Microbiology and Computation
Analysis of the control and productivity of microorganisms
Revolution: genomics and bioinformatics
Does all that DNA explain Life?
First, let me tell you…..
Ever noticed?
The Cell: dead structures
The Cell: live processes
Main laws of biochemistry
In short: Life=f(processes(enzymes(genes)))
But…………...
Now important: Integrative Biology
What is BioComplexity?
Molecular Cell Physiology: where Life begins
Mathematical Biochemistry: how Life works
Analysis of the control and productivity of microorganisms: contents
How do enzymes communicate? Structure or reactivity?
How do enzymes communicate? Reactivity
Enzym kinetics
Implication of enzyme steady state
Michaelis constant, KM
Reaction rate:
Michaelis/Menten equation: [P]=0
Kinetics; zero product
Elasticity coefficient: extent of listening
Listening is not always the same: 1 or 0
Substrate elasticity zero product
Kinetics; product not zero
Cell at steady state
Enzyme systems at steady state
How important is each enzyme for steady state performance (flux, concentrations)?
Metabolic Control Analysis: Introduction
Criteria originally in use
Many enzymes when deleted eliminate the flux: essential
Problems arising
Metabolic Control Analysis take 1
Metabolic Control Analysis
Control Coefficient
Flux Control Coefficient
Metabolic Control Analysis take 2
Three ways to determine a control coefficient
PPT Slide
Surprise: nobody and everyone was right: distributed control
Energetics; uphill ATP synthesis driven by proton gradient
But is it really that important?
Measurement of flux control: Tunable promoter
Tunable promoter up front H+-ATPase operon
Example: Control by H+-ATPase: very small
Control by H+-ATPase: very small
Now we know how to measure the extent to which each enzyme controls the flux
How do enzymes communicate again?
Metabolic Control Analysis take 3
Metabolic Control Analysis: laws
The summation theorem for flux control
The connectivity theorem for flux control
Implication of summation plus connectivity theorem
The summation theorem for concentration control
The connectivity theorem for concentration control
Implications of summation plus connectivity theorem
Inversion law
Overexpress enzyme with high control coefficient, etc, etc (come and talk)
Rational drug design; Trypanosomes
Glycosome glycolysis
Control of glycolysis
Everybody was looking at the wrong place:
Control hierarchy: covalent modification/signal transduction
Hierarchical Control: Additional control!
Control hierarchy: gene expression
Democratic Hierarchy
DNA supercoiling
From structure to function: calculating structure dynamics of DNA in the cell
DNA gyrase reduces Linking number in steps of two
Hierarchical Control Analysis
In vitro gyrase dependent supercoiling depends on [ATP]/[ADP]
In vivo gyrase dependent supercoiling depends on [ATP]/[ADP]
In vivo supercoiling depends on gyrase activity
In vivo supercoiling depends on topoisomerase I activity
Metabolic Control Analysis take 4
Control distributed over levels
The end……….. ?? …. Or the beginning?
Email: HW@Bio.VU.NL
Home Page: http://www.bio.vu.nl/hwconf
Other information: Lecture held by Hans V. Westerhoff at the UvA course on Microbiology and Computation, May 18, 2001