http:// EnzKin.de.vu

Enzyme Kinetics: Personal Views, Program, Scriptum & Postscriptum

Sidney A. Bernhard
Obituary:
Recollections of Sidney Bernhard (1927-1988) M. F. Dunn and G. L. Rossi (1990) Trends Biochem. Sci. 15, 84-85

As a newcomer at Caltech, I was provided with all the technical support for up-to-date structural studies on proteins. In the center of interest were F-19 labelling techniques for investigating symmetry relations of oligomeric proteins (hemoglobin) and enzymes by NMR . My model was the good old glycolytic enzyme glyceraldehyde-3-phosphate-dehydrogenase (GPDH / GAPDH, ref. 9, 10).

Structure is one thing, function another. Trying to perform enzyme kinetics, I felt lonely at this world-renowned Institute. This changed when Sidney Bernhard, Professor at the University of Orgegon (Eugene) , was invited for a seminar and until he and Rick Dahlquist enabled my visit at “UofO” from January to March 1974. From thereon the (then controversial) phenomenon of “half-of-the-sites reactivity” and/or “pre-existing asymmetry” of homo-oligimeric enzymes was in the center of our interest (ref. 10) - forcefully supported by X-ray analyses performed by Michael Rossmann´s group at Purdue University. I realized the unique chance not only to learn about enzyme kinetics but also to make use of the newly acquired “Schoeffel” fluorescence machine (ref. 4-8, 23). More than anything else I got a deep appreciation for quantitative approaches and Bernhard´s views on “The Structure and Function of Enzymes” (W. A. Benjamin, Inc. NY 1968 “...We do not imagine a program lacking in the subject matter of ´classical biology`. Rather we are thinking of a program in which the teaching of many of the more classical biological subjects will be firmly based on the student´s background in biochemistry and molecular biology”).

From the Annals: Course BC2/BB3
“Enzymkinetik und -Mechanismus”

1 - SS1976

12 - SS1984

24 - WS1995

2 - WS76/77

13 - SS1985

25 - WS1996

3 - SS1977

14 - SS1986

26 - WS1997

4 - WS77/78

15 - SS1987

27 - WS1998

5 - SS1978

16 - SS1988

28 - WS1999

6 - WS78/79

17 - SS1989

29 - WS2000

7 - SS1980

18 - SS1990

30 - WS2001

8 - WS80/81

20 - SS1991

31 - WS2002

9 - SS1981

21 - WS1992

32 - WS2003

10 - SS1982

22 - WS1993

33 - WS2004

11 - SS1983

23 - WS1994

34 - WS2005

Probe des Ernstfalls!

 

With this in mind I joined the GMBF (Gesellschaft für Molekularbiologische Forschung, later GBF) in 1974. Even in my new field, the structure and interactions within nucleosomal core particles, I found many applications for the concepts deriving from enzyme kinetics. To spread these approaches, I held a first course in “Enzyme Kinetics and -Mechanisms” for students of the TU Braunschweig in 1976 and I have continued to do so ever since. While data evaluation by ´paper-and-pencil´ was still common, mostly using the more than popular ´Lineweaver-Burk´  formalism, a very radical change occured when I came across Ron G. Duggleby´s paper “A NONLINEAR REGRESSION PROGRAM FOR SMALL COMPUTERS” (Analyt. Biochem 1109, 9-18. 1981) written in plain “BASIC”. Being the proud owner of a home computer (the classic Sinclair ZX81), I immediately realized the strength of this approach and introduced both (the ZX and the program) into the course - under the mild laughter of my students. Later on and with the intense help of Ron I was able to adopt and extend the program always accompanied by his great expertise and sense of humor. Although they date back to the past ages of DOS, they are still running on Windows XP and I am very willing to share them for teaching or self-education (just mail or e-mail). Some functions can be activated from the menu below. Feed-back will always be welcome!

 

 

 

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You may try to use programs  1, 2 , 3 , 4, 5 , 6 and 7 (just click). Essentials are found in a WORD-file and more in our manuscript.

Enzyme Kinetics and Biochemistry: More Opinions

I became an enzyme kineticist by accident when, as a young assistant professor, I was asked to teach a first-year graduate level course in biochemistry. Kinetics was one of the topics, and I rapidly discovered that the field was in a very unsatisfactory state. I began to play with equations, and this led to the theoretical papers in Biochimica et Biophysica Acta in 1963, the first of which was an earlier Citation Classic. As we began to do experimental kinetics, it became obvious that statistical analysis of the data was needed, and I wrote FORTRAN programs that made least-squares fits to the rate equations using the method of Wilkinson. ....It feels good to know that programs written in a 1963 version of FORTRAN are still useful and are the standard tools for statistical analysis of enzyme kinetic data over 20 years later. W. Wallace Cleland, December 14, 1984

Die Enzymkinetik ist ein in allgemeingültigen Gesetzmäßigkeiten, Begriffen und Theorie abgeschlossener Teil der Biochemie; Fortschritte sind daher in diesem klassischen Haus nicht zu erwarten, nur Ausbauten. So haben die Methoden der Auswertung und Datenverarbeitung durch elektronische Schnellrechner Routine gewonnen. Statistik ist keine Mühsal mehr sondern nur einen Knopfdruck weit entfernt......die zitierte Literatur geht in Einzelfällen bis in die neuere Zeit, aber man sieht doch, dass die Enzymkinetik ihren Höhepunkt in der vorigen Generation hatte - jetzt bewährt sie sich in der Praxis und hat dadurch eine hoffnungsvolle Renaissance.
Lothar Jänicke (1994) zu “
Enzymkinetik - Theorie und Methoden” von Hans Bisswanger; VCH 1994; N 3-527-30032-5 - gleichzeitig (m)eine Literaturempfehlung

I have been interested in enzyme and enzyme kinetics ever since I got my first job (1966), working as a research assistant in the food industry. We were supposed to find a way of stopping frozen potatoes turning strange colours when they thawed out. My boss thought it had something to do with polyphenol oxidase. I didn't agree, but I got to play with an enzyme and haven't really stopped playing since.  (Ronald Duggleby)

When reviewing a book, one feels rather exposed; without the safety of anonymity, it is tempting to say nice things. Who knows when the book’s author might review one of your papers or grants; best to play safe and be complimentary, eh? Fortunately, Cornish-Bowden’s recently revised “Fundamentals of Enzyme Kinetics” allows me to offer praise while retaining my self respect, for this is a truly excellent book.... I have not compared this book with the previous edition, mainly because my copy of that book was borrowed (permanently) by a person unknown. This is probably an indication of the value of the previous edition. I shall be guarding my copy of the present book more carefully. Ronald Duggleby, Department of Biochemistry and Molecular Biology, The University of Queensland, Brisbane Qld 4072, Australia in Protein Science 5, 181,1996

Ein Biologe ohne enzymkinetische Grundkenntnisse ist wie ein Haus ohne Fundament...
Leopold Flohé (zwischen Tür und Angel, 2000)

 

 Enzyme Kinetics: Postscriptum

 After almost thirty years, our course on “Enzyme Kinetics and -mechanism” will be discontinued in its original form due to many reorganizations and the introduction of Bachelor Courses in Biology and Biotechnology. This happens at a time when many pieces of the traditional equipment (Berthold Luminometer, Eppendorf Fluorimeter) signal their age. The course will probably be condensed and it is my impression that only a fraction of the experimental approaches will have a chance to survive. While I will continue to incorporate this traditional field into my lectures “Introduction to Biochemistry”, the experimental setup will be given into other hands together with my sincere offer to provide any advice I can - including the nonlinear regression programs - to any colleague worldwide who might be interested. Another sources of information (in German language) about the subject is “Wikipedia”:

Allosterie, Cori-Zyklus, Crabtree-Effekt, Energieladung, Enzymaktivität und katalytische Effizienz, Enzymhemmung, Enzymkinetik, exergon, Fließgleichgewicht, Freie Enthalpie, Glucokinase, Gluconeogenese, Glykolyse (Mitw), Glyoxylat-Zyklus, Gruppenübertragungspotential, Isoenzym, Katalase, Kooperativität, Mehrsubstratreaktion, Methode der kleinsten Quadrate (Abschnitt "Enzymkinetik"), Michaeliskonstante, Michaelis-Menten-Theorie, Multienzymkomplexe, Oxalessigsäure, Pasteur-Effekt, Phosphofructokinase, Pyruvat (Mitw.), Redox-Potential, Regressionsanalyse, second Messenger, Sidney A. Bernhard, Substratzyklus, Wechselzahl

Juergen Bode, December 17, 2005
 

Background picture to this site: how identical “protomers” can adopt non-identical structures in space - pseudo-isologous binding of domains in the formation of dimers  (Sidney Bernhard, 1974)

 

bode.juergen@mh-hannover.de
juergenbode@gmx.de

Semester