Evolution and Molecules Basic questions of biology seen with - PowerPoint PPT Presentation

GGCUAUCGUACGUUUACCCAAAAGUCUACGUUGGACCCAGGCAUUGGACG G G A U C U G A C CC C A GG G G C U UGGA A U C UACG U G U C A G U AAG UC U A U C C C AA One error neighborhood – Surrounding of an RNA molecule in sequence and shape space

G GGCUAUCGUACGUUUACCC AAAGUCUACGUUGGACCCAGGCAUUGGACG GGCUAUCGUACGUUUACCCAAAAGUCUACGUUGGACCCAGGCAUUGGACG G G A U C U G A C CC C A GG G U G U G C A U A C G U A A A A G G C U A C U A C G U U C G U A C A G A C A G C G G C G U A G U G U A C G U C A A U C U A C G G C A C G U G G A C A G G C U G U U A G C U UGGA A U C UACG U G U C A G U AAG UC U A U C C C AA One error neighborhood – Surrounding of an RNA molecule in sequence and shape space

U C A G U G C G G U A C C G A U G U G U U U A A C C C G G A C C G C A AA G C A U G C G U U U A C G G GGCUAUCGUACGUUUACCC AAAGUCUACGUUGGACCCAGGCAUUGGACG GGCUAUCGUACGUUUACCCAAAAGUCUACGUUGGACCCAGGCAUUGGACG G G A U C U G A C G CC C A GG G C U UGGA A U C UACG U G U C A G U AAG UC U A U C C C AA One error neighborhood – Surrounding of an RNA molecule in sequence and shape space

U C A A G G C U U C G U C C C C A G G G A G G G G U A C C G G A C UGG U U G U U G A U U U U A A C C UACG U G C C G U G A C A C C G G C A U AAG UC AA G C U A A U U C G C G U C U C AA U A C G U G GGCUAUCGUACGUUUACCCAAAAGUCUACGUUGG CCCAGGCAUUGGACG GGCUAUCGUACGUUUACCC AAAGUCUACGUUGGACCCAGGCAUUGGACG GGCUAUCGUACGUUUACCCAAAAGUCUACGUUGGACCCAGGCAUUGGACG G G A U C U G A C G CC C A GG G C U UGGA A U C UACG U G U C A G U AAG UC U A U C C C AA One error neighborhood – Surrounding of an RNA molecule in sequence and shape space

U C A A G G C U U C G U C C C C A G G G A G G G G U A C C G G A C UGG U U G U U G A U U U U A A C C UACG U G C C G U G A C A C C G G C A U AAG UC AA G C U A A U U C G C G U C U C AA U A C G U G GGCUAUCGUACGUUUACCCAAAAGUCUACGUUGG CCCAGGCAUUGGACG GGCUAUCGUACGUUUACCC AAAGUCUACGUUGGACCCAGGCAUUGGACG GGCUAUCGUACGUUUACCCAAAAGUCUACGUUGGACCCAGGCAUUGGACG G G A U C U G A C C G CC C A GG GGCUAUCGUACGUUUACCCAAAAGUCUACGUUGGACCCAGGCA UGGACG G C U UGGA A U C UACG U G U C A A G C C U U AAG UC C C C AG G G A G U G A U G C G C C C AA C UGG A U A U C UACG U G U C A G U AAG UC U A U C C C AA One error neighborhood – Surrounding of an RNA molecule in sequence and shape space

U C A A G G C U U C G U C C C C A G G G A G G G G U A C C G G A C UGG U U G U U G A U U U U A A C C UACG U G C C G U G A C A C C G G C A U AAG UC AA G C U A A U U C G C G U C U C AA U A C G U G GGCUAUCGUACGUUUACCCAAAAGUCUACGUUGG CCCAGGCAUUGGACG GGCUAUCGUACGUUUACCC AAAGUCUACGUUGGACCCAGGCAUUGGACG GGCUAUCGUACGUUUACCCAAAAGUCUACGUUGGACCCAGGCAUUGGACG G G A U C U G A C C G G CC C A GG GGCUAUCGUACGUUUACCCAAAAGUCUACGUUGGACCCAGGCA UGGACG GGCUAUCGUACGU UACCCAAAAGUCUACGUUGGACCCAGGCAUUGGACG G C U UGGA A U A C G C G UACG U G G U C A U A G G C C A U C G U U AAG UC C C C AG G G A G U C G A U G G C U G G A C C C AA A C UGG A U C A U U ACC C C G UACG U G G U U G C A A G U U C U AAG UC G G U A C U U C A G C C AA U U A U C C C G C A A A A One error neighborhood – Surrounding of an RNA molecule in sequence and shape space

GGCUAUCGUA U GUUUACCCAAAAGUCUACGUUGGACCCAGGCAUUGGACG GGCUAUCGUACGUUUACCCAAAAGUCUACGUUGGACCCAGGCAUU A GACG GGCUAUCGUACGUUUAC U CAAAAGUCUACGUUGGACCCAGGCAUUGGACG GGCUAUCGUACG C UUACCCAAAAGUCUACGUUGGACCCAGGCAUUGGACG GGC C AUCGUACGUUUACCCAAAAGUCUACGUUGGACCCAGGCAUUGGACG GGCUAUCGUACGUUUACCCAAAAGUCUACGUUGGACCCAGGCAUUGGACG GGCUAUCGUACGU G UACCCAAAAGUCUACGUUGGACCCAGGCAUUGGACG GGCUA A CGUACGUUUACCCAAAAGUCUACGUUGGACCCAGGCAUUGGACG GGCUAUCGUACGUUUACCCAAAAGUCUACGUUGGACCC U GGCAUUGGACG GGCUAUCGUACGUUUACCCAAAAGUCUACGUUGGACCCAGGCA C UGGACG G G A U GGCUAUCGUACGUUUACCCAAAAGUCUACGUUGG U CCCAGGCAUUGGACG C U GGCUA G CGUACGUUUACCCAAAAGUCUACGUUGGACCCAGGCAUUGGACG G A GGCUAUCGUACGUUUACCC G AAAGUCUACGUUGGACCCAGGCAUUGGACG C G CC C A GG GGCUAUCGUACGUUUACCCAAAAG C CUACGUUGGACCCAGGCAUUGGACG G C U UGGA A U C UACG U G U C A G U AAG UC U A U C C C AA One error neighborhood – Surrounding of an RNA molecule in sequence and shape space

Number Mean Value Variance Std.Dev. Total Hamming Distance: 150000 11.647973 23.140715 4.810480 Nonzero Hamming Distance: 99875 16.949991 30.757651 5.545958 Degree of Neutrality: 50125 0.334167 0.006961 0.083434 Number of Structures: 1000 52.31 85.30 9.24 1 (((((.((((..(((......)))..)))).))).))............. 50125 0.334167 2 ..(((.((((..(((......)))..)))).)))................ 2856 0.019040 3 ((((((((((..(((......)))..)))))))).))............. 2799 0.018660 4 (((((.((((..((((....))))..)))).))).))............. 2417 0.016113 5 (((((.((((.((((......)))).)))).))).))............. 2265 0.015100 6 (((((.(((((.(((......))).))))).))).))............. 2233 0.014887 7 (((((..(((..(((......)))..)))..))).))............. 1442 0.009613 8 (((((.((((..((........))..)))).))).))............. 1081 0.007207 9 ((((..((((..(((......)))..))))..)).))............. 1025 0.006833 10 (((((.((((..(((......)))..)))).))))).............. 1003 0.006687 11 .((((.((((..(((......)))..)))).))))............... 963 0.006420 12 (((((.(((...(((......)))...))).))).))............. 860 0.005733 13 (((((.((((..(((......)))..)))).)).)))............. 800 0.005333 14 (((((.((((...((......))...)))).))).))............. 548 0.003653 15 (((((.((((................)))).))).))............. 362 0.002413 16 ((.((.((((..(((......)))..)))).))..))............. 337 0.002247 G G A U 17 (.(((.((((..(((......)))..)))).))).).............. 241 0.001607 C U 18 (((((.(((((((((......))))))))).))).))............. 231 0.001540 G A 19 ((((..((((..(((......)))..))))...))))............. 225 0.001500 C G CC C A GG 20 ((....((((..(((......)))..)))).....))............. 202 0.001347 G C U UGGA A U C UACG U G U C A G U AAG UC U A U C Shadow – Surrounding of an RNA structure in shape space – AUGC alphabet C C AA

1. Replication and mutation 2. Quasispecies and error thresholds 3. Fitness landscapes and randomization 4. Lethal mutations 5. Ruggedness of natural landscapes 6. Simulation of stochastic phenomena 7. Biology in its full complexity

Structure of Phenylalanyl-tRNA as andomly chosen target structure initial sequence

Evolution in silico W. Fontana, P. Schuster, Science 280 (1998), 1451-1455

Evolution of RNA molecules as a Markow process and its analysis by means of the relay series

Replication rate constant (Fitness) : f k = � / [ � + � d S (k) ] � d S (k) = d H (S k ,S � ) Selection pressure : The population size, N = # RNA moleucles, is determined by the flux: ≈ ± N ( t ) N N Mutation rate : p = 0.001 / Nucleotide � Replication The flow reactor as a device for studying the evolution of molecules in vitro and in silico .

In silico optimization in the flow reactor: Evolutionary Trajectory

28 neutral point mutations during a long quasi-stationary epoch Transition inducing point mutations Neutral point mutations leave the change the molecular structure molecular structure unchanged Neutral genotype evolution during phenotypic stasis

Randomly chosen initial structure Phenylalanyl-tRNA as target structure

Evolutionary trajectory Spreading of the population on neutral networks Drift of the population center in sequence space

Spreading and evolution of a population on a neutral network: t = 150

Spreading and evolution of a population on a neutral network : t = 170

Evolution and Molecules Basic questions of biology seen with - PowerPoint PPT Presentation

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