文档介绍：Biomolecular Processes as putation: Modeling Molecular Processes in the p-calculus Process Algebra
Intracellular biochemical processes
Metabolic pathways
Signal transduction
Transcriptional regulation
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Signal transduction (ST) pathways
Pathways of molecular interactions that munication between the cell membrane and intracellular end-points, leading to some change in the cell.
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Modular at domain, component and pathway level
MAPKKK
MAPKK
MAPK
Multiple connections:
feedback, cross talk
G protein receptors
Cytokine receptors
DNA damage, stress sensors
RTK
RTK
RhoA
GCK
RAB
PAK
RAC/Cdc42
?
JNK1/2/3
MKK4/7
MEKK1,2,3,4
MAPKKK5
C-ABL
HPK
P38 a/b/g/d
MKK3/6
MLK/DLK
ASK1
Gg
Gb
Ga
Ca+2
PYK2
Cell division, Differentiation
Rsk, MAPKAP’s
Kinases, TFs
Inflammation, Apoptosis
TFs, cytoskeletal proteins
PP2A
MOS
TLP2
PKA
GAP
GRB2
SHC
SOS
RAS
ERK1/2
MKK1/2
RAF
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What is missing from the picture?
Information about
Dynamics
Molecular structure
Biochemical detail of interaction
The Power to
simulate
pare
Formal semantics
Script:
Characters +Plot
Movie
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Our Goal
A formal representation language for molecular processes
Powerful and essential
Dynamic and executable (simulation)
Analyzable (comparative and functional studies)
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The molecule as putational process
Represent a structure by its potential behavior: by the process in which it can participate
Example: An enzyme as the enzymatic reaction process, in which it may participate
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Example: ERK1 Ser/Thr kinase
Binding MP1 molecules
Regulatory T-loop: Change conformation
Kinase site: Phosphorylate Ser/Thr residues (PXT/SP motifs)
ATP binding site: Bind ATP, and use it for phsophorylation
Binding to substrates
Structure
Process
COOH
Nt lobe
Catalytic core
Ct lobe
NH2
p-Y
p-T
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The correspondence between molecular putational processes
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The p-calculus
A program specifies work of interacting processes
Processes are defined by their munication ac