Transcript pdb-d.eng.uiowa.edu

Pathways
Prediction and analysis
12-05-01
What is a pathway?


A series of interconected enzymatic steps
linked by the production of intermediates that
are used in the next enzymatic step (Note
this definition will change)
May also include signaling pathways as well
were one input may cause several effects
Why is it good to find pathways?


Better understand the physiology of the
organism
Predict the effect of a drug
 Predict
the weaknesses or side effects of a drug
 Predict
good or bad drug combinations

Understand disease processes

Gene function assignment

Make a “perfect” simulation of cellular
function to use as an experimental model
A high level of understanding

Many tools “feed” into this understanding
 Microarrays
 Homology
tools (BLAST, alignments COGS)
 Biochemical
 Genomic
literature
sequence


Any holes in these tools lead to problems in
the pathway analysis
A complex problem
 35,000
genes either on or off (huge
simplification!!!!) would have 2^35,000 solutions
 Things
can be simplified by grouping and finding
key genes which regulate many other genes and
genes which may only interact with on other
gene
 Lots
of subtile interactions
Two ways of looking at the
problem

Top down or bottom up
 Either
look at the whole organism and abstract
large portions of it
 Or
try to understand each small piece and then
after understanding every small piece assemble
into the whole
Bottom up is traditionally how it is
done
 You
would study a pathway in detail not worrying
about how that pathway might interact with other
elements in the cell.
 You
would strive to understand a gene or
pathway in great detail, eventually you might
extend this knowledge to other organisms and
compare and contrast.

With top down you need other tools...
Graph theory, networks

Two types of networks
 Exponential
and scale
free
 Most
cellular networks
are scale free
 It
makes the most
sense to study the
interactions of the
central nodes not the
outer nodes
A better definition of a pathway:

Voet and Voet say:a series of consecutive
enzymatic reactions that produce specific
products.
 Does
this include pathways that feed into this
pathway or branches to the pathway or .....

A more rigorous definition is needed
 A set
of pathways could be defined as the
possible routes through a “black box” given a set
of enzymes and metabolic inputs
Elementary modes

A minimal set of enzymes that could operate
at steady state with the enzymes weighted by
the relative flux the need to carry for the node
to function
 If
one enzyme is removed the steady state would
be destroyed
How to transform this
Into this...
Several methods for doing this:
Steps for reducing the matrix:

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Left hand side metabolites
Right hand side keeps
track of the origin

Top reversable

Bottom irreversable
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Linear combination is
done to further reduce the
set
Different types go to
irreversable
00100|1000
0-1 0 2 0 | 0 1 0 0
____________________
0 0 0-1 0 | 0 0 10
10000|0001
Metatool


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A program to do this for you:
http://www2.bioinf.mdcberlin.de/metabolic/metatool/
Download the program and the example.dat
file

Try to compile with “gcc meta*.c”

Fix the header
Cogs

What is COGS
 http://www.ncbi.nlm.nih.gov/COG/
 Basically
a method for finding orthologous
proteins from fully sequenced genomes by using
a cross species comparison.
 What
does this have to do with pathways?
Databases of enzymatic reactions



http://www.genome.ad.jp/kegg/ is a good
starting place
EMP and http://www.expasy.ch/enzyme/ are
other good places to look
These can also be good places to look to get
overviews of unfamilar pathways or reactions
rather than a biochem textbook
EC numbers

EC Enzyme commision number
 1.1.1.49
= Glucose-6-phosphate 1dehydrogenase
 Hierarchal
assignment
1.x.x.x = Oxidoreductases
 1.1.x.x = Acting on the CH-OH group of donors
 1.1.1.x = With NAD or NADP as acceptor
 1.1.1.49 = using glucose-6-phosphate as a donor

 Unifies
and codifies enzyme nomenclature
Http://www.chem.qmw.ac.uk/iubmb/enzyme/index.
html