1. The structural organization within proteins Kevin Slep June 13 th, 2012

2. From Linear Peptide to a 3D Fold 1951 Herman BransonLinus PaulingRobert Corey

3. The Amino Acid The Building Blocks of Proteins

4. The 20 Amino Acids The Building Blocks of Proteins

5. The Peptide Chain, Primary Structure Assembled by the Ribosome During Translation

6. Peptide Backbone: Phi Psi Angles Limits to their distribution

7. Ramachandran Plot Energy limits to the Phi Psi Distribution

8. The Globular Protein Fold Exterior: Hydrophillic Interior: Hydrophobic Soluble Proteins: How would the organization of a Membrane Protein compare? L A G S V E T R K D I P N Q F Y M H C W Packing Cross Section of a Globular Protein

9. Interactions That Stabilize Protein Folds

10. Secondary Structure Helices Strands and Loops

11. First: How do we determine structure? Our Tools: Solution NMR Nuclear Magnetic Resonance Distance Constraints Dynamic Snapshot X-ray Crystallography Electron Density Static Snapshot

12. Secondary Structure: The  -Helix 3.6 residues per turn

13. Secondary Structure: The  -Helix Helical Axis

14. Secondary Structure: The  -Helix Helical Wheel – Hydropathy Plots Helical Axis

15. Forms of Helices

16. Secondary Structure: The  -Sheet: Parallel  -Strands

18. Secondary Structure: The  -Sheet: Anti-Parallel  -Strands

19. Secondary Structure: Loops Linkers, Variable Structrure, Active Site

20. Cystine: The Disulfide Bond Two Cysteines Covalently Bond (Oxidation) Provides Added Stabilization to a Fold

21. Secondary Structure Prediction Tools Online Sites: Predict Protein http://www.predictprotein.org/ Phyre http://www.sbg.bio.ic.ac.uk/phyre/ Jpred3 http://www.compbio.dundee.ac.uk/~www-jpred/

22. Secondary Structure:

23. Structure is Conferred by Main Chain Conformation and Side Chain Conformation – Packing Rotamers: Favored Geometries/Energy States Phenylalanine

24. How Secondary Structure is Organized: Motifs and Tertiary Structure

25. Topology Diagrams Jane Richardson (Duke Univ.) Triose Phosphate Isomerase

26. Structural Motifs  Hairpin

27. Structural Motifs Helix-Loop-Helix

28. Structural Motifs EF-Hand Calmodulin: 4 EF Hands

29. Structural Motifs Zinc_Finger Two Histidines on a Helix Two Cysteines on a Loop

30. Structural Motifs Greek Key

31. Pre-albumin

32. Structural Motifs Jelly Roll

33. Structural Motifs 

34. Structural Motifs Rossmann Fold Nucleotide Binding

35. Helix-Turn-Helix DNA Binding Proteins

36. Four-Helix Bundle

37. Catalytic Triad Aspartate, Histidine, Serine

38. TIM Barrel Domain

39.  -Barrel

40.  -Propeller Domain Neuraminidase

41. Non-Protein Molecules That Play a Role in Structure and Function The Heme Group in Hemoglobin Cofactors

42. Non-Protein Molecules That Play a Role in Structure and Function Water in Prealbumin First Hydration Shell Ordered Water

43. Non-Protein Molecules That Play a Role in Structure and Function Ions Water in Prealbumin

44. How Do Proteins Fold? Moving from a linear peptide To a Motif To a Domain

45. Protein Folding: Energy Landscape

46. Protein Folding: Pathways

47. Protein Folding: Help From Chaperones

48. Protein Domains Built from Motifs

49.  Domains  solenoid – a curved structure peridinin-chlorophyll-containing protein - trimer

50.  Domains WD40 protein

51.  Domains Helices and Strands Alternate in the peptide

52.  Domains  Saddle

53.  and  Domains Helices and Strands Are separated in the peptide DNA Clamp PCNA

54. Irregular Folds Conotoxin, disulfide in yellow

55. Examples of Protein Structure Structure Confers Function

56. Membrane Proteins Porins

57. Membrane Proteins Aquaporins

58. Membrane Proteins G-Protein Coupled Receptors GPCR: Rhodopsin

59. Membrane Proteins Ion Channels Potassium Channel

60. Viral Proteins Reovirus Core

61. Immunoglobulins

62. Signaling Molecules: G-protiens

63. Structural Proteins Clathrin

64. Structural Proteins Actin Filaments: Actinh

65. Structural Proteins Microtubules: Tubulin

66. Motor Proteins Kinesin

67. Motor Proteins Myosin

68. Protein Folds – as of 2008 1056 2008

69. Various Folds Confer Dynamic Properties T4 Lysozyme

70. Various Folds Confer Dynamic Properties G-proteins Nucleotide-dependent Conformational change

71. Quaternary Structure Oligomerization of the same protein, or multiple different proteins HomodimerHeterodimer HomotrimerHeterotrimer HomotetramerHeterotetramer The Coiled Coil A common dimerization motif

72. Quaternary Structure

73. Quaternary Structure  -globin E6V Mutation: Sickle Cell Anemia Sickle Cell Malaria Heterozygotes are protected from malaria Pauling Hemoglobin is responsible

74. PyMol Demonstration

75. Discussion Questions Open discussion on the PNAS paper by Pauling, Corey and Branson What is the importance of tertiary structure for an active site? Why is it important to study secondary and tertiary structure? How important is it to know structure and what does structure tell us about function? Can you predict the tertiary structure from primary or secondary structure. Can you predict the quaternary structure from primary, secondary or tertiary Structure? Why are some protein folds seen over and over again in nature – and used for different functions.