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Chapter 3 - Proteins

Chapter 3 - Proteins. Test Your Knowledge About Basic Protein Structure. Name one polar and one nonpolar amino acid, then make a list of all the additional amino acids that you remember. What are the four weak (noncovalent) interactions that determine the conformation of a protein?

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Chapter 3 - Proteins

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  1. Chapter 3 - Proteins

  2. Test Your Knowledge About Basic Protein Structure • Name one polar and one nonpolar amino acid, then make a list of all the additional amino acids that you remember. • What are the four weak (noncovalent) interactions that determine the conformation of a protein? • (True/False) A protein is at a near entropy minimum (point of lowest disorder, or greatest order) when it is completely stretched out like a string and when it is properly folded up. Explain. • (True/False) Loops of polypeptide that protrude from the surface of a protein often form the binding sites for other molecules. Explain. • (True/False) For a family of related genes that do not match genes of known function in the sequence database, it should be possible to deduce their function using “evolutionary tracing” to see where conserved amino acids cluster on their surfaces. Explain.

  3. Also Pro, Phe, Met, Trp, Gly, Cys

  4. Reactions that promote protein folding

  5. Adapted from L. Wu et al., 1995, Nature Struc. Biol.2:281; courtesy of J. Harris and P. S. Kim

  6. Molecular chaperones Chaperones Video – chaperone-aided protein folding

  7. Average length ≈ 10 residues ≈ 15 Å. • Minimum length = 4 residues: how many H-bonds? • Maximum length = 40 residues.

  8. Pleated - look edge-on • Strands ~ 5 Å apart • Note direction of H-bonds will differ in anti-parallel & mixed sheets

  9. Loops & Turns • Connect secondary structural elements. • Loops often carry the functional groups. • Hairpin turns: Shortest possible loops (2 residues). • Gly often in tight turns.

  10. Motifs (protein folds) Domains/Modules Beta-Hairpins I Beta-Hairpins II Beta Corners Beta Barrels Helix Hairpins Alpha-Alpha Corners E-F Hand Helix-Turn-Helix Beta-Alpha-Beta Motifs Greek Key Motifs Pyruvate kinase

  11. B sheet core with protruding loops • Loops for binding interactions • N and C terminals at opposite poles or form “plug-ins” Domain shuffling

  12. Families/Clans Pyruvate kinase This is a member of the Pyruvatekinase-likeTIM barrel superfamily Other families

  13. Serine Protease family

  14. Other Important Protein Structural Features • Subunits • Dimers, tetramers, large assemblies of monomers • Filamentous proteins • Globular proteins Video – clathrin assembly

  15. Test Your Knowledge Now Table 1. Proportions of amino acids that are inaccessible to solvent in a study of twelve proteins. Small proteins may have only one or two amino acid side chains that are totally inaccessible to solvent. Even in large proteins, only about 15% of the amino acids are fully buried. A list of buried side chains from a study of twelve proteins is shown in Table 1. The list is ordered by the proportion of amino acids of each type that are fully buried. What types of amino acids are most commonly buried? Least commonly buried? Are there any surprises? If so, why?

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