29.6°C), located ~ 500 Km to the north of the Amazon River mouth, was characterized by the presence of coastal diatoms in the top 8 m of the water column. Sampling was conducted between 0700 and 0900 local time by gently impeller pumping (modified Rule 1800 submersible sump pump) surface water through 10 m of tygon tubing (3 cm) to the ship's deck where it then flowed through a 156 µm mesh into 20 L carboys. In the lab, cells were partitioned into two size fractions by sequential filtration (using a Masterflex peristaltic pump) of the pre-filtered seawater through a 2.0 µm pore-size, 142 mm diameter polycarbonate (PCTE) membrane filter (Sterlitech Corporation, Kent, CWA) and a 0.22 µm pore-size, 142 mm diameter Supor membrane filter (Pall, Port Washington, NY). Metagenomic and non-selective metatranscriptomic analyses were conducted on both pore-size filters; poly(A)-selected (eukaryote-dominated) metatranscriptomic analyses were conducted only on the larger pore-size filter (2.0 µm pore-size). All filters were immediately submerged in RNAlater (Applied Biosystems, Austin, TX) in sterile 50 mL conical tubes, incubated at room temperature overnight and then stored at -80oC until extraction. Filtration and stabilization of each sample was completed within 30 min of water collection. -
Suzanne Pfeffer
July 2010 ASBMB PreSidentiAl PriMer: Suzanne Pfeffer American Society for Biochemistry and Molecular Biology AAdjuvdjuvAAntnt IImmunothermmunotherAApypy ususIIngng KKrnrn70007000 KRN7000 (α-Galactosyl Ceramide) Avanti Number 867000 Supplier: Funakoshi Co. Ltd. Hepatic metastasis is a major clinical problem in cancer treatment. We examined antitumor ac- tivity of alpha-galactosylceramide (KRN7000) on mice with spontaneous liver metastases of re- ticulum cell sarcoma M5076 tumor cells (spontaneous metastasis model). In this model, all mice that were s.c. challenged with one million tumor cells developed a solid s.c. mass by day 7 and died of hepatic metastases. In the current study, we administered 100 microg/kg of KRN7000 to the model mice on days 7, 11, and 15. This treatment suppressed the growth of established liver metastases and resulted in the prolongation of survival time. Fluorescence-activated cell sorter analysis of phenotypes of spleen cells, hepatic lymphocytes, and regional lymph node cells around the s.c. tumor revealed that CD3+NK1.1+ (NKT) cells increased in hepatic lym- phocytes of the KRN7000-treated mice. Cytotoxic activity and IFN-gamma production of hepatic lymphocytes were augmented in comparison with those of spleen cells and regional LN cells. At the same time, interleukin (IL)-12 production of hepatic lymphocytes was markedly enhanced. Neutralization of IL-12 using a blocking monoclonal antibody diminished the prolonged survival time. These results showed that the in vivo antitumor effects of KRN7000 on spontaneous liver metastases were dependent on the endogenous IL-12 production, where NKT cells in the liver are suggested to be involved. Adjuvant immunotherapy using KRN7000 could be a promising modality for the prevention of postoperative liver metastases. -
NIH Conflict of Interest Regs Revised
OCTOBEROCTOBER 2005 www.asbmb.org Constituent Society of FASEB AMERICAN SOCIETY FOR BIOCHEMISTRY AND MOLECULAR BIOLOGY NIH Conflict of Interest Regs Revised SEE PAGE 30 FOR NEW CLARA BENSON TRAVEL FELLOWSHIP AWARD Held in conjunction with EB2006 Custom Antibodies Your Way! Choose the protocol that is right for you! QwikScreen ™: 65 day, 2 rabbit protocol - 4 immunizations, 3 bleeds/rabbit (~100ml serum), customer supplied peptide/protein - Options: Peptide synthesis, immunograde Conjugation to carrier u ELISA u u Animal extensionsMS analysis $685 Standard: 80 day, 2 rabbit protocol - 5 immunizations, 5 bleeds/rabbit (~ 200ml ser Options: um), ELISA, customer supplied peptide/pr Peptide synthesis MS Check™ peptide sequence confirmation u HPLC purified peptide Affinity purification otein - Pinnacle: $975 u HPLC and MS analysis u Complete Affinity Purified Protocol- Animal extensions 2 rabbit pr 5 bleeds/rabbitotocol, (~ 200mlepitope serum), design, peptide PhD technical synthesis support, (up to 20mer),5 immunizations, HPLC purified to ~85%, 5+mg peptide to customer, ELISA, evaluation period, affinity purification, and morMS Check™ peptide sequence confirmationNo Hidden Charges! e… - Discounts for Multiple Protocols$1795 , Includes peptide sequencing by CID MS/MS– u Guaranteed Peptide Let our enthusiasm for scienceExpert workTechnical for SupportFidelity! P: 508.303.8222 www.21stcenturybio.com Toll-free: 877.217.8238 F: 508.303.8333 you! E: [email protected] www.asbmb.org AMERICAN SOCIETY FOR BIOCHEMISTRY AND MOLECULAR BIOLOGY OCTOBER