Commemorating the 1913 Michaelismenten
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Single Molecule Enzymology À La Michaelis-Menten
Single molecule enzymology à la Michaelis-Menten Ramon Grima1, Nils G. Walter2 and Santiago Schnell3* 1 School of Biological Sciences and SynthSys, University of Edinburgh, Edinburgh, UK 2 Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA 3 Department of Molecular & Integrative Physiology, Department of Computational Medicine & Bioinformatics, and Brehm Center for Diabetes Research, University of Michigan Medical School, Ann Arbor, Michigan, USA * To whom the correspondence should be addressed. E-mail: [email protected] Review article accepted for publication to FEBS Journal special issue on Enzyme Kinetics and Allosteric Regulation 1 Abstract In the past one hundred years, deterministic rate equations have been successfully used to infer enzyme-catalysed reaction mechanisms and to estimate rate constants from reaction kinetics experiments conducted in vitro. In recent years, sophisticated experimental techniques have been developed that allow the measurement of enzyme- catalysed and other biopolymer-mediated reactions inside single cells at the single molecule level. Time course data obtained by these methods are considerably noisy because molecule numbers within cells are typically quite small. As a consequence, the interpretation and analysis of single cell data requires stochastic methods, rather than deterministic rate equations. Here we concisely review both experimental and theoretical techniques which enable single molecule analysis with particular emphasis on the major developments in the field of theoretical stochastic enzyme kinetics, from its inception in the mid-twentieth century to its modern day status. We discuss the differences between stochastic and deterministic rate equation models, how these depend on enzyme molecule numbers and substrate inflow into the reaction compartment and how estimation of rate constants from single cell data is possible using recently developed stochastic approaches. -
Covalent Modification of Reduced Flavin Mononucleotide in Type-2 Isopentenyl Diphosphate Isomerase by Active-Site-Directed Inhibitors
Covalent modification of reduced flavin mononucleotide in type-2 isopentenyl diphosphate isomerase by active-site-directed inhibitors Takuya Nagaia,1, Hideaki Unnob,1, Matthew Walter Janczakc,1, Tohru Yoshimuraa, C. Dale Poulterc,2, and Hisashi Hemmia,2 aDepartment of Applied Molecular Bioscience, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan; bDivision of Chemistry and Materials Science, Graduate School of Engineering, Nagasaki University, Bunkyo-machi, Nagasaki, Nagasaki 852-8521, Japan; and cDepartment of Chemistry, University of Utah, 315 South 1400 East RM2020, Salt Lake City, UT 84112 Contributed by C. Dale Poulter, October 11, 2011 (sent for review July 9, 2011) Evidence for an unusual catalysis of protonation/deprotonation by not detect signals for putative radical intermediates (9). Attempts a reduced flavin mononucleotide cofactor is presented for type-2 to inhibit the enzyme by incubation with a cyclopropyl analogue isopentenyl diphosphate isomerase (IDI-2), which catalyzes isomer- of IPP, designed to rearrange to a homoallylic structure by a ization of the two fundamental building blocks of isoprenoid bio- radical clock mechanism, were unsuccessful (12, 13). Instead, the synthesis, isopentenyl diphosphate and dimethylallyl diphosphate. analogue was an alternate substrate that isomerized to the cor- The covalent adducts formed between irreversible mechanism- responding DMAPP derivative without a cyclopropylcarbinyl- based inhibitors, 3-methylene-4-penten-1-yl diphosphate or 3-oxi- homoallyl radical rearrangement. ranyl-3-buten-1-yl diphosphate, and the flavin cofactor were inves- Mechanism-based inhibitors of IDI-1, which are activated by tigated by X-ray crystallography and UV-visible spectroscopy. Both protonation of epoxide and diene moieties in these compounds, the crystal structures of IDI-2 binding the flavin-inhibitor adduct – and the UV-visible spectra of the adducts indicate that the covalent also inactivate IDI-2 (12 15). -
Peptide Chemistry up to Its Present State
Appendix In this Appendix biographical sketches are compiled of many scientists who have made notable contributions to the development of peptide chemistry up to its present state. We have tried to consider names mainly connected with important events during the earlier periods of peptide history, but could not include all authors mentioned in the text of this book. This is particularly true for the more recent decades when the number of peptide chemists and biologists increased to such an extent that their enumeration would have gone beyond the scope of this Appendix. 250 Appendix Plate 8. Emil Abderhalden (1877-1950), Photo Plate 9. S. Akabori Leopoldina, Halle J Plate 10. Ernst Bayer Plate 11. Karel Blaha (1926-1988) Appendix 251 Plate 12. Max Brenner Plate 13. Hans Brockmann (1903-1988) Plate 14. Victor Bruckner (1900- 1980) Plate 15. Pehr V. Edman (1916- 1977) 252 Appendix Plate 16. Lyman C. Craig (1906-1974) Plate 17. Vittorio Erspamer Plate 18. Joseph S. Fruton, Biochemist and Historian Appendix 253 Plate 19. Rolf Geiger (1923-1988) Plate 20. Wolfgang Konig Plate 21. Dorothy Hodgkins Plate. 22. Franz Hofmeister (1850-1922), (Fischer, biograph. Lexikon) 254 Appendix Plate 23. The picture shows the late Professor 1.E. Jorpes (r.j and Professor V. Mutt during their favorite pastime in the archipelago on the Baltic near Stockholm Plate 24. Ephraim Katchalski (Katzir) Plate 25. Abraham Patchornik Appendix 255 Plate 26. P.G. Katsoyannis Plate 27. George W. Kenner (1922-1978) Plate 28. Edger Lederer (1908- 1988) Plate 29. Hennann Leuchs (1879-1945) 256 Appendix Plate 30. Choh Hao Li (1913-1987) Plate 31. -
Maud Menten, a Physician and Biochemist
Maud Menten Canadian medical researcher Maud Menten (1879-1960) has been called the "grandmother of biochemistry," a "radical feminist 1920s flapper," and a "petite dynamo." Not only was she an author of Michaelis-Menten equation for enzyme kinetics (like the plot in indigo in my portrait), she invented the azo-dye coupling for alkaline phosphatase, the first example of enzyme histochemistry, still used in histochemistry imaging of tissues today (which inspired the histology background of the portrait), and she also performed the first electrophoretic separation of blood haemoglobin in 1944! Born in Port Lambton, Ontario, she studied at the University of Toronto, earning her bachelor's in 1904, and then graduated from medical school (M.B., bachelor's of medicine) in 1907. She published her first paper with Archibald Macallum, the Professor of Physiology at U of T (who went on to set up the National Research Council of Canada), on the distribution of chloride ions in nerve cells in 1906. She worked a year at the Rockefeller Institute in New York, where along with Simon Flexner, first director of the Institute, she co-authored a book on radium bromide and cancer, the first publication produced by the Institute - barely 10 years after Marie Curie had discovered radium. She completed the first of two fellowships at Western Reserve University (now Case Western Reserve University), then she earned a doctorate in medical research in 1911 at U of T. She was one of the first Canadian women to earn such an advanced medical degree. She then moved to Berlin (travelling by boat, unfazed by the recent sinking of the Titanic) to work with Leonor Michaelis. -
Leonor Michaelis and Maud Leonora Menten Celebrating 100 Years of the Michaelis–Menten Equation
ARTICLE-IN-A-BOX Leonor Michaelis and Maud Leonora Menten Celebrating 100 years of the Michaelis–Menten Equation Leonor Michaelis was an honoured German biochemist and Maud Leonora Menten an honoured Canadian pathologist, during the nineteenth century. Though Michaelis sustained his interest in enzymology and biochemistry, Menten moved to pathology and became a renowned pathologist later in her career. The research collaboration of Michaelis and Menten was phenomenal resulting in the celebrated ‘Michaelis–Menten Equation’. Michaelis and Menten’s classic paper titled ‘Die Kinetik der Invertin wirkung’, published in Biochemische Zeitschrift in 1913 marks its centenary this year. This seminal paper which proved vital for the teaching of enzyme kinetics, was acknowledged with so much appreciation and attention that no textbook in biology for undergraduate and graduate students across the world is complete without a discussion of the Michaelis–Menten Equation. An earlier paper by Victor Henri and Brown lacked one important insight which was reported by Michaelis and Menten: that insight was the analysis of reaction in terms of the initial rate. Michaelis and Menten introduced the concept of measuring the initial activity of the enzyme by mixing it with substrate so that product accumulation would not inhibit the activity. Leonor Michaelis (1875–1949) Leonor Michaelis was born in Berlin, Germany on January 16, 1875. He graduated from the ‘humanistic’ Koellnisches Gymnasium in 1893. This gymnasium was special as unlike the other humanistic gymnasiums, it also included chemistry and physics labs which were not in general use and it was only the keen initiative of two professors that enabled interested students learn the subjects. -
Maud Leonora Menten
Regulars Past Times A woman at the dawn of biochemistry Maud Leonora Menten Athel Cornish-Bowden Ask an average biochemist who was the first to realize that variant proteins could be detected by (Bioénergétique et Ingénierie electrophoresis and sedimentation, and had used this understanding to recognize different forms of des Protéines, CNRS and haemoglobin, the reply would probably refer to Linus Pauling and his work on sickle cell disease. Yet, Aix-Marseille Université, although this work was certainly important, that would be the wrong answer, because Maud Leonora France) and John Lagnado Menten, who sometimes seems to be remembered for one paper only, had this idea several years (Honorary Archivist, the before him, and used it to recognize the differences between foetal and adult haemoglobin1. She was Biochemical Society) unfortunate, however, in that her paper appeared in war time, and was eclipsed a few years later by a far more high-profile study2. In 2013 we celebrate two important centenaries not only of Director, and later the person who appointed Leonor the admission of women to the Biochemical Society (why Michaelis to his position there. With Flexner and James W. did it take so long?), but also of the publication of a paper Jobling, she wrote a book (the first monograph emanating by Maud Menten, who was one of the first women to leave from the Rockefeller Institute) on the effects of radium her mark in biochemistry, with a paper that is cited more bromide on tumours of animals, published in 1910 – often in the 21st Century than it was in the 20th. -
The Biological Laboratory
LONG ISLAND BIOLOGICAL ASSOCIATION ANNUAL REPORT OF THE BIOLOGICAL LABORATORY COLD SPRING HARBOR LONG ISLAND, NEW YORK 1939 LONG ISLAND BIOLOGICAL ASSOCIATION INCORPORATED 1924 ANNUAL REPORT OF THE BIOLOGICAL LABORATORY FOUNDED 1890 FIFTIETH YEAR 1939 SCIENTIFIC ADVISORY COMMITTEE J. H. Bodine, Chairman,State University of Iowa Harold A. Abramson,College of Physicians and Surgeons, Columbia University Edgar Allen, Yale University,School of Medicine Stanley A. Cain, Universityof Tennessee Robert Chambers, WashingtonSquare College, New York University Harry A. Charipper,Washington Square College, New York University Kenneth S. Cole, College of Physiciansand Surgeons, Columbia University William H. Cole, Rutgers University Henry S. Conard, GrinnellCollege George W. Corner, Universityof Rochester, School of Medicine and Dentistry W. J. Crozier, Harvard University Charles B. Davenport, Carnegie Institution of Washington Alden B. Dawson, Harvard University S. R. Detwiler, College of Physicians and Surgeons,Columbia University Hugo Fricke, The Biological Laboratory Robert Gaunt, Washington Square College, New York University A. J. Grout, Newfane, Vt. Ross G. Harrison, Yale University Hans 0. Haterius, Wayne University, College of Medicine S.I. Kornhauser, University of Louisville Medical School Duncan A. Maclnnes, The Rockefeller Institute for Medical Research fHarold Mestre, Bard College Stuart Mudd, University of Pennsylvania, School of Medicine Hans Mueller, Massachusetts Institute of Technology J.S. Nicholas, Yale University W. J. V. Osterhout, The Rockefeller Institute for Medical Research Eric Ponder, The Biological Laboratory Asa A. Schaeffer, Temple University Herman T. Spieth, College of the City of New York 'Charles R. Stockard, Cornell University Medical College W. W. Swingle, Princeton University Ivon R. Taylor, Brown University Harold C. Urey, Columbia University H. -
Explicit Treatment of Non Michaelis-Menten and Atypical Kinetics in Early Drug Discovery
Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 8 October 2020 doi:10.20944/preprints202010.0179.v1 Explicit Treatment of Non Michaelis-Menten and Atypical Kinetics in Early Drug Discovery Bharath Srinivasan#,1 # Mechanistic Biology and Profiling, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK [email protected]; +44 7508382559 Abstract: Biological systems are highly regulated. They are also highly resistant to sudden perturbations enabling them to maintain the dynamic equilibrium essential for sustenance of life. This robustness is conferred by regulatory mechanisms that influence the activity of enzymes/proteins within their cellular context, to adapt to changing environmental conditions. However, the initial rules governing the study of enzyme kinetics were tested and implemented for mostly cytosolic enzyme systems that were easy to isolate and/or recombinantly express. Moreover, these enzymes lacked complex regulatory modalities. Now, with academic labs and pharmaceutical companies turning their attention to more complex systems (for instance, multi-protein complexes, oligomeric assemblies, membrane proteins and post-translationally modified proteins), the initial axioms defined by Michaelis- Menten (MM) kinetics are rendered inadequate and the development of a new kind of kinetic analysis to study these systems is required. The current review strives to present an overview of enzyme kinetic mechanisms that are atypical and, oftentimes, do not conform to the classical MM kinetics. Further, it presents -
Chemical Reactor Design
Chemical Reactor Design Youn-Woo Lee School of Chemical and Biological Engineering Seoul National University 155-741, 599 Gwanangro, Gwanak-gu, Seoul, Korea ywlee@snu. ac.kr http://sfpl. snu. ac. kr 第7章 化學反應裝置設計 Chemical Reactor Design Reaction Mechanisms , Pathways, Bioreactions and Bioreactors Seoul National University Objective Discuss the pseudo-steady-state-hypothesis and explain how it can be used to solve reaction engineering problems Write reaction pathways for complex reactions. Explain what an enzyme is and how it acts as a catalyst. Describe Michealis-Menten enzyme kinetics and rate law along with its temperature dependence. Discss h ow t o di stin gui sh th e diff er ent t ypes of enz yme inhibition. Discuss stages of cell growth and rate laws used to describe growth. Write material balances on cells, substrates, and products in bioreactors to size chemostats and plot concentration-time trajectoriesin batch reactors. Describe how physiologically-based pharmocokinetic models can be used to model alcohol metabolism. Seoul National University 7.1 Active Intermediates and Nonelementary Rate law • Elementary rate law - the reaction order of each species is identical with the stoichiometric coefficient of that species for the reaction as written n rA kC A • Non-elementary rate law - no direct correspondence between reaction order and stoichiometry 3 / 2 CH CHO CH + CO r kC 3 4 CH 3CHO CH 3CHO k C C 3/ 2 1 H 2 Br2 H2+Br+ Br2 2HBr rHBr CHBr k2CBr Seoul National University Non-elementary Reaction Non-elementary rate laws involve a number of elementary reactions and at least one active intermediate. -
Enzyme Kinetics at the Molecular Level∗
GENERAL ARTICLE Enzyme Kinetics at the Molecular Level∗ Arti Dua The celebrated Michaelis–Menten (MM) expression provides a fundamental relation between the rate of enzyme cataly- sis and substrate concentration. The validity of this classical expression is, however, restricted to macroscopic amounts of enzymes and substrates and, thus, to processes with negligi- ble fluctuations. Recent experiments have measured fluctu- ations in the catalytic rate to reveal that the MM equation, though valid for bulk amounts, is not obeyed at the molecu- Arti Dua is an Associate lar level. In this review, we show how new statistical measures Professor in the Indian of fluctuations in the catalytic rate identify a regime in which Institute of Technology Madras. She is a theoretical the MM equation is always violated. This regime, character- chemist, working in the area ized by temporal correlations between enzymatic turnovers, of stochastic reaction is absent for a single enzyme and is unobservably short in the dynamics and statistical classical limit. mechanics of complex fluids. 1. Classical Enzyme Kinetics Enzymes are biological catalysts that accelerate chemical reac- tions manyfold, without getting consumed in the catalytic pro- cess. Several biological processes involving the conversion of substrates to products, thus, rely crucially on the catalytic activity of enzymes. Specific enzymes control and regulate a wide range of life-sustaining processes that vary from digestion, metabolism, absorption, and blood clotting to reproduction. While specificity Keywords depends on the detailed chemical structure of enzyme proteins, Biological catalysts, enzymes, rate kinetics, stochastic enzyme the rate at which the enzymes carry out the catalytic conversion kinetics, Michaelis–Menten depends less on their chemical structure but more on the physical mechanism, enzymatic velocity, parameters, including the amounts of enzymes, substrates, tem- molecular noise. -
Die Kinetik Der Invertinwirkung Von L. Michaelis and Miss Maud L. Menten (Received 4 February 1913.) with 19 Figures in Text
Die Kinetik der Invertinwirkung Von L. Michaelis and Miss Maud L. Menten (Received 4 February 1913.) With 19 Figures in Text. The Kinetics of Invertase Action translated by Roger S. Goody1 and Kenneth A. Johnson2 The kinetics of enzyme3) action have often been studied using invertase, because the ease of measuring its activity means that this particular enzyme offers especially good prospects of achieving the final aim of kinetic research, namely to obtain knowledge on the nature of the reaction from a study of its progress. The most outstanding work on this subject is from Duclaux4), Sullivan and Thompson5), A.J. Brown6) and in particular V. Henri7). Henri’s investigations are of particular importance since he succeeded, starting from rational assumptions, in arriving at a mathematical description of the progress of enzymatic action that came quite near to experimental observations in many points. We start from Henri’s considerations in the present work. That we have gone to the lengths of reexamination of this work arises from the fact that Henri did not take into account two aspects, which must now be taken so seriously that a new investigation is warranted. The first point to be taken into account is the hydrogen ion concentration, the second the mutarotation of the sugar(s). The influence of the hydrogen ion concentration has been clearly demonstrated by the work of Sörensen8) and of Michaelis and Davidsohn9). It would be a coincidence if Henri in all his experiments, in which he did not consider the hydrogen ion concentration, had worked at the same hydrogen ion concentration. -
ADOLF BUTENANDT (1903–1995) Robert N. Proctor
Forschungsprogramm „Geschichte der Kaiser-Wilhelm-Gesellschaft im Nationalsozialismus“ Research Program “History of the Kaiser Wilhelm Society in the National Socialist Era” ADOLF BUTENANDT (1903–1995) NOBELPREISTRÄGER, NATIONALSOZIALIST UND MPG-PRÄSIDENT EIN ERSTER BLICK IN DEN NACHLASS Robert N. Proctor Ergebnisse 2 IMPRESSUM Ergebnisse. Vorabdrucke aus dem Forschungsprogramm „Geschichte der Kaiser-Wilhelm-Gesellschaft im Nationalsozialismus“ Herausgegeben von Carola Sachse im Auftrag der Präsidentenkommission der Max-Planck-Gesellschaft zur Förderung der Wissenschaften e. V. Alle Rechte vorbehalten. Copyright © 2000 by Robert N. Proctor Lektorat: Astrid Becker Redaktion: Christine Rüter Bezugsadresse: Forschungsprogramm „Geschichte der Kaiser-Wilhelm- Gesellschaft im Nationalsozialismus“ c/o Max-Planck-Institut für Wissenschaftsgeschichte Wilhelmstraße 44 D-10117 Berlin Tel.: 0049–(0)30–2 26 67–154 Fax: 0049–(0)30–2 26 67–333 Email: [email protected] Umschlaggestaltung: punkt 8, Berlin ([email protected]) INHALT Kurzfassung/Abstract 4 Schuld und Sühne 5 Historiographie und „die ganze Wahrheit“ 7 Der Mann und seine Partei 10 Blutforschung und die Zusammenarbeit mit der Luftwaffe 16 TBC-Abwehrforschung mit Verschuer und die Zusammenarbeit mit Hillmann 21 Die Nachkriegsverteidigung Verschuers 26 Butenandts Beziehung zu Neuberg 31 Saubere Wissenschaft – Schmutzige Politik 33 Quellenverzeichnis 36 Literaturverzeichnis 37 Personenregister 40 Autor 41 KURZFASSUNG/ABSTRACT Die Person Adolf Butenandts ist nicht unumstritten in der