1. Computer modeling of cellular processes
Glycolysis: a few reactions By
Raquell M. Holmes, Ph.D.
Boston University

2. Computational Biology
Computational Biology  Bioinformatics
More than sequences, database searches, and statistics.
A part of Computational Science
Using mathematical modeling, simulation and visualization
Complementing theory and experiment

3. Today’s journey Bioinformatics Metabolic behaviors
From protein sequence
Metabolic pathway databases
Metabolic behaviors
Computer modeling glycolysis

4. Pathway for discussion
Karp: Cell and Molecular Biology Textbook

5. Bioinformatics
Common starting point

6. Many types of Protein Databases
Sequence (103):
publication, organism, sequence type, function
Protein properties (80):
Motifs, active sites, individual families, localization
Structure (15)
Resolution, experiment type, type of chain, space group.
Why do we have so many databases of the same kind? So many types of data and lots of curation. For example, let’s look at the protein databases. For sequences without much additional information…we get 7 minimum fields desired.
Nucl. Ac. Res. 32, D3 2004

7. Generic Protein Seq. Record
Sequence: hexokinase
E.C. #:
Publication: Stachelek et al 1986
Organism: Yeast
Function: main glucose phosphorylating enzyme
Links: other databases or tools
Pre-determined Properties:
families, folds…
Swissprot example for enzyme.

8. What we learn from protein sequence?
Similarity searches :
Homology with other proteins
Conserved domains
Active sites
How do we find the related pathway?
Are there metabolism databases?

9. Databases on Molecular Networks
Metabolic Pathways from NAR (5):
EcoCyc:
Began with E. coli Genes and Metabolism
BioCyc includes additional genomes
KEGG:
Encyclopedia of genes and genomes
Others: WIT2, PathDB, UMBDD

10. Metabolism pathway databases
What is a metabolic pathway?
Contains a series of reactions.
Reactions: Substrate, product (metabolites), enzyme, co-factors.
Metabolism pathway databases
Search by name or sequence
Pathway, Compounds, Reactions, Genes

11. Example search results
KEGG: search by compound or enzyme by key word.
Glucose: 82 hits
1.cpd:C00029 UDPglucose; UDP-D-glucose; UDP-glucose; Uridine diophosphate glucose
2. cpd:C00031 D-Glucose; Grape sugar; Dextrose
3. cpd:C00092 D-Glucose 6-phosphate; Glucose 6-phosphate; Robison ester
…….
79. cpd:C11911 dTDP-D-desosamine; dTDP-3-dimethylamino-3,4,6-trideoxy-D-glucose
80. cpd:C11915 dTDP-3-methyl-4-oxo-2,6-dideoxy-L-glucose
81. cpd:C11922 dTDP-4-oxo-2,6-dideoxy-D-glucose
82. cpd:C11925 dTDP-3-amino-3,6-dideoxy-D-glucose
Grape sugar:
FORMULA C6H1206
NAME D-Glucose grape sugar Dextrose
List of reactions involving compound
List of enzymes acting on compound
Enzyme
Reaction
Pathway
Compounds
R0029
Map0010
C00031

12. Home page Navigation bar List of categories Compounds List of results
All-Carbohydrates
a sugar
a sugar phosphate
a sugar-1-phosphate
Aldonic-Acids
Carbohydrate-Derivatives
Carbohydrates
Disaccharides
Oligosaccharides
Polysaccharides
Fructans
Glycogens
Large-branched-glucans
Long-linear-glucans
Pectin
Short-glucans
Starch

13. KEGG: E.coli
EcoCyc: E.Coli

14. Summary I Protein ->enzyme->pathway database
Pathway Database Content:
Species specific (BioCyc), general (KEGG)
Known and proposed enzymes, co-factors, metabolites.
Searches return similar results (compounds, reactions…) with different appearance.

15. From Data to Dynamics Static Data What is the behavior of the pathway?
Expression data
Dynamics

16. Expression data KEGG: EcoCyc:
retrievable expression data sets
EcoCyc:
input expression data to view in relation to metabolic data.
Expression data is one way of viewing the behavior of a system.

17. Submitted by: Hirotada MORI
Organism: E.coli
Raw data

18. MicroArray Data: fold changes in expression Enzyme Aerobic Anaerobic
Hypothetical data
Enzyme
Aerobic
Anaerobic
hexokinase
++++
isomerase
---- ++
Changes in gene expression:
Single time point
Various conditions

19. Dynamics: Answering different questions
If glucose concentration is 300 mM outside of the cell,
How quickly is glucose converted to glucose 6-phosphate?
How does the concentration of glucose 6 phosphate change over time?

20. Yeast Glycolysis suspended immobile Liquid, flasks, temp, ph
Experiment:
Sample media or characterize cell content over time
Repeat under different conditions
immobile
Agar, temp, ph

21. Results may look like

22. Computer Modeling
Method for analyzing what we know about a biological process
Used to describe mechanisms behind changes
Determines what can be seen or predicted

23. Walking through a Computational Model
Concept Map
Factors and relationships between factors
Describe relationships mathematically
Solve equations: using computer tools
View and interpret results

24. Designing a dynamic experiment
What components are involved?
Glucose, glucose 6 phosphate, fructose 6 phosphate…
What chemical reactions involved?
Transport, chemical conversions…

25. Glycolysis: Concept Map
Often drawings, schematics or chemical reactions v1 v2 v3 v4
Glucose
6-phosphate
Fructose
6-phosphate
Glucose
Internal
Glucose
Ethanol
Cell

26. Examples of relationships
Glucose
6-phosphate
Fructose v1 v2
Internal
Glucose
[Glucose 6-phosphate] is determined by increase from Glucose conversion and decrease by conversion to Fructose 6-phosphate
Amount of glucose 6 phosphate= amount produced- amount converted

27. Designing a dynamic experiment
Describing relationship mathematically

28. Relationship in terms of rates of change
The rate of change of Glucose-6-phosphate (S2) is the rate of Glucose conversion (v1) minus
the rate of conversion (v2) to Fructose-6-phosphate.

29. Designing a dynamic experiment
Describing relationship mathematically
What rate laws are known to describe the enzymatic reaction?
Types of rate laws/kinetic models
Constant, mass action, michaelis menten…

30. Simplify
Glucose transport (v1)
Facilitated diffusion

31. Rate Equations Substrates Glucose: Glucose- 6-phosphate:
Rate constants
Enzyme1:
Enzyme2:
Mass action kinetics are used here to describe the enzymatic reactions.
This is a simplification of the enzyme kinetics for this example.

32. Initial conditions Concentrations of components Enzymatic rates
External glucose (i.e. 300mM)
Enzymatic rates
Rate constant k (i.e. 50mM/min)
Michaelis-Menten constants, Hill Coefficients

33. The model Glucose 6-phosphate Fructose v1 v2 Internal S1=300mM
Ordinary differential equation
Rate equations
Initial conditions
S1=300mM
k1=55mM/min
k2=9.8mM/min

34. Walking through a Computational Model
Concept Map
Factors and relationships between factors
Describe relationships mathematically
Solve equations: using computer tools
View and interpret results

35. Some Available Tools General Stella
Install
Mac or PC
Excel
Customized
GEPASI
Virtual Cell
Browser: Java
Concept mapping and system dynamics (changes over time).
Discrete events, algebraic equations
Biochemical kinetics and kinetic analyses.
Icon mapping, dynamics and space

36. Stella
Concept Map
Rules as math
Initial Conditions

37. GEPASI
Chemical
Equations
Math

38. Online Glycolysis models
Concept map
Math-rule
Initial conditions

39. Results
Fructose 6-phosphate
Glucose 6 phosphate

40. Conclusions… Model based discoveries in glycolysis::
Oscillations in concentrations of some but not all metabolites.
Control of process distributed throughout pathway
Development of theoretical models
Method integrates knowledge of pathway factors to examine pathway behaviors.

41. Examples of other models
Calcium dynamics: Wave patterns in neuronal cells
Virtual Cell
Receptor signaling: IgE triggering mast cells
Personal computer codes
Cell cycle regulation: length of wee 1 mutant cell divisions
Matlab, Mathematica, personal computer codes

43. Calcium dynamics in neuroblastoma cells

44. Modeling Requires formalizing assumptions Worst case scenario
Rate equations
Inclusion or exclusion from model
Worst case scenario
See what you believe
Best case scenario
See something unexplainable
Create new laboratory experiments