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A BioNetGen2 Tutorial Jim Faeder Theoretical Biology and Biophysics Group Los Alamos National Laboratory How to find BioNetGen• Web site is http://cellsignaling.lanl.gov• Web interface is athttp://cellsignaling.lanl.gov/bionetgen/bionetgen2.html• Send email to faeder@lanl.gov torequest an account, source code, or forother questions.Introduction to the GraphicalRepresentationSignaling proteins and theircomplexes are represented asGraphsA multi-subunit receptor~Y ~Y Component states~pY ~pYMoleculeComponentsFcεRIThe high affinityreceptor for IgEα β γβ γβ γA kinasetSH2 L~YL~pYLA~YAA~pYSykSyk!!!!A molecular complexLig%~P%~P !#~U $ $ !#~UFc!"RI Fc!"RItSH2L~UA~PSyk!!!!!!!!Patterns select groups ofchemical speciesA pattern that selects a receptorwith free ligand binding siteList of selected species "%~U !$~U "Unspecified Fc!#RIcomponents Fc!#RImay be in any binding or %~P !$~U "internal state.Fc!#RI...%~P $~U "Fc!#RItSH2L~UList contains 24 speciesA~Pfor 354 state model.Syk!!!!!!!!!!Another pattern exampleA pattern that selects a receptorwith bound ligand siteList of selected species $LigFilled circle Fc!"RI %~U #~U $indicates that component has Fc!"RIone or more ...unspecified bonds. LigThis species is %~P%~P !#~U $ $ !#~Uselected twice becuaseit contains two Fc!"RIFc!"RI Fc!"RI molecules that match... the pattern. Lig%~P !#~U $Fc!"RItSH2List contains ...

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A BioNetGen2 Tutorial

Jim Faeder

Theoretical Biology and
Biophysics Group
Los Alamos National Laboratory
How to find BioNetGen
• Web site is http://cellsignaling.lanl.gov
• Web interface is at
http://cellsignaling.lanl.gov/bionetgen/bionetgen2.html
• Send email to faeder@lanl.gov to
request an account, source code, or for
other questions.Introduction to the Graphical
RepresentationSignaling proteins and their
complexes are represented as
Graphs
A multi-subunit receptor
~Y ~Y Component states~pY ~pY
Molecule
Components
FcεRI
The high affinity
receptor for IgE
α β γ
β γ
β γA kinase
tSH2 L~Y
L~pYL
A~YA
A~pY
Syk
Syk!
!
!
!
A molecular complex
Lig
%~P%~P !#~U $ $ !#~U
Fc!"RI Fc!"RItSH2
L~U
A~P
Syk!
!
!
!
!
!
!
!
Patterns select groups of
chemical species
A pattern that selects a receptor
with free ligand binding site
List of selected species
"
%~U !$~U "
Unspecified
Fc!#RIcomponents
Fc!#RI
may be in any
binding or %~P !$~U "
internal state.
Fc!#RI
...
%~P $~U "
Fc!#RItSH2
L~U
List contains 24 species
A~P
for 354 state model.
Syk!
!
!
!
!
!
!
!
!
!
Another pattern example
A pattern that selects a receptor
with bound ligand site
List of selected species
$
Lig
Filled circle Fc!"RI %~U #~U $
indicates that
component has
Fc!"RIone or more ...
unspecified
bonds. Lig
This species is %~P%~P !#~U $ $ !#~U
selected twice becuase
it contains two Fc!"RI
Fc!"RI Fc!"RI molecules that match
... the pattern.
Lig
%~P !#~U $
Fc!"RItSH2List contains 324 species
L~Ufor 354 state model.
A~P
Syk!
!
!
!
!
!
!
!
Reaction rules generate
species and reactions
Ligand binding (48 reactions)
Rule
k" +Lig LigLig+
"kFc!#RI $Lig
Fc!#RI
Example
Lig
&~P !%~U "&~P !%~U " k2 +LigLig+
k Fc!#RIFc!#RI tSH2tSH2 $Lig
L~UL~U
A~PA~P
SykSyk!
!
!
!
Another rule example
Syk transphosphorylation (64 reactions)
Connectivity of receptors is suppressed
p
SS
"~P "~P"~P "~P
tSH2 tSH2 tSH2 tSH2
L~U L~UL~U L~U
A~U A~UA~U A~P
Syk Syk Syk Syk
Green = Enzyme Red = Substrate