1. Virtual modelling of proteins Jacek Leluk Interdyscyplinarne Centrum Modelowania Matematycznego i Komputerowego, Uniwersytet Warszawski

2. Main functions of proteins (selected): Enzymes Immunoglobulins Transport factors (e.g.hemoglobin) Hormones, neurotransmitters Structural and storage proteins Contractile proteins (muscles, flagella) Jacek Leluk

3. Protein – a polymer of amino acids. Proteins consists of one or more chains. Some proteins contain other components ( sugars, lipids, nucleotides, metal ions, other compounds... ) – proteids. The basic unit of a protein is amino acid. There are 20 biogenic amino acids (genetically encoded).

4. Jacek Leluk Amino acids Amino acid – organic compound that contains amino group and acidic group (usually it is carboxyl group) AlanineGeneral formula

5. Jacek Leluk Amino acid – polypeptide – protein

6. Jacek Leluk Protein chain folding

7. Jacek Leluk Diversity of proteins Glucagon ROP proteinInsulin

8. Jacek Leluk Light „harvesting” protein from purple bacteria Diversity of proteins

9. Jacek Leluk Sequence – structure - function At first the central dogma of molecular biology assumed very strict relationship between genetic information, protein structure and function: 1 gene 1 sequence 1 structure 1 function At present this dogma is still valid but not in as strict form as before. These relationships are not strictly univocal. e.g. a protein of the same sequence may reveal different secondary and tertiary structures. ???

10. Jacek Leluk All information about protein structure (and function as well) is included in its amino acid sequence, which is unique for each protein. In order to be able to apply these relationships for protein modelling, first we have to learn to read and understand the information „written” in amino acid sequence. The current level of our understanding this „writing” depends on the protein complexity and the prediction accuracy is between 20% and 80%. Sequence – structure - function

11. Jacek Leluk What do we have? Biomolecular databases (genomic, protein and bibliographic) Tools for theoretical analysis of biomolecules Labs for experimental verification of the results Knowledge (theories, hypotheses, theoretical models)

12. Jacek Leluk Regular types of structure (secondary structure) helix  -helix

13. Jacek Leluk sheet  -chain (  -sheet) Regular types of structure (secondary structure)

14. Jacek Leluk 3D protein structures Structure-function relationship Sea anemone - toxin Snake - toxin

15. Jacek Leluk Bacterial RNase Mammalian RNase Rnase inhibitor (inhibits both RNases) 3D protein structures Structure-function relationship

16. Jacek Leluk Errors (mutations) and resulting implications Sickle cell anemia Sickle cell anemia – genetic disease caused by a single amino acid substitution in hemoglobin  -chain (one of 146). S hemoglobin has Val instead of Glu in  -chain. Homozygotes (HbSS) are lethal, heterozygotes (Hb AS) are anemic, but resistant to malaria. Normal hemoglobin –  chain VHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPK VKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFG KEFTPPVQAAYQKVVAGVANALAHKYH S Hemoglobin –  chain VHLTPVEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPK VKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFG KEFTPPVQAAYQKVVAGVANALAHKYH

17. Jacek Leluk Hemoglobin NormalAltered Mutations and resulting implications Sickle cell anemia

18. Jacek Leluk Mutations and resulting implications Sickle cell anemia

19. Jacek Leluk Mutations and resulting implications Sickle cell anemia

20. Jacek Leluk Glucagon (pig) – hormone, 29 amino acids HSQGTFTSDYSKYLDSRRAQDFVQWLMNT Glucagon (synthetic) – hormone, 29 amino acids HSQGTFTSDYSKYLDSKKAQEFVQWLMNT

21. Jacek Leluk Glucagon (pig) – HSQGTFTSDYSKYLDSRRAQDFVQWLMNT Glucagon (synth.) – HSQGTFTSDYSKYLDSKKAQEFVQWLMNT Hydrophobic amino acids: L, I, V, F, M, Y, (W) „Gluca con” modelling Gluca con LAALIAAVAAAIAAVLRRIAEVLAIVAAL

22. Jacek Leluk „Gluca con” design - results Glucagon (pig) – HSQGTFTSDYSKYLDSRRAQDFVQWLMNT Glucagon (synth.) – HSQGTFTSDYSKYLDSKKAQEFVQWLMNT Gluca con – LAALIAAVAAAIAAVLRRIXEVLAIVAAL

23. Jacek Leluk Can we „improve” the Nature at molecular level? What for? Our goal is to get the knowledge about natural mechanisms and then to apply this knowledge for our needs, but not to alter the evolved mechanisms that naturally occur.

24. Jacek Leluk Role and significance of theoretical protein modeling and design Time economy Money economy Work and material economy Increasing our knowledge Supporting the experimental work

25. Jacek Leluk The value of virtual protein design =