Protein Structure

1. Protein Structure • Biochemistry Free For All

2. Peptide Bonds From Amino Acids to Proteins Alpha Carboxyl Alpha Amine In Ribosomes

3. Linear sequence of amino acids Joined by Peptide Bonds Translated from mRNA using Genetic Code Synthesis begins at amino end and terminates at carboxyl end Ultimately determines all properties of a protein Primary Protein Structure

4. A simple view Free Carboxyl Group Amino Terminus Alternating Orientations of R-groups Peptide Bond Peptide Bond Peptide Bond Polypeptides Carboxyl Terminus Free Alpha Amine Peptide Bond Peptide Bond Alternating Orientations of R-groups

5. Chemical Character Double Bond Behavior Peptide Bonds Alpha Carbons Usually Trans-oriented

6. Alpha Carbons Trans Separated bulky groups Proteins Steric Hindrance Alpha Carbons Cis Separated bulky groups Interacting Bulky Groups

7. Multiple Peptide Bond Planes Free Rotation Polypeptides

8. Phi Angle Psi Angle Omega Angle Peptide Bond Phi and Psi Angles Peptide Bond

9. Bond Angles Ramachandran Plot Primary Angles of Stability

10. Alpha Helix Secondary Structure

11. Alpha Helix Hydrogen bonds stabilize structure Secondary Structure Hydrogen bonds stabilize structure

12. Beta Strands / Beta Sheets Hydrogen Bonds Secondary Structure Anti-Parallel Parallel

13. Beta-Sheet Interactions

14. Secondary / Supersecondary Structures

15. Ramachandran Plot Labeled

16. Fibrous Proteins Secondary Structure • Collagen • Connective tissue • Keratin • Hair / nails • Fibroin • Silk

17. Collagen Partial Sequence Primary Structure Hydroxyproline Proline in Helix Abundant Glycine Occasional Lysine

18. Structural Proteins • Keratins • Fibrous • 50 in Humans • Intermediate Filaments of Cytoskeleton • Hair, nails, horns

19. Fibroin Silk Beta sheets Repeating glycines

20. Secondary Structure Types • Alpha Helix • Beta Strands / Beta Helix • Reverse turns (5 types) • 310 Helix

21. Tendencies of Amino Acids High Propensity for Reverse Turns Secondary Structure High Propensity for Beta Strands High Propensity for Alpha Helices

22. Amino Acid Hydropathy

23. Hydrophobic Amino Acid Bias In Bilayer Hydrophobic Amino Acid Bias Inside Soluble vs. Membrane Bound Proteins Hydrophilic Amino Acid Bias Outside Hydrophilic Amino Acid Bias Outside of Bilayer

24. Reverse Turns

25. Folding and Turns Alpha Helices Random Coil Beta Strands Turns Tertiary Structure

26. Folding of a Globular Protein

27. Unfolding of a Globular Protein

28. Forces Stabilizing Tertiary Structure Hydrogen Bonds

29. Forces Stabilizing Tertiary Structure Disulfide Bonds (Covalent)

30. Forces Stabilizing Tertiary Structure

31. Denaturing/Unfolding Proteins • Break forces stabilizing them Mercaptoethanol/dithiothreitol - break disulfide bonds Detergent - disrupt hydrophobic interactions Heat - break hydrogen bonds pH - change charge/alter ionic interactions Chelators - bind metal ions

32. Denaturing/Unfolding Proteins

33. Folding of a Globular Protein

34. Energetics of Folding

35. Protein Structural Domains • Leucine Zipper - Prot.-Prot. and Prot.-DNA • Helix Turn Helix - Protein-DNA • Zinc Fingers • SH2 Domains - Protein-Protein • Pleckstrin Homology Domains - Signaling (Membrane) Zinc Finger Leucine Zipper Pleckstrin Domains SH2 Domain Leucine Zipper Helix-Turn-Helix

36. Folding Errors

37. Prion Replication Model

38. Amyloids and Disease • Amyloids - a collection of improperly folded protein aggregates found in the human body. • When misfolded, they are insoluble and contribute to some twenty human diseases including important neurological ones involving prions. • Amyloid diseases include (affected protein in parentheses) - • Alzheimer’s disease (Amyloid β) • Parkinson’s disease (α-synuclein) • Huntington’s disease (huntingtin), • Rheumatoid arthritis (serum amyloid A), • Fatal familial insomnia (PrPSc)

39. Chaperonins - Proper folding - environment for hydrophobic sequences Protein Processing GroEL / GroEL-GroES Proteasomes - Degradation to oligopeptides of about 8 amino acids each

40. Role of Ubiquitin • Flag for protein destruction by proteasome

41. Intrinsically Disordered Proteins Not all proteins folded into stable structures Intrinsically Disordered Proteins (IDPs) have regions favoring disorder IDP regions tend to lack hydrophobic residues Rich in polar amino acids and proline IDPs may favor adaptation to binding another protein IDPs may favor being modified IDPs may be more involved in signaling and regulation Non-IDPs more involved in catalysis and transport Metamorphic Proteins May adopt more than one stable structure Lymphotactin - monomeric receptor. Binds heparin as dimer

42. Protein Structure • Primary – Amino Acid Sequence • Secondary / Supersecondary – Repeating Structures – short range forces • Tertiary – Folded structures – longer range interactions