Proteins: Structure and Function

1. Proteins: Structure and Function

2. Proteins • Cellular Overview • Functions • Key Properties • Core Topics • Amino Acids: properties, classifications, pI • Primary Structure, Secondary Structure, and Motifs • Tertiary Structure • Fibrous vs. Globular • Quaternary Structure

3. Amazing Proteins: Function • The largest class of proteins, accelerate rates of reactions • Catalysts (Enzymes) • Transport & Storage DNA Polymerase CK2 Kinase Catalase Ovalbumin Casein Ion channels Hemoglobin Serum albumin

4. Amazing Proteins: Function • Structural • Generate Movement Collagen Keratin Silk Fibroin Actin Myosin

5. Amazing Proteins: Function • Regulation of Metabolism and Gene Expression • Protection Lac repressor Insulin Thrombin and Fibrinogen Ricin Venom Proteins Immunoglobulin

6. Amazing Proteins: Function • Signaling and response (inter and intracellular) Apoptosis Membrane proteins Signal transduction

7. Amazing Proteins: Properties • Biopolymers of amino acids • Contains a wide range of functional groups • Can interact with other proteins or other biological macromolecules to form complex assemblies • Some are rigid while others display limited flexibility

8. a-Amino Acids: Protein Building Blocks R-group or side-chain a-amino group Carboxyl group a-carbon

9. Amino acids are zwitterionic • “Zwitter” = “hybrid” in German • Fully protonated forms will have specific pKa’s for the different ionizable protons • Amino acids are amphoteric (both acid and base)

10. Stereochemistry of amino acids

11. Stereochemistry of amino acids (AA) • AA’s synthesized in the lab are racemic mixtures. AA’s from nature are “L” isomers • These are all optically-active except for glycine (why?)

12. Synthesis of Proteins + H2O

13. Synthesis of Proteins

14. N-Terminal End C-Terminal End Synthesis of Proteins

15. Synthesis of Proteins = ≠

16. Synthesis of Proteins = ≠

17. Synthesis of Proteins ≠ ≠

18. 20 common amino acids make up the multitude of proteins we know of COMMON AMINO ACIDS

19. Amino Acids With Aliphatic Side Chains

20. Amino Acids With Aliphatic Side Chains

21. Amino Acids With Aliphatic Side Chains

22. Amino Acids With Aromatic Side Chains

23. Amino Acids with Aromatic Side Chains Can Be Analyzed by UV Spectroscopy

24. Amino Acids With Hydroxyl Side Chains

25. Amino Acid with a Sulfhydryl Side Chain

26. Disulfide Bond Formation

27. Amino Acids With Basic Side Chains

28. Amino Acids With Acidic Side Chains and Their Amide Derivatives

30. There are some important uncommon amino acids we shall still encounter later on.

31. pH and Amino Acids Net charge: +1 Net charge: -1 Net charge: 0

32. Basic amino acids High pKa Function as bases at physiological pH Side chains with N Acidic amino acids Low pKa Negatively charged at physiological pH Side chains with –COOH Predominantly in unprotonated form Characteristics of Acidic and Basic Amino Acids

33. Protein Structure We use different “levels” to fully describe the structure of a protein.

34. Primary Structure • Amino acid sequence • Standard: Left to Right means N to C-terminal • Eg. Insulin (AAA40590) • The info needed for further folding is contained in the 1o structure. MAPWMHLLTVLALLALWGPNSVQAYSSQHLCGSNLVEALYMTCGRSGFYRPHDRRELEDLQVEQAELGLEAGGLQPSALEMILQKRGIVDQCCNNICTFNQLQNYCNVP

35. Secondary Structure • The regular local structure based on the hydrogen bonding pattern of the polypeptide backbone • α helices • β strands (β sheets) • Turns and Loops • WHY will there be localized folding and twisting? Are all conformations possible?

36. α Helix • First proposed by Linus Pauling and Robert Corey in 1951. • 3.6 residues per turn, 1.5 Angstroms rise per residue • Residues face outward

37. α Helix • α-helix is stabilized by H-bonding between CO and NH groups • Except for amino acid residues at the end of the α-helix, all main chain CO and NH are H-bonded

38. α Helix representation

40. β strand • Fully extended • β sheets are formed by linking 2 or more strands by H-bonding • Beta-sheet also proposed by Corey and Pauling in 1951.

42. PARALLEL ANTIPARALLEL

43. The Beta Turn • (aka beta bend, tight turn) • allows the peptide chain to reverse direction • carbonyl C of one residue is H-bonded to the amide proton of a residue three residues away • proline and glycine are prevalent in beta turns

44. Mixed β Sheets

45. Twisted β Sheets

47.  Loops

48. What Determines the Secondary Structure? • The amino acid sequence determines the secondary structure • The α helix can be regarded as the default conformation – Amino acids that favor α helices: Glu, Gln, Met, Ala, Leu – Amino acids that disrupt α helices: Val, Thr, Ile, Ser, Asx, Pro

49. What Determines the Secondary Structure? • Branching at the β-carbon, such as in valine, destabilizes the α helix because of steric interactions • Ser, Asp, and Asn tend to disrupt α helices because their side chains compete for H-bonding with the main chain amide NH and carbonyl • Proline tends to disrupt both α helices and β sheets • Glycine readily fits in all structures thus it does not favor α helices in particular

50. Can the Secondary Structure Be Predicted? • Predictions of secondary structure of proteins adopted by a sequence of six or fewer residues have proved to be 60 to 70% accurate • Many protein chemists have tried to predict structure based on sequence • Chou-Fasman: each amino acid is assigned a "propensity" for forming helices or sheets • Chou-Fasman is only modestly successful and doesn't predict how sheets and helices arrange • George Rose may be much closer to solving the problem. See Proteins 22, 81-99 (1995)