Fundamentals of protein and nucleic acid structure

1. Fundamentals of protein and nucleic acid structure Lecture 2 Structural Bioinformatics Dr. Avraham Samson 81-871

2. Tree of Life All known life forms use the same building blocks suggesting there was a common ancestor

3. The tree of life is not that simple! Gene transfer across kingdoms continually occurs (cyanobacteria became chlorophylls, proteobacteria mitochondria, viruses)

4. Inside living cells

5. 29 atoms of life Most common elements:H, O, C, N, P, S (97% of organismweight) Most common ions: Ca2+, K+, Na+, Mg2+, Cl-

6. Forces affecting structure: • H-bonding • Van der Waals • Electrostatics • Hydrophobicity • Disulfide Bridges d 2.6 Å < d < 3.1Å 150° < θ < 180°

7. Forces affecting structure: • H-bonding • Van der Waals • Electrostatics • Hydrophobicity • Disulfide Bridges Repulsion דחייה Attraction משיכה d 3 Å < d < 4Å

8. Forces affecting structure: • H-bonding • Van der Waals • Electrostatics • Hydrophobicity • Disulfide Bridges d d = 2.8 Å “IONIC BOND” יוניקשר “SALT BRIDGE” מלחגשר E = Energy k = constant D = Dielectric constant (vacuum = 1; H2O = 80) q1 & q2 = electronic charges (Coulombs) r = distance (Å) Coulomb’s law

9. Forces affecting structure: • H-bonding • Van der Waals • Electrostatics • Hydrophobicity • Disulfide Bridges

10. Forces affecting structure: • H-bonding • Van der Waals • Electrostatics • Hydrophobicity • Disulfide Bridges Other names: cystine bridge disulfide bridge Hair contains lots of disulfide bonds which are broken and reformed by heat

11. Levels of protein structure Primary: Amino acid sequence Secondary: Local fold pattern of small subsequence Tertiary: Fold of entire protein chain Quaternary: Complex of multiple chains

12. Primary (1o)structure The amino acid sequence is the primary structure

13. Primary (1o)structure 20 amino acids

14. Primary (1o)structure

15. Primary (1o)structure

16. pKa = pH of 50% dissociation

17. Amino acid nomenclature Primary (1o)structure

18. Primary (1o)structure • Amino acids polymerize through peptide bonds to form polypeptides

19. Primary (1o)structure • N-terminal is the start of a polypeptide chain • Amino acids are also called residues

20. side chains צדדישייר שלד backbone Primary (1o)structure

21. Primary (1o)structure • Post translational modification are important because they can change the function of proteins (i.e. phosphorylation, acetylation, hydroxylation, carbohydrate and lipid modifications) N-terminal acetylation hydroxyproline O-phosphotyrosine γ-carboxyglutamate

22. Amino acids chirality Enantiomers –mirror images - תמונת ראי- אננטיומרים chiral center Cכיראלימרכז Dextro-Laevus in Latin

23. Most proteins: only L amino acids C chiral center is L configuration • איך לקבועקונפיגורציה L וD- • סדר את האטומים לפי עדיפותעלפיהכללים הבאים • כלל .1 אטום עם מספר אטומי יותר גבוה בעל סדר עדיפות יותר גבוה. • (I > Cl > O > N> C > H) • כלל .2 אם האטומים זהים, העדיפותעלפי האטומים המתמירים • (C(CH3)3 > CH(CH3)2 > CH2CH3 > CH3) • שים את האטום עם סדר העדיפות הכי נמוך מאחור. • קבע את כיווןהחץ , מסדר עדיפות הכי גבוה לככוון הכי נמוך. אם החץ: • עםכיוון השעוןקונפיגורציה D • נגד כיוון השעון קונפיגורציה L רמז יותר קל בשביל לזכור :) CORNתירס (

24. Bond angles

25. Torsion angles w, φ, and ψ • Unlike w, the two backbone dihedral angles φ and ψ are free to rotate • This rotation freedom allows protein folding Dihedral angles: -180o <φ < +180o -180o < ψ < +180o w is 0o or 180o w

26. Peptide bond is planar Cα, C, O, N, H, Cα all lie in the same plane

27. Torsion angle (w) is usually trans Steric hindrance Question: What other residues can be cis?

28. Except for X-Pro bond in which cis is preferred Steric hindrance Steric hindrance Steric hindrance allows both cis and trans (4:1 ratio)

30. Ramachandran Diagrams • Steric hindrance dictates torsion angle preference • Ramachandran plot show preferred regions of φ and ψ dihedral angles Preferred regions

31. Secondary (2o)structure Helices • a-helix • 310-helix • p-helix b Sheets • Antiparallel • Parallel Turns • b,g,a,and p Unstructured • α-helix is the most common • 3.6 residues per turn (number of residues in one full rotation of 360°) • 5.4 Å pitch (translation along axis for one full rotation of 360°) Hydrogen bond: i→i+4

32. Secondary (2o)structure Helices • a-helix • 310-helix • p-helix b Sheets • Antiparallel • Parallel Turns • b,g,a,and p Unstructured 310-helices are rare in proteins: 3.1 residues per turn (number of residues in one full rotation of 360°) 6 Å pitch (translation along axis for one full rotation of 360°) Hydrogen bond: i→i+3

33. Secondary (2o)structure Helices • a-helix • 310-helix • p-helix b Sheets • Antiparallel • Parallel Turns • b,g,a,and p Unstructured π-helices are rare in proteins 4.3 residues per turn (number of residues in one full rotation of 360°) 6 Å pitch (translation along axis for one full rotation of 360°) Hydrogen bond: i→i+5

34. Hydrogen bonding in helices • CO of residue (n) forms an h-bond with NH of residue: • (n+4) → α-helix • (n+3) → 310-helix • (n+5) → π-helix

35. Ribbon diagram of α-helix

36. Ramachandran of α-helix

37. Secondary (2o)structure Helices • a-helix • 310-helix • p-helix b Sheets • Antiparallel • Parallel Turns • b,g,a,and p Unstructured • In antiparallel b-sheets • Adjacent β-strands run in opposite directions • Hydrogen bonds (dashed lines) between NH and CO stabilize the structure • The side chains (in green) are above and below the sheet

38. Secondary (2o)structure Helices • a-helix • 310-helix • p-helix b Sheets • Antiparallel • Parallel Turns • b,g,a,and p Unstructured • In parallel b-sheets • Adjacent β-strands run in same direction • Hydrogen bonds (dashed lines) between NH and CO stabilize the structure • The side chains (in green) are above and below the sheet

39. Ribbon diagram of β sheet • In addition to being purely parallel or antiparallel, β sheets can be mixed, with strands running in both parallel and antiparallel directions • Arrow pointing to C-terminal end

40. Ramachandran of β-sheet

41. Secondary (2o)structure CO of residue i forms h-bonds with NH of either residue i+2, i+3, i+5, or i+4 β-turn i→i+3 H-bond (most common) γ-turn: i→i+2 H-bond α-turn i→i+4 H-bond π-turn i→i+5 H-bond Helices • a-helix • 310-helix • p-helix b Sheets • Antiparallel • Parallel Turns • b,g,a,and p Unstructured

42. Secondary (2o)structure Helices • a-helix • 310-helix • p-helix b Sheets • Antiparallel • Parallel Turns • b,g,a,and p Unstructured

43. Tertiary (3o)structure • Proteins fold into compact tertiary structures with hydrophobic cores. (spacefill representation) Structural classification: http://www.cathdb.info/cgi-bin/cath/GotoCath.pl?link=class.html

44. Tertiary (3o)structure • It is a bit difficult to see and understand anything here (sticks representation)

45. Tertiary (3o)structure • To simplify representation, secondary structure diagrams are used

46. Quaternary (4o)structure Dimer of identical subunits (Cro protein of bacteriophage lambda)

47. Quaternary structure • Coat of rhinovirus • (common cold) • 60 copies of 4 • different subunits, • 3 outside, • red, blue, green

48. Protein structure databases • Primary: UniProthttp://www.uniprot.org/ • Secondary: DSSP http://rcsb.org • Tertiary: PDB http://rcsb.org • Quaternary: PQS http://www.ebi.ac.uk/pdbe/pqs/

49. DNA and RNA Structure • NOTE: • Components • Sugar • Base • Phosphate • 5’ to 3’ direction • T->U in RNA • RNA - extra –OH at 2’ of pentose sugar • DNA - deoxyribose • Numbering • Single vs double strands • DNA more stable Voet, Donald and Judith G. Biochemistry. John Wiley & Sons, 1990, p. 792.

50. NOTE: • Pyrimadines and Purines • T->U in RNA • Names • Numbering • Bonding character • Position of hydrogen • Tautomers Purines The 5 Basesof DNA and RNA Pyrimadines