1. Wrong assumptions and misinterpretations in explanations of biological models, phenomena and processes Jacek Leluk ICM UW or Is biologist logical, and computer scientist alive?

2. How is it, that your genome is in 98% the same as genome of chimpanzee and only in 50% as your own father’s genome? "O składności członów człowieczych" Dlaczego ptacy mleka nie dają? Bo musiałyby mieć cyce, które by im wadziły ku lataniu. Andrzej z Kobylina (XVI w.)

3. Is biology „bilogical”? Nomenclature chaos: Mitochondria or chondriosomes? Is papain a proteolytic enzyme? definition of identity, similarity an homology Misinterpretaion: Amino acid sequence of gene? Why squash inhibitors are inhibitors? Is wheat aglutinin to aglutinate rabbit red cells? Incomplete knowledge Stochastic index matrices Statistical description of biological processes

4. The problem of terminology BPTI - Basic Pancreatic Trypsin Inhibitor - Bovine Pancreatic Trypsin Inhibitor - Basic Protein Trypsin Inhibitor PAM - Point Accepted Mutations - Percent Accepted Mutations Kunitz trypsin inhibitor - BPTI - mammalian organs - STI - soybean trypsin inhibitor

5. What may everybody do wrong? Monte Carlo approach in structure analysis and prediction - – what state do we predict? Mathematical modelling of life processes – - Markov chains and protein evolution and differentiation - significance similarity estimation

6. What may biologists do wrong? Amino acids and proteins – - do proteins consist of amino acids as we describe? Definitions and theory – - definition of species and theory of evolution - definitions and biology Correlated mutations – - dispersed correlation

7. What may theoreticians do wrong? Primitive or ancestral? – - (Cyanophyta, Archaebacteria, ape and human) Global and local energy minima – - can we predict the exact conformation at exact time? Microscopic/mesoscopic/macroscopic processes - - water molecule and tsunami Assumptions and conclusions – - incomplete assumptions and wrong conclusions - deformations by simplifying - is the protein sequence just a string of characters?

8. Sequence identity estimation in proteomics and genomics Identity threshold – does it make sense?

9. WHAT IS IMPORTANT IN THE PROTEIN SIMILARITY SEARCH ? 1) Contribution (%) of identical positions 2) Length of the compared strings (sequences) 3) Distribution of the identical positions along the analyzed sequence

10. WHAT IS IMPORTANT IN THE PROTEIN SIMILARITY SEARCH ? 4) Residues at the conservative positions 5) Structural/genetic similarity of the amino acids at non-conservative positions

11. Sequence multiple alignment Problem of gap manipulation Any protein can be aligned with each other as homologous/similar anybiologicalstring anybilogicalstrip anybiologicalstri-ng anybi-logicalstrip anyprotein canbealigned -an-yprote--i-n canb-----ealigned

12. Statistical approaches vs. accuracy How far may they be improved? Protein secondary structure prediction – accuracy 70-72% (not much changed since 1978) 100% accuracy requires the complete database for all possible structures. For 30 AA polypeptides – 20 30 sequences/secondary structures Searching the database for appropriate sequence/structure with the rate 10 12 sequences/sec. would proceed 1.8 bilion times longer than the age of the Universe.

13. Genetic conditioning of the amino acid replacement probabilities and spectrum in molecular evolution

14. The Markov model assumes that the substitution probability of amino acid AA 1 by AA 2 is the same, regardless of what the initial residue AA 1 was transformed from ( AA x, AA y ) The currently used statistical algorithms are based on Markovian model of the amino acid replacement (they directly use stochastic matrices of replacement frequency indices) AA 1 AA 2 AA x PaPa AA 1 AA 2 AA y PbPb P a = P b

15. BLOSUM62 matrix of amino acid replacements Why tryptophane is here the most conservative residue?

16. Replacemant Arg  Lys according to the statistical interpretation using stochastical matrix indices Arg Lys PAM250 3 BLOSUM62 2 BLOSUM35 2 BLOSUM45 3 BLOSUM100 3

17. Arginine-to-lysine mutational replacements Gln CAR Arg AGR Arg AGR Ser AGY Arg CGR His CAY Lys AAR Leu CTR Lys AAR Met ATG Lys AAG

18. Thr Ser UCG Ser AGU IleAsn ArgCys Gly Trp UGG AlaThrPro TrpSerLeu (UAG) Asn AAU Possible one-point-mutational processing of serine with respect to its origin

19. Possible codons for arginine: AGA AGG CGA CGG CGC CGT Is arginine the same as arginine?

20. Diagram of amino acid genetic relationshipsDiagram of codon genetic relationships

21. H H – – Y Y E E D D K K N N R R – W C C G G G G R S S P P P P S S S S A A A A T T T T L L L L L L F F V V V V I I I Genetic relationships between Arg and Met/Gln M R R Q R Q

22. What part of the codon contains the information about the previous amino acid that occurred at certain position of the protein sequence? At most 2/3 of the entire codon. Ala GCG Val GUG

23. How long is the information about codons of preceeding amino acids stored? Theoreticaly the longest period is infinite The shortest storage period is 3 transitions/transversions Ala GCG Val GUG Met AUG Ile AUA Ser UCC Ser UCU Thr ACU Ser AGU Lys AAA Asn AAC Asp GAC His CAC Gln CAG Glu GAG Asp GAU His CAU Asn AAU Lys AAG Gln CAG His CAC Tyr UAU...

24. Correlated mutations The phenomenon of several mutations occurring simultaneously and dependent on each other According to the current hypothesis of molecular positive Darwinian selection, correlated mutations are related to the changes occurring in their neighborhood, they reflect the protein-to-protein interaction and they preserve the biological activity and structural properties of the molecule

25. The current explanation of correlated mutations occurrence (example)

26. The three types of distribution of correlated positions present in myoglobins The residue location and relative distribution is shown on tertiary structure of human myoglobin (P0244, pdb1bzp) The spot correlation cluster Position no. and occurring residues Correlation versus position 127 127 [AMSTV]A (58)S (7) 27 [ADEFLNT]ADEFNTE 31 [GKRS]GKRSR 78 [AKLQ]KALQ 109 [DEGNT]DEGTE 116 [AEHKQST]AEHKQSA 117 [AEKNQS]AEKQSE 122 [BDEN]BDEND

27. The three types of distribution of correlated positions present in Bowman-Birk inhibitor family The residue location and relative distribution is shown on tertiary structure of Bowman- Birk inhibitor from soybean (P01055) The narrow correlation cluster Position no. and occurring residues Correlation versus position 13 13 [–ADFIKLMPRSTV]L (11)M (10) A (8) 4 [–RSTVY]V–SS 5 [–KPST]K–SS 7 [AEGKP]APP 11 [EFHIKLQRST]TEHQS 21 [EFIKMQT]TQEQ

28. The three types of distribution of correlated positions present in eglin-like proteins. The residue location and relative distribution is shown on tertiary structure of eglin C (P01051) Position no. and occurring residues Correlation versus position 67 67 [–DGNT]D (8)G (9) 10 [–ELNQRST]ETLNQRS The dispersed correlation

29. The three types of distribution of correlated positions present in lysozymes The residue location and relative distribution is shown on tertiary structure of lysozyme from rat (P00697, pdb5lyz) The dispersed correlation Position no. and occurring residues Correlation versus position 80 80 [GHKNR]G (7)H (31)N (16) 30 [ILMV]MVILMVV 40 [DFKNR]DNNFKNR

30. The observed number and contribution of three correlation types in four different protein families The correlation sets consist of 2 to over 20 residues The protein family (number of correlated positions/set) The correlation statistics Total number of correlation sets observed Number of dispersed sets Number of narrow clusters Number of undirected clusters Number of sets related to active center Eglin-like proteins (2-13)207761 Bowman-Birk proteinase inhibitors (2-28) 2341369 Myoglobins (2- 29) 412399n.a. Lysozymes (2-15)4125979 All families125 (100%)59 (47.2%)38 (30.4%)28 (22.4%)-

31. Bowls are concave Bowls are convex A mathematician – biologist dialogue The communication problem

32. ...not always the first conclusion is correct and the first impression consistent with the reality In entire splendour of natural phenomena...

33. Thank you for your attention !!!