Lecture 10 (10/4/17) Lecture 10 (10/4/17)

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1 Lecture 10 (10/4/17) Reading: Ch4; 125, , Problems: Ch4 (text); 7, 9, 11 Ch4 (study guide); 1, 2 NEXT Reading: Ch4; 125, (structure determination) Ch4; (Collagen) Problems: Ch4 (text); 10, 15 (may add some more on website) Lecture 10 (10/4/17) OUTLINE I. Protein Structure A. Tertiary 1. Depiction; the Protein Database 2. Examples of Types 3. Domains 4. Intrinsically unstructured 5. Energetics B. Quaternary 1. Nomenclature 2. Energetics 1

2 Tertiary Structure Bovine Carboxypeptidase A Carboxypeptidase A PDBid 3CPA 2

3 Picturing protein structure Space-fill Backbone trace Ribbon Triose-phosphate Isomerase (TIM) 5 Picturing protein structure Ribbon Surface Ribbon with Spacecontour side-chains filling Sperm-whale Myoglobin (Mb) 3

4 Protein Classification: α, β, or α/β Cytochrome b562 PDBid 256B Human immunoglobulin fragment PDBid 7FAB Dogfish lactate dehydrogenase PDBid 6LDH Protein Classification: α Cytochrome b562 PDBid 256B Growth hormone 4

5 Protein Classification: α Protein Classification: β Human immunoglobulin fragment PDBid 7FAB Immunoglobulin-fold 5

6 Protein Classification: α/β Flavodoxin Can you find the Rossmann Fold? Protein Classification: α/β Flavodoxin Can you find the Rossmann Fold? 6

7 Protein Topology: 8- Stranded β Barrels Human retinol binding protein PDBid 1RBP Peptide-N 4 -(N-acetyl-b-D-glucosaminyl) asparagine amidase PDBid 1PNG Triose phosphate isomerase PDBid 1TIM Protein Topology: 8- Stranded β Barrels Human retinol binding protein PDBid 1RBP b-meander 7

8 Protein Topology: 8- Stranded β Barrels Peptide-N 4 -(N-acetyl-b-D-glucosaminyl) asparagine amidase PDBid 1PNG Greek key ( ) Protein Topology: 8- Stranded β Barrels Triose phosphate isomerase PDBid 1TIM a/b-barrel 8

9 Protein Topology: 8- Stranded β Barrels a/b-barrels 17 Protein Domains Domains: Separate folded structures with hinge all with one polypeptide chain g-b Crystallin Hinge region 9

10 Protein Domains Dogfish lactate dehydrogenase PDBid 6LDH a/b-saddle & Rossmann Fold (b-a-b-a-b) Protein Domains 2-Domain Protein : GAPDH Hinge region Glyceraldehyde-3-phosphate dehydrogenase PDBid 1GD1 a/b-saddle & Rossmann Fold (b-a-b-a-b) 10

11 Intrinsically Disordered Proteins: Tachystatin Unstructured domains: Part of primary structure without any defined conformation, changeable, dynamic, several possible structures depending on binding partners in cells Tachystatin 21 Intrinsically Disordered Proteins: p53 C N N E3 ubiquitin-protein ligase Mdm

12 Intrinsically Disordered Proteins: p53 C N N E3 ubiquitin-protein ligase Mdm2 23 Intrinsically Disordered Proteins: p53 12

13 Intrinsically Disordered Proteins: CREB CREB (camp response element-binding protein) Kinase-inducible domain of CREB PDBid 1KDX 3 structure is a collection of 2 structures in motifs and/or domains Sum of weak interactions 3 structure held together with side-chain interactions lysozyme Hydrophobic effect Salt bridges Hydrogen bonds Dispersion forces Disulfide bonds 13

14 Hydrophobic effect drives protein folding Globular proteins a hydrophobic core and a hydrophilic surface 28 14

15 Problem Which residue would be more likely to be? 1. On a protein s surface: Trp or Gln 2. In the protein interior: Ser or Val 3. In the middle of an alpha-helix: Gly or Leu 4. In a beta-sheet: His or Pro 29 Quaternary Structure 15

16 Protein Structure-Quaternary homo trimer a 3 a 4 a 2 b 2 a 2 b 2 g 2 hetero tetramer homo tetramer hetero hexamer Multiple subunits held together by primarily noncovalent interactions Nomenclature: homo vs. hetero subunits indicated with Greek letters (a (1 st ), b (2 nd ), g (3 rd ), etc. 31 Protein Structure-Quaternary Same weak interactions determine 4 structure Hydrophobic effect Hydrogen bonds Salt bridges Dispersion forces 16

17 4 structure held together with side-chain interactions Sum of weak interactions Ferredoxin (Fd) Protein Structure-Quaternary Phytochromobilin synthase (HY2) Intermolecular salt bridges formed by conserved, charged residues stabilize HY2-Fd interaction. HY2-bound substrate and the iron-sulfur cluster on AtFd2 are shown in stick representation. Important charged residues in AtFd2-HY2 binding interface are viewed from the top of Fd side of the docking complex. Residues identified in this study are shown in stick representation with blue (HY2) and brown (AtFd2) carbon atoms. Red circles indicate the salt bridges in-between two proteins. Hydrophobic effect Hydrogen bonds Salt bridges Dispersion forces Protein Structure-Summary 34 17