Computer modeling of cellular processesGlycolysis: a few reactionsByRaquell M. Holmes, Ph.D.Boston University

Computational BiologyComputational Biology BioinformaticsMore than sequences, database searches, and statistics.

A part of Computational ScienceUsing mathematical modeling, simulation and visualizationComplementing theory and experiment

Todays journeyBioinformaticsFrom protein sequenceMetabolic pathway databases

Metabolic behaviorsComputer modeling glycolysis

Pathway for discussionKarp: Cell and Molecular Biology Textbook

BioinformaticsCommon starting point

Many types of Protein DatabasesSequence (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.Nucl. Ac. Res. 32, D3 2004

Generic Protein Seq. RecordSequence: hexokinaseE.C. #: 2.7.1.1Publication: Stachelek et al 1986Organism: YeastFunction: main glucose phosphorylating enzymeLinks: other databases or toolsPre-determined Properties:families, foldsSwissprot example for enzyme.

What we learn from protein sequence?Similarity searches : Homology with other proteinsConserved domains Active sites

How do we find the related pathway?Are there metabolism databases?

Databases on Molecular NetworksMetabolic Pathways from NAR (5):EcoCyc:http://ecocyc.PangeaSystems.com/ecocyc/Began with E. coli Genes and MetabolismBioCyc includes additional genomesKEGG: http://www.genome.ad.jp/kegg/Encyclopedia of genes and genomesOthers: WIT2, PathDB, UMBDD

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

Example search results KEGG: search by compound or enzyme by key word.Glucose: 82 hits1.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-glucose80. cpd:C11915 dTDP-3-methyl-4-oxo-2,6-dideoxy-L-glucose 81. cpd:C11922 dTDP-4-oxo-2,6-dideoxy-D-glucose82. cpd:C11925 dTDP-3-amino-3,6-dideoxy-D-glucose Grape sugar:FORMULA C6H1206NAME D-Glucose grape sugar DextroseList of reactions involving compoundList of enzymes acting on compound

EnzymeReactionPathwayCompounds2.7.1.1R0029Map0010C00031

Home pageNavigation bar List of categoriesCompoundsList 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

KEGG: E.coliEcoCyc: E.Coli

Summary IProtein ->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.

From Data to DynamicsStatic Data

What is the behavior of the pathway?Expression dataDynamics

Expression dataKEGG: retrievable expression data setsEcoCyc: input expression data to view in relation to metabolic data.Expression data is one way of viewing the behavior of a system.

Raw dataSubmitted by: Hirotada MORIOrganism: E.coli

MicroArray Data: fold changes in expressionChanges in gene expression:Single time pointVarious conditionsHypothetical data

EnzymeAerobicAnaerobichexokinase++++++++isomerase----++

Dynamics:Answering different questionsIf 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?

Yeast GlycolysisLiquid, flasks, temp, phAgar, temp, phExperiment:Sample media or characterize cell content over time

Repeat under different conditions

Results may look like

adhoc

in first 10-15 minutes

Glucoserate14.5ethanol26.7

mMdt1

03000

1285.526.7

227153.4

3256.580.1

4242106.8

5227.5133.5

6213160.2

7198.5186.9

8184213.6

9169.5240.3

10155267

11140.5293.7

12126320.4

13111.5347.1

1497373.8

1582.5400.5

adhoc

00

00

00

00

00

00

00

00

00

00

00

00

00

00

00

00

ethanol

glucose

time

mM conc.

changing external concentrations

Chart1

300

285.5

271

256.5

242

227.5

213

198.5

184

169.5

155

140.5

126

111.5

97

82.5

68

53.5

39

24.5

external glucose

time (minutes)

Glucose (mM)

Glucose

stella1

constants and mass action

K*Cell

timeethanolglucosetimeethanolglucosetimeethanolglucosetimeethanolglucose

00300001000030000100

114.5285.5114.585.510285.51085.5

2292712297122927122971

343.5256.5343.556.5329256.532956.5

4582424584245824245842

572.5227.5572.527.5558227.555827.5

6872136871368721368713

7101.5198.571000787198.57870

811618481000811618481000

9130.5169.5910009116169.591000

1014515510100010145155101000

11159.5140.511100011145140.5111000

1217412612100012174126121000

13188.5111.513100013174111.5131000

14203971410001420397141000

15217.582.51510001520382.5151000

16232681610001623268161000

17246.553.51710001723253.5171000

18261391810001826139181000

19275.524.51910001926124.5191000

20290102010002029010201000

213000211000212900211000

223000221000223000221000

233000231000233000231000

243000241000243000241000

253000251000253000251000

263000261000263000261000

273000271000273000271000

283000281000283000281000

293000291000293000291000

303000301000303000301000

313000311000313000311000

323000321000323000321000

333000331000333000331000

343000341000343000341000

353000351000353000351000

363000361000363000361000

373000371000373000371000

383000381000383000381000

393000391000393000391000

Final3000Final1000Final3000Final1000

uptakeReg

Glucose 6 phoshpate balances to 0.5 after initial step regardless of concentration even at 300dosen't quite make sense

feedback=-2.1no feedback

timeglucoseethanolg6puptaketimeglucoseethanolg6puptaketimeglucoseethanolg6ptimeglucoseethanolg6puptake

03000014.3477503000100003000014.50300010014.5

1286.5212.980.513.4427081288.39111.110.513.4427081285.513.960.5414.51285.5113.960.5414.5

2273.0826.420.513.4427082274.94124.550.513.442708227128.460.5414.52271128.460.5414.5

3259.6439.860.513.4427083261.51380.513.4427083256.542.960.5414.53256.5142.960.5414.5

4246.1953.30.513.4427084248.06151.440.513.442708424257.460.5414.54242157.460.5414.5

5232.7566.750.513.4427085234.62164.880.513.4427085227.571.960.5414.55227.5171.960.5414.5

6219.3180.190.513.4427086221.17178.320.513.442708621386.460.5414.56213186.460.5414.5

7205.8693.630.513.4427087207.73191.770.513.4427087198.5100.960.5414.57198.5200.960.5414.5

8192.42107.070.513.4427088194.29205.210.513.4427088184115.460.5414.58184215.460.5414.5

9178.98120.520.513.4427089180.84218.650.513.4427089169.5129.960.5414.59169.5229.960.5414.5

10165.54133.960.513.44270810167.4232.090.513.44270810155144.460.5414.510155244.460.5414.5

11152.09147.40.513.44270811153.96245.540.513.44270811140.5158.960.5414.511140.5258.960.5414.5

12138.65160.850.513.44270812140.52258.980.513.44270812126173.460.5414.512126273.460.5414.5

13125.21174.290.513.44270813127.07272.420.513.44270813111.5187.960.5414.513111.5287.960.5414.5

14111.77187.730.513.44270814113.63285.870.513.4427081497202.460.5414.51497302.460.5414.5

1598.32201.170.513.44270815100.19299.310.513.4427081582.5216.960.5414.51582.5316.960.5414.5

1684.88214.620.513.4427081686.75312.750.513.4427081668231.460.5414.51668331.460.5414.5

1771.44228.060.513.4427081773.3326.190.513.4427081753.5245.960.5414.51753.5345.960.5414.5

1857.99241.50.513.4427081859.86339.640.513.4427081839260.460.5414.51839360.460.5414.5

1944.55254.940.513.4427081946.42353.080.513.4427081924.5274.960.5414.51924.5374.960.5414.5

2031.11268.390.513.4427082032.98366.520.513.4427082010289.460.5414.52010389.460.5414.5

2117.67281.830.513.4427082119.53379.960.513.4427082103000021040000

224.22295.270.513.442708226.09393.410.513.4427082203000022040000

23030000230400002303000023040000

24030000240400002403000024040000

25030000250400002503000025040000

26030000260400002603000026040000

27030000270400002703000027040000

28030000280400002803000028040000

29030000290400002903000029040000

30030000300400003003000030040000

31030000310400003103000031040000

32030000320400003203000032040000

33030000330400003303000033040000

34030000340400003403000034040000

35030000350400003503000035040000

36030000360400003603000036040000

37030000370400003703000037040000

38030000380400003803000038040000

39030000390400003903000039040000

Final03000Final04000Final03000Final04000

adhoc

in first 10-15 minutes

Glucoserate14.5ethanol26.7

mMdt1

03000

1285.526.7

227153.4

3256.580.1

4242106.8

5227.5133.5

6213160.2

7198.5186.9

8184213.6

9169.5240.3

10155267

11140.5293.7

12126320.4

13111.5347.1

1497373.8

1582.5400.5

adhoc

00

00

00

00

00

00

00

00

00

00

00

00

00

00

00

00

ethanol

glucose

time

mM conc.

changing external concentrations

Chart1

300

285.5

271

256.5

242

227.5

213

198.5

184

169.5

155

140.5

126

111.5

97

82.5

68

53.5

39

24.5

external glucose

time (minutes)

Glucose (mM)

Glucose in the exernal media

Chart2

0

14.5

29

43.5

58

72.5

87

101.5

116

130.5

145

159.5

174

188.5

203

217.5

232

246.5

261

275.5

290

ethanol

time (minutes)

ethanol (mM)

Ethanol

stella1

constants and mass action

K*Cell

timeethanolglucosetimeethanolglucosetimeethanolglucosetimeethanolglucose

00300001000030000100

114.5285.5114.585.510285.51085.5

2292712297122927122971

343.5256.5343.556.5329256.532956.5

4582424584245824245842

572.5227.5572.527.5558227.555827.5

6872136871368721368713

7101.5198.571000787198.57870

811618481000811618481000

9130.5169.5910009116169.591000

1014515510100010145155101000

11159.5140.511100011145140.5111000

1217412612100012174126121000

13188.5111.513100013174111.5131000

14203971410001420397141000

15217.582.51510001520382.5151000

16232681610001623268161000

17246.553.51710001723253.5171000

18261391810001826139181000

19275.524.51910001926124.5191000

20290102010002029010201000

213000211000212900211000

223000221000223000221000

233000231000233000231000

243000241000243000241000

253000251000253000251000

263000261000263000261000

273000271000273000271000

283000281000283000281000

293000291000293000291000

303000301000303000301000

313000311000313000311000

323000321000323000321000

333000331000333000331000

343000341000343000341000

353000351000353000351000

363000361000363000361000

373000371000373000371000

383000381000383000381000

393000391000393000391000

Final3000Final1000Final3000Final1000

uptakeReg

Glucose 6 phoshpate balances to 0.5 after initial step regardless of concentration even at 300dosen't quite make sense

feedback=-2.1no feedback

timeglucoseethanolg6puptaketimeglucoseethanolg6puptaketimeglucoseethanolg6ptimeglucoseethanolg6puptake

03000014.3477503000100003000014.50300010014.5

1286.5212.980.513.4427081288.39111.110.513.4427081285.513.960.5414.51285.5113.960.5414.5

2273.0826.420.513.4427082274.94124.550.513.442708227128.460.5414.52271128.460.5414.5

3259.6439.860.513.4427083261.51380.513.4427083256.542.960.5414.53256.5142.960.5414.5

4246.1953.30.513.4427084248.06151.440.513.442708424257.460.5414.54242157.460.5414.5

5232.7566.750.513.4427085234.62164.880.513.4427085227.571.960.5414.55227.5171.960.5414.5

6219.3180.190.513.4427086221.17178.320.513.442708621386.460.5414.56213186.460.5414.5

7205.8693.630.513.4427087207.73191.770.513.4427087198.5100.960.5414.57198.5200.960.5414.5

8192.42107.070.513.4427088194.29205.210.513.4427088184115.460.5414.58184215.460.5414.5

9178.98120.520.513.4427089180.84218.650.513.4427089169.5129.960.5414.59169.5229.960.5414.5

10165.54133.960.513.44270810167.4232.090.513.44270810155144.460.5414.510155244.460.5414.5

11152.09147.40.513.44270811153.96245.540.513.44270811140.5158.960.5414.511140.5258.960.5414.5

12138.65160.850.513.44270812140.52258.980.513.44270812126173.460.5414.512126273.460.5414.5

13125.21174.290.513.44270813127.07272.420.513.44270813111.5187.960.5414.513111.5287.960.5414.5

14111.77187.730.513.44270814113.63285.870.513.4427081497202.460.5414.51497302.460.5414.5

1598.32201.170.513.44270815100.19299.310.513.4427081582.5216.960.5414.51582.5316.960.5414.5

1684.88214.620.513.4427081686.75312.750.513.4427081668231.460.5414.51668331.460.5414.5

1771.44228.060.513.4427081773.3326.190.513.4427081753.5245.960.5414.51753.5345.960.5414.5

1857.99241.50.513.4427081859.86339.640.513.4427081839260.460.5414.51839360.460.5414.5

1944.55254.940.513.4427081946.42353.080.513.4427081924.5274.960.5414.51924.5374.960.5414.5

2031.11268.390.513.4427082032.98366.520.513.4427082010289.460.5414.52010389.460.5414.5

2117.67281.830.513.4427082119.53379.960.513.4427082103000021040000

224.22295.270.513.442708226.09393.410.513.4427082203000022040000

23030000230400002303000023040000

24030000240400002403000024040000

25030000250400002503000025040000

26030000260400002603000026040000

27030000270400002703000027040000

28030000280400002803000028040000

29030000290400002903000029040000

30030000300400003003000030040000

31030000310400003103000031040000

32030000320400003203000032040000

33030000330400003303000033040000

34030000340400003403000034040000

35030000350400003503000035040000

36030000360400003603000036040000

37030000370400003703000037040000

38030000380400003803000038040000

39030000390400003903000039040000

Final03000Final04000Final03000Final04000

Computer ModelingMethod for analyzing what we know about a biological process

Used to describe mechanisms behind changes

Determines what can be seen or predicted

Walking through a Computational Model

Concept MapFactors and relationships between factorsDescribe relationships mathematically

Solve equations: using computer toolsView and interpret results

Designing a dynamic experimentWhat components are involved?Glucose, glucose 6 phosphate, fructose 6 phosphate

What chemical reactions involved?Transport, chemical conversions

Glycolysis: Concept MapOften drawings, schematics or chemical reactionsGlucoseGlucose6-phosphateFructose6-phosphateInternalGlucoseEthanolv1v2v3v4Cell

Examples of relationshipsInternal Glucose[Glucose 6-phosphate] is determined by increase from Glucose conversion and decrease by conversion to Fructose 6-phosphateAmount of glucose 6 phosphate= amount produced- amount converted

Designing a dynamic experimentDescribing relationship mathematically

Relationship in terms of rates of changeThe 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.

Designing a dynamic experimentDescribing relationship mathematically

What rate laws are known to describe the enzymatic reaction?Types of rate laws/kinetic modelsConstant, mass action, michaelis menten

SimplifyGlucose transport (v1)Facilitated diffusion

Rate EquationsSubstratesGlucose: Glucose-6-phosphate:

Rate constantsEnzyme1:Enzyme2: Mass action kinetics are used here to describe the enzymatic reactions.

This is a simplification of the enzyme kinetics for this example.

Initial conditionsConcentrations of componentsExternal glucose (i.e. 300mM)

Enzymatic ratesRate constant k (i.e. 50mM/min)Michaelis-Menten constants, Hill Coefficients

The modelS1=300mMk1=55mM/mink2=9.8mM/minOrdinary differential equationRate equationsInitial conditions

Walking through a Computational Model

Concept MapFactors and relationships between factorsDescribe relationships mathematically

Solve equations: using computer toolsView and interpret results

Some Available ToolsGeneralStellaInstall Mac or PCExcelInstall Mac or PCCustomizedGEPASIInstall Mac or PCVirtual CellBrowser: JavaMac or PC

Concept mapping and system dynamics (changes over time).

Discrete events, algebraic equations

Biochemical kinetics and kinetic analyses. Icon mapping, dynamics and space

StellaConcept MapRules as mathInitial Conditions

GEPASIChemical EquationsMathhttp://www.gepasi.org/gepasi.html

Online Glycolysis modelshttp://jjj.biochem.sun.ac.za/database/Concept mapMath-ruleInitial conditions

ResultsGlucose 6 phosphateFructose 6-phosphate

ConclusionsModel based discoveries in glycolysis:: Oscillations in concentrations of some but not all metabolites. Control of process distributed throughout pathwayDevelopment of theoretical models

Method integrates knowledge of pathway factors to examine pathway behaviors.

Examples of other modelsCalcium dynamics: Wave patterns in neuronal cellsVirtual Cell

Receptor signaling: IgE triggering mast cellsPersonal computer codes

Cell cycle regulation: length of wee 1 mutant cell divisions Matlab, Mathematica, personal computer codes

Calcium dynamics in neuroblastoma cells

ModelingRequires formalizing assumptionsRate equationsInclusion or exclusion from modelWorst case scenarioSee what you believeBest case scenarioSee something unexplainable Create new laboratory experiments

Why do we have so many databases of the same kind? So many types of data and lots of curation. For example, lets look at the protein databases. For sequences without much additional informationwe get 7 minimum fields desired.