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Chapter 7 continued Mass Spec Sequencing

Page 172

Figure 7-8a The generation of the gas phase ions required for the mass spectrometric analysis of proteins. (a) By electrospray ionization (ESI).

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Figure 7-9 The ESI-MS spectrum of the 16,951-D horse heart protein apomyoglobin.

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Figure 7-10 The use of a tandem mass spectrometer (MS/MS) in amino acid sequencing.

Figure 7-11 The tandem mass spectrum of the doubly charged ion of the 14-residue human

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[Glu1]fibrinopeptide B (m/z = 786).

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Figure 7-12a Peptide mapping.

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Figure 7-12b Peptide mapping.

Genetic Defect in Sickle Cell Anemia • Change is in beta chain of hemoglobin • Protein sequence changed from Glu to Val at position 6 Homozygous patients have sickle cell anemia

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Figure 7-18a Scanning electron microscope of human erythrocytes. (a) Normal human erythrocytes revealing their biconcave disklike shape.

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Figure 7-18bScanning electron microscope of human erythrocytes. (b) Sickled erythrocytes from an individual with sickle-cell anemia.

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Figure 7-20 A map indicating the regions of the world where malaria caused by P. falciparum was prevalent before 1930.

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Figure 7-21 Phylogenic tree of cytochrome c.

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Figure 7-22 Rates of evolution of four unrelated proteins.

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Figure 7-24 Phylogenetic tree of the globin family.

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Figure 7-34 Flow diagram for polypeptide synthesis by the solid phase method.

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Figure 7-35 A selection of amino acids with benzylprotected side chains and a Boc-protected α-amino acid group.

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Figure 7-36 The native chemical ligation reaction.

Polypeptide Synthesis • Some achievements – 99 amino acid HIV protease, fully active when denatured and refolded – 99 D-amino acid HIV protease, active against D-amino acid target but not L-amino acid target. – Complete synthesis of a virus

Bioinformatics This topic, covering both protein and nucleic acid sequence information,will be covered later in the semester in a lecture by Dr. Edward Marcotte

Chapter 8 Three Dimensional Structure of Proteins

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Figure 7-1

The structural hierarchy in proteins.

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Figure 8-1

The trans-peptide group.

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Figure 8-2

The cis-peptide group.

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Figure 8-3 A polypeptide chain in its fully extended conformation showing the planarity of each of its peptide groups.

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Figure 8-4

The torsional degrees of freedom in a peptide unit.

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Figure 8-5

.

Conformations of ethane

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Figure 8-6

Steric interference between adjacent residues.

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Figure 8-7

The Ramachandran diagram.

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Figure 8-8

Conformation angles in proteins.

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Figure 8-9

The Ramachandran diagram of Gly residues in a polypeptide chain.

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Figure 8-10 Examples of helices.

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Figure 8-11 The right-handed α helix.

Animations of Alpha Helix See Biochemical Interactions CD with Voet & Voet Also go to www.boyerbiochem.com and try your hand at the “Structure Tutorials.

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Figure 8-12 Stereo, space-filling representation of an α helical segment of sperm whale myoglobin (its E. helix) as determined by X-ray crystal structure analysis.

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Figure 8-13 The hydrogen bonding pattern of several polypeptide helices.

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Figure 8-14 Comparison of the two polypeptide helices that occasionally occur in proteins with the commonly occurring α helix.

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Figure 8-15 The polyproline II helix.

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Figure 8-16a β pleated sheets. (a) The antiparallel β pleated sheets.

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Figure 8-16b β pleated sheets. (b) The parallel β pleated sheets.

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Figure 8-17 A two-stranded β antiparallel pleated sheet drawn to emphasize its pleated appearance.

Figure 8-18 Stereo, space-filling representation of the 6stranded antiparallel β pleated sheet in jack bean

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concanavalin A as determined by crystal X-ray analysis.

Figure 8-19a Polypeptide chain folding in proteins illustrating the right-handed twist of β sheets. (a) Bovine

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carboxypeptidase A.

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Figure 8-19b Polypeptide chain folding in proteins illustrating the right-handed twist of β sheets. (b) Chicken muscle triose phosphate isomerase.

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Figure 8-20 Connections between adjacent polypeptide strands in β pleated sheets.

Figure 8-21 Origin of a right-handed crossover

.

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connection

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Figure 8-22 Reverse turns in polypeptide chains.

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Figure 8-23 Space-filling representation of an Ω loop comprising residues 40 to 54 of cytochrome c.

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Figure 8-24 X-Ray diffraction photograph of a fiber of Bombyx mori silk.

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Figure 8-25 The microscopic organization of hair.

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Figure 8-26 The structure of α keratin.

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Figure 8-27a The two-stranded coiled coil. (a) View down the coil axis showing the interactions between the nonpolar edges of the α helices.

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Figure 8-27bThe two-stranded coiled coil. (b) Side view in which the polypeptide back bone is represented by skeletal (left) and space-filling (right) forms.

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Table 8-2

The Most Abundant Types of Collagen.

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Figure 8-28 The amino acid sequence at the C-terminal end of the triple helical region of the bovine α1(I) collagen chain.

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Figure 8-29 The triple helix of collagen.

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Figure 8-30a X-Ray structure of the triple helical collagen model peptide (Pro-Hyp-Gly)10 in which the fifth Gly is replaced by Ala. (a) Ball and stick representation.

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Figure 8-30bX-Ray structure of the triple helical collagen model peptide (Pro-Hyp-Gly)10 in which the fifth Gly is replaced by Ala. (b) View along helix axis.

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Figure 8-30c X-Ray structure of the triple helical collagen model peptide (Pro-Hyp-Gly)10 in which the fifth Gly is replaced by Ala. (c) A schematic diagram.

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Figure 8-31 Electron micrograph of collagen fibrils from skin.

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Figure 8-32 Banded appearance of collagen fibrils.

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Table 8-3 The Arrangement of Collagen Fibrils in Various Tissues.

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Figure 8-33 A biosynthetic pathway for cross-linking Lys, Hyl, and His side chains in collagen.

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Figure 8-34 Distorted structure in abnormal collagen.

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Figure 8-35 X-Ray diffraction photograph of a single crystal of sperm whale myoglobin.

X-Ray Crystallography and NMR

• Dr. Hackert and Dr. Hoffman will cover these topics later in the semester

Figure 8-39a Representations of the X-ray structure of sperm whale myoglobin. (a) The protein and its bound

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heme are drawn in stick form.

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Figure 8-39bRepresentations of the X-ray structure of sperm whale myoglobin. (b) A diagram in which the protein is represented by its computer-generated Cα backbone.

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Figure 8-39c Representations of the X-ray structure of sperm whale myoglobin. (c) A computer-generated cartoon drawing in an orientation similar to that of Part b.

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Figure 8-40 The X-ray structure of jack bean protein concanavalin A.

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Figure 8-41 Human carbonic anhydrase.

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Figure 8-42a The X-Ray structure of horse heart cytochrome.

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Figure 8-42bThe X-Ray structure of horse heart cytochrome.

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Figure 8-43a The H helix of sperm whale myoglobin. (a) A helical wheel representation in which the side chain positions about the α helix are projected down the helix axis onto a plane.

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Figure 8-43b The H helix of sperm whale myoglobin. (b) A skeletal model, viewed as in Part a.

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Figure 8-43c The H helix of sperm whale myoglobin. (c) A space-filling model, viewed from the bottom of the page in Parts a and b and colored as in Part b.

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Figure 8-44 A space-filling model of an antiparallel β sheet from concanavalin A.

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Figure 8-45 One subunit of the enzyme glyceraldehyde3-phosphate dehydrogenase from Bacillus stearothermophilus.

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Figure 8-46abc Schematic diagrams of supersecondary structures

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Figure 8-46dSchematic diagrams of supersecondary structures.

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Figure 8-47a X-Ray structures of 4-helix bundle proteins. (a) E. coli cytochrome b562.

Figure 8-47b X-Ray structures of 4-helix bundle proteins.

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(b) Human growth hormone.

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Figure 8-48 The immunoglobulin fold.

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Figure 8-49 Retinol binding protein.

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Figure 8-50a X-Ray structure of the C-terminal domain of bovine γ-β crystallin. (a) A topological diagram showing how its two Greek key motifs are arranged in a β barrel.

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Figure 8-50bX-Ray structure of the C-terminal domain of bovine γ-β crystallin. (b) The 83-residue peptide backbone displayed in ribbon form.

Figure 8-51a X-Ray structure of the enzyme peptide-N4-(Nacetyl-β-D-glucosaminyl)asparagine amidase F from

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Flavobacterium meningosepticum.

Figure 8-51bX-Ray structure of the enzyme peptide-N 4(N-acetyl-β-D-glucosaminyl)asparagine amidase F from

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Flavobacterium meningosepticum.

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Figure 8-52 left The X-ray structure of the 247-residue enzyme triose phosphate isomerase (TIM) from chicken muscle.

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Figure 8-53 Topological diagrams of (a) carboxypeptidase A and (b) the N-terminal domain of glyceraldehyde-3phosphate dehydrogenase.

Figure 8-54a X-Ray structures of open β sheet-containing enzymes. (a) Dogfish lactate dehydrogenase, N-terminal

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domain (residues 20-163 of this 330-residue protein).

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Figure 8-54bX-Ray structures of open β sheet-containing enzymes. (b) Porcine adenylate kinase (195 residues).

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Figure 8-55 Doubly wound sheets.

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Table 8-4 (top) Structural Bioinformatics Websites (URLs).

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Table 8-4 (middle) Structural Bioinformatics Websites (URLs).

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Table 8-4 (bottom) Structural Bioinformatics Websites (URLs)

Protein Stability • • • •

Electrostatic Forces Hydrogen Bonding Hydrophobic Forces Disulfide Bonds

• Protein Denaturation

Page 258

Figure 8-56 A GRASP diagram of human growth hormone.

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Figure 8-57 Dipole-dipole interactions.

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Table 8-5 Thermodynamic Changes for Transferring Hydrocarbons from Water to Nonpolar Solvents at 25°C.

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Figure 8-58 The orientational preference of water molecules next to a nonpolar solute.

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Figure 8-59 Structure of the clathrate (n-C4H9)3S+F– •23H2O

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Figure 8-60 Hydropathic index plot for bovine chymotrypsinogen.

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Table 8-6

Hydropathy Scale for Amino Acid Side Chains.

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Figure 8-61 Protein denaturation.

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Figure 8-62 Melting temperature of RNase A as a function of the concentration of various salts.

Quaternary Structure

The three dimensional structure of proteins containing multiple subunits

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Figure 8-63 The quaternary structure of hemoglobin.

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Figure 8-64a Some possible symmetries of proteins with identical protometers. (a) Assemblies with the cyclic symmetries C2, C3, and C5.

Figure 8-64bSome possible symmetries of proteins with identical protometers. (b) Assemblies with the dihedral symmetries D2, D4, and D3.

Figure 8-64c Some possible symmetries of proteins with identical protometers. (c) Assemblies with T, O, and I symmetries.

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Figure 8-65 A dimer of transthyretin as viewed down its twofold axis (red lenticular symbol).

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Figure 8-66a X-Ray structure of glutamine synthetase from Salmonella typhimurium.

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Figure 8-66bX-Ray structure of glutamine synthetase from Salmonella typhimurium.

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Figure 8-67 A helical structure composed of a single kind of subunit.

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Figure 8-68 Cross-linking agents.

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Figure 8-69 Stereo drawing of a tetrahedron inscribed in a cube.

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Table 8-7 (top)Torsion Angles (φ, ψ), for Residues 24 to 73 of Hen Egg White Lysozyme.

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