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The Three-Dimensional Structure of Proteins Part 1 Chapter 4.

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1 The Three-Dimensional Structure of Proteins Part 1 Chapter 4

2 Proteins: Structure, Function, Folding –Structure and properties of the peptide bond –Structural hierarchy in proteins –Structure and function of fibrous proteins –Structure analysis of globular proteins –Protein folding and denaturation Learning goals: to Know:

3 Structure of Proteins Unlike most organic polymers, protein molecules adopt a specific three- dimensional conformation. This structure is able to fulfill a specific biological function This structure is called the native fold The native fold has a large number of favorable interactions within the protein There is a cost in conformational entropy of folding the protein into one specific native fold

4 Favorable Interactions in Proteins Hydrophobic effect –Release of water molecules from the structured solvation layer around the molecule as protein folds increases the net entropy Hydrogen bonds –Interaction of N-H and C=O of the peptide bond leads to local regular structures such as  -helices and  -sheets London dispersion –Medium-range weak attraction between all atoms contributes significantly to the stability in the interior of the protein Electrostatic interactions –Long-range strong interactions between permanently charged groups –Salt-bridges, esp. buried in the hydrophobic environment strongly stabilize the protein

5 Folding  Final Structure: Chymotrypsin and Glycine 75 Daltons 21,000 Daltons, 3 polypeptides

6 Protein Conformation Stabilized by weak bonds: ΔG separating folded and unfolded is small Bond: H bonds, hydrophobic interatction, ionic interaction and –S-S-. Proteins possess a “solvation layer” The extent of which depends on surface amino acid R groups Overall structural patterns: Hydrophobic areas buried in protein interior Number of H-bonds is maximized

7 The Peptide Bond

8 Only non-planar Bonds Rotate Each α-Carbon has a Φ and Ψ

9 Getting the Angles

10 Many Angles are Prohibited due to Steric Overlap

11 Ramachandran Plot

12 Pauling and Corey and the Alpha Helix

13 How To Determine Protein Structure The Classic Method – X-ray Crystallography Methods to form Crystals take Proteins to their Solubility Minimum

14 Proteins Crystals in Electron Microscopy

15 X-ray Diffraction

16 X-ray Diffraction Pattern of Myoglobin and DNA Fourier Transform to convert X-ray pattern to Electron Density Map

17 X ray Diffraction Patterns from Different Proteins

18 Fitting Electron Density Map to Structure

19 Fitting Electron Density Map to Primary Structure

20 X-ray Crystallography at Fine Resolution

21 Proton Nuclear Magnetic Resonance of a Protein

22 2 Dimensional NMR

23 NMR Structure of Myoglobin NMR is limited to small proteins

24 TROSY NMR Transverse Relaxation Optimized Spectroscopy  increases time overwhich NMR signals from neighboring methyl groups can be detected. The trick is to deuterate the protein then protonate methyls…. A look into a Proteasome cavity. This protein is 670 kD! (20S) Red groups = methyls that are mobile Yellow groups = active site…protein degradation. C+E News Feb 5, 2007

25 Here Is How It Worked Nature 445:618 Feb 8, 2007

26 Proteasome Function Core Proteasome Ubiquitin Binding Sites top and bottom

27 4 th Edition: See pages 1075- 1076, Fig 27-41 5 th Edition: See pages 1107- 1109, Fig 27-47, 48 Ubiquitin Targeting a Cytoplasmic Protein Protein AminoTerminal-aaHalf-life stabilizing M, G, A, S, T, V>20 hrs destabilizing I, N, Y, D, P, L, F, K, R 30 – 2 min

28 What’s New: Free-Electron Lasers X-ray pulses, in series of femtoseconds on drops containing microcrystals. Free-electron X ray source at Stanford only one ($300 million), Resolution 2Å. Schichting, I. May, 2012 Max-Plank Gesellschaft

29 Alpha Helix Stabilized by H-bonding to every 4 th Amino Acid

30 Alpha Helix Stabilized by Dipole Moments and Hydrogen Bonds Can be Right or Left Handed

31 Alpha Helix H-bonding - Stability H-bonds to every 4 th amino acid So, amino acid-8 in a 15 aa α-helix is H-bonded to aa-11 and aa-5. What about amino acids at the N- and C-terminal ends? Instability is brought about by: 1. electrostatic repulsion or attraction – charged R groups. 2.adjacent bulky R groups. 3.interaction with R groups 3-4 aa’s up or down the helix. 4.occurrence of G. 5.interaction of aa’s at C-terminal and N-terminal ends with any near aa-R group.

32 table 4-1 A

33 How Long is an 80 amino acid alpha helix? FACTS to KNOW: One turn: 3.6 aa’s, 5.4 Å long NOW DO IT

34 How Long is an 80 amino acid alpha helix? FACTS to KNOW: One turn: 3.6 aa’s, 5.4 Å long 80 aa’s / (3.6 aa’s/turn) = 22.2 turns 22.2 turns x 5.4 Å/turn = 120 Å long

35  Sheets The planarity of the peptide bond and tetrahedral geometry of the  -carbon create a pleated sheet- like structure Sheet-like arrangement of backbone is held together by hydrogen bonds between the backbone amides in different strands Side chains protrude from the sheet alternating in up and down direction

36 Beta (Pleated Sheet) Structure


38 Antiparallel Beta-turns

39 Antiparallel Beta-turns with Proline Normal = transIn Beta-turns, Proline is cis

40 Ramachandran Plot showing 2 o Structures

41 Ramachandran Plot of Pyruvate Kinase Excludes Glycines – they are too flexible


43 Frequency of Amino Acids in 2 o Structure

44 Circular Dichroism Spectra A Difference in right handed and left handed polarized light on the extinction coefficient.

45 Tertiary structure refers to the overall spatial arrangement of atoms in a protein Stabilized by numerous weak interactions between amino acid side chains.  Largely hydrophobic and polar interactions  Can be stabilized by disulfide bonds Interacting amino acids are not necessarily next to each other in the primary sequence. Two major classes – Fibrous and globular (water or lipid soluble) Protein Tertiary Structure

46 Fibrous Proteins: From Structure to Function

47 Alpha Keratin Structure – Almost All Alpha Helix


49 Biochemists at the Hairdressers Why a Permanent is not a Temporary!

50 Chicken Feather α-keratin Carbonizing (under O 2 free environment) makes the fiber into a graphite- like material = light weight, high strength, low cost polymer)

51 Silk Fibroin is almost all Beta Structure

52 Silk A

53 Spinnerets of a Spider – SEM, Artificially Colored

54 Things to Know and Do Before Class 1.The peptide bond and why it is planar. 2.Rotation around the alpha carbon, Ramachandran Plot. 3.Basic idea of X-ray crystallography and how it is used to get 3-D structure. 4.Alpha helix and B-structure. 5.Circular Dichroism spectra: what they demonstrate. 6.Fibrous proteins that are essentially all alpha helix or beta structure. 7.EOC problems 1-4. We will do some in class and a case study with music.

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