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Mechanisms of molecular cooperation Peter Schuster Institut fr - - PowerPoint PPT Presentation
Mechanisms of molecular cooperation Peter Schuster Institut fr - - PowerPoint PPT Presentation
Mechanisms of molecular cooperation Peter Schuster Institut fr Theoretische Chemie, Universitt Wien, Austria and The Santa Fe Institute, Santa Fe, New Mexico, USA Homo Sociobiologicus Evolution of human cooperation
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Web-Page for further information: http://www.tbi.univie.ac.at/~pks
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1977 1988 1971
Chemical kinetics of molecular evolution
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1. Cyclic reaction networks ¨ catalysts
- 2. Cyclic catalytic networks ¨ autocatalysts
- 3. Cyclic autocatalytic networks ¨ hypercycles
- 4. Neutrality – a source for coexistent competitors
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- 1. Cyclic reaction networks ¨ catalysts
- 2. Cyclic catalytic networks ¨ autocatalysts
- 3. Cyclic autocatalytic networks ¨ hypercycles
- 4. Neutrality – a source for coexistent competitors
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The Bethe - vonWeizsäcker catalytic cycle ist responsible – in part – for the energy production in massive stars.
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The tricarboxylic acid or citric acid cycle is fuelling the metabolic reactions of the cell.
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The citric acid
- r Krebs cycle
(enlarged) The reaction network of cellular metabolism published by Boehringer-Mannheim.
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A B C D E F G H I J K L 1
Biochemical Pathways
2 3 4 5 6 7 8 9 10
The reaction network of cellular metabolism published by Boehringer-Mannheim.
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1. Cyclic reaction networks ¨ catalysts
- 2. Cyclic catalytic networks ¨ autocatalysts
- 3. Cyclic autocatalytic networks ¨ hypercycles
- 4. Neutrality – a source for coexistent competitors
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Complementary () replication of RNA as an example
- f an autocatalytic cycle.
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A synthetic oligopeptide ligase becomes a replicator for E = P
- K. Severin, D.H. Lee, A.J. Kennan, M.R. Ghadiri, Nature 389, 706-709, 1997
D.H. Lee, J.R. Granja, J.A. MartinezK. Severin, M.R. Ghadiri, Nature 382, 525-528, 1996
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Cross-catalysis of peptide replicators
D.H. Lee, K. Severin, Y. Yokobayashi, M.R. Ghadiri, Nature 390, 591-594, 1997
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A chiroselective peptide replicator
- A. Saghatelian, Y. Yokobayashi, K. Soltani, M.R. Ghadiri, Nature 409, 797-801, 2001
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Cross-catalysis of two RNA enzymes leads to self-sustained replication
Tracey A. Lincoln, Gerald F. Joyce, Science 323, 1229-1232, 2009
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Exponential growth levels off when the reservoir is exhausted (l.h.s.). RNA production in serial transfer experiments (r.h.s.)
Tracey A. Lincoln, Gerald F. Joyce, Science 323, 1229-1232, 2009
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RNA evolution of recombinant replicators
Tracey A. Lincoln, Gerald F. Joyce, Science 323, 1229-1232, 2009
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1. Cyclic reaction networks ¨ catalysts
- 2. Cyclic catalytic networks ¨ autocatalysts
- 3. Cyclic autocatalytic networks ¨ hypercycles
- 4. Neutrality – a source for coexistent competitors
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Hypercycles with one and two members are common in nature.
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Hypercycle dynamics for n=3
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Hypercycle dynamics for n=4
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Hypercycle dynamics for n=6
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1. Cyclic reaction networks ¨ catalysts
- 2. Cyclic catalytic networks ¨ autocatalysts
- 3. Cyclic autocatalytic networks ¨ hypercycles
- 4. Neutrality – a source for coexistent competitors
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Chemical kinetics of replication and mutation as parallel reactions
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A fitness landscape including neutrality
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Motoo Kimura
Is the Kimura scenario correct for frequent mutations?
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5 . ) ( ) ( lim
2 1
= =
→
p x p x
p
dH = 1
a p x a p x
p p
− = =
→ →
1 ) ( lim ) ( lim
2 1
dH = 2 dH ≥3
1 ) ( lim , ) ( lim
- r
) ( lim , 1 ) ( lim
2 1 2 1
= = = =
→ → → →
p x p x p x p x
p p p p
Random fixation in the sense of Motoo Kimura Pairs of genotypes in neutral replication networks
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Neutral network: Individual sequences n = 10, = 1.1, d = 1.0
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Consensus sequence of a quasispecies of two strongly coupled sequences of Hamming distance dH(Xi,,Xj) = 1.
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Neutral network: Individual sequences n = 10, = 1.1, d = 1.0
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Consensus sequence of a quasispecies of two strongly coupled sequences of Hamming distance dH(Xi,,Xj) = 2.
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N = 7 Neutral networks with increasing : = 0.10, s = 229
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N = 24 Neutral networks with increasing : = 0.15, s = 229
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N = 70 Neutral networks with increasing : = 0.20, s = 229
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JN1LH
1D 1D 1D 2D 2D 2D R R R
G GGGUGGAAC GUUC GAAC GUUCCUCCC CACGAG CACGAG CACGAG
- 28.6 kcal·mol
- 1
G/
- 31.8 kcal·mol
- 1
G G G G G G C C C C C C A A U U U U G G C C U U A A G G G C C C A A A A G C G C A A G C /G
- 28.2 kcal·mol
- 1
G G G G G G GG CCC C C C C C U G G G G C C C C A A A A A A A A U U U U U G G C C A A
- 28.6 kcal·mol
- 1
3 3 3 13 13 13 23 23 23 33 33 33 44 44 44
5' 5' 3’ 3’
J.H.A. Nagel, C. Flamm, I.L. Hofacker, K. Franke, M.H. de Smit, P. Schuster, and C.W.A. Pleij. Structural parameters affecting the kinetic competition of RNA hairpin formation. Nucleic Acids Res. 34:3568-3576, 2006.
An RNA switch
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A ribozyme switch
E.A.Schultes, D.B.Bartel, Science 289 (2000), 448-452
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Two ribozymes of chain lengths n = 88 nucleotides: An artificial ligase (A) and a natural cleavage ribozyme of hepatitis--virus (B)
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The sequence at the intersection: An RNA molecules which is 88 nucleotides long and can form both structures
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Two neutral walks through sequence space with conservation of structure and catalytic activity
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Web-Page for further information: http://www.tbi.univie.ac.at/~pks
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