1. Applied Bioinformatics The amino acids

2. Overview Proteins (sneak preview) – Primary structure – Secondary structure – Tertiary structure The amino acids – One amino acid – Our first protein – A closer look at the amino acids – Secondary structure preferences

3. Our goal for today: (a little) understanding of the relation between amino acids and protein structure

4. Proteins Primary structure – A.K.A. “the sequence” Secondary structure – Short stretches form distinct ‘substructures’ Helices Sheets Turns & Loops Tertiary structure – The arrangement of secondary structure elements with respect to each other

5. Primary structure

6. Proteins Primary structure – A.K.A. “the sequence” Secondary structure – Short stretches form distinct ‘substructures’ Helices Sheets Turns & Loops Tertiary structure – The arrangement of secondary structure elements with respect to each other

7. Secondary structure - α helix

8. Secondary structure – β sheets

9. Secondary structure – turns & loops

10. Proteins Primary structure – A.K.A. “the sequence” Secondary structure – Short stretches form distinct ‘substructures’ Helices Sheets Turns & Loops Tertiary structure – The arrangement of secondary structure elements with respect to each other

12. Protein structure (secondary & tertiary) is largely determined by its primary structure.

13. When you understand the amino acids, you understand everything

14. The amino acids A short introduction

15. One amino acid - Cα is at the heart of the amino acid - Cα, C N and O are called backbone atoms - R can be any of the 20 side chains

16. Our first protein

17. The 20 amino acids AAlaAlanine C CysCysteine D Asp Aspartic acid (Aspartate) E GluGlutamic acid (Glutamate) F PhePhenylalanine G GlyGlycine H HisHistidine I IleIsoleucine K LysLysine L LeuLeucine M MetMethionine N AsnAsparagine P ProProline Q GlnGlutamine R ArgArginine S SerSerine T ThrThreonine V ValValine W TrpTryptophan Y TyrTyrosine

18. The 20 amino acids The side chains, R, determine the differences in the structural and chemical properties of the 20 ‘natural’ amino acids. The 20 amino acids can, for example, be classified as follows: Hydrophobic AliphaticAla, Leu, Ile, Val AromaticPhe, Tyr, Trp, (His) Hydrophilic PolarAsn, Gln AlcoholicSer, Thr, (Tyr) ChargedArg, Lys, Asp, Glu, (His) Inbetween: Sulfur-containingMet, Cys SpecialGly (no R), Pro (cyclic) Several amino acids belong in more than one category.

19. There are many ways to characterize the properties of amino acids. The ones most useful and most commonly used are: Hydrophobicity Size Charge Secondary structure preference Alcoholicity Aromaticity And on top of that there are some special characteristics like bridge forming by cysteines, rigidity of prolines, titrating at physiological pH of histidine, flexibility of glycines, etc.

20. Aromatic

21. Charged

22. Sulfur - containing

23. Really special

24. Cysteines are extra special

25. amino acids don’t fall neatly into classes--they are different combinations of small/large, charged/uncharged, polar/nonpolar properties the properties of a residue type can also vary with conditions/environment Key points about the character of amino acid side chains

26. Secondary structure preferences

27. Obviously, there are relations between the physico-chemical characteristics of the amino acids and their secondary structure preference.

28. Chou Fasman parameters Take all protein structures Calculate for each secondary structure type how many amino acids are in that structure type (in % of all amino acids) Calculate for each amino acid type the distribution across secondary structure types (in % of all amino acids of that type) Calculate the preference score

29. Chou Fasman parameters Say your dataset is 1000 amino acids and 350 of them are in alpha-helix conformation. This is 35%. There are 50 Alanines in your set and 25 of them are in alpha-helix conformation. This is 50%. The helix preference parameter P for Ala is 50/35=1,43

30. helix strand turn Alanine 1.42 0.83 0.66 Arginine 0.98 0.93 0.95 Aspartic Acid 1.01 0.54 1.46 Asparagine 0.67 0.89 1.56 Cysteine 0.70 1.19 1.19 Glutamic Acid 1.39 1.17 0.74 Glutamine 1.11 1.10 0.98 Glycine 0.57 0.75 1.56 Histidine 1.00 0.87 0.95 Isoleucine 1.08 1.60 0.47 Leucine 1.41 1.30 0.59 Lysine 1.14 0.74 1.01 Methionine 1.45 1.05 0.60 Phenylalanine 1.13 1.38 0.60 Proline 0.57 0.55 1.52 Serine 0.77 0.75 1.43 Threonine 0.83 1.19 0.96 Tryptophan 1.08 1.37 0.96 Tyrosine 0.69 1.47 1.14 Valine 1.06 1.70 0.50

31. ©CMBI 2006 Chou Fasman parameters Take home message: Preference parameter > 1.0  specific residue has a preference for the specific secondary structure. Preference parameter = 1.0  specific residue does not have a preference for, nor dislikes the specific secondary structure Preference parameter < 1.0  specific residue dislikes the specific secondary structure.

32. Secondary structure - helix

33. Helices pack because of the hydrogen bonds and because of the hydrophobic packing of side chains along the length of the helix. Certain residues do this hydrophobic packing better than others, and those residues are thus good for a helix. Remember: AMELK

34. Secondary structure - strands

35. Also strands pack because of the hydrogen bonds between the strands and hydrophobic packing of side chains along the length of the strand. Certain residues do this hydrophobic packing better than others, and those residues are thus good for a strands.  -branched residues (Ile, Thr, Val) are very good for strands, and so are the large hydrophobic residues. Remember: VITWYF

36. Secondary structure - turn

37. Secondary structure - turns To create a turn the backbone needs to be bent pretty sharply, and some residues are really good at that. Glycine is special because it is so flexible, so it can easily make the sharp turns and bends needed in a  -turn. Proline is special because it is so rigid; you could say that it is pre-bent for the turn. Aspartic acid, asparagine, and serine have in common that they have short side chains that can form hydrogen bonds with the own backbone. These hydrogen bonds compensate the energy loss caused by bending the chain into a turn Remember: PSDNG

39. Hydrophobicity When hydrophobic objects come together in water, the number of unhappy waters go down, and that is good for stability. Free waters are happy waters.

40. Hydrophobicity Hydrophobicity is the most important characteristic of amino acids. It is the hydrophobic effect that drives proteins towards folding. Actually, it is all done by water. Water does not like hydrophobic surfaces. When a protein folds, exposed hydrophobic side chains get buried, and release water of its sad duty to sit against the hydrophobic surfaces of these side chains. Water is very happy in bulk water because there it has on average 3.6 H-bonds and about six degrees of freedom. So, whenever we discuss protein structure, folding, and stability, it is all the entropy of water, and that is called the hydrophobic effect.