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The Ramachandran diagram. Allowed phi and psi torsion angles in proteins. The Ramachandran diagram of Gly residues in a polypeptide chain. Cis/Trans Isomerization: Proline. trans. cis. Energy difference between these forms is small.

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slide4

Cis/Trans Isomerization: Proline

trans

cis

Energy difference between these forms is small.

Nearly all Xaa-Pro linkages are biosynthesized in the trans form.

~10% of these peptide bonds are in the cis form in globular proteins.

Interconversion catalyzed by peptidyl prolyl cis-trans isomerases

slide5

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

slide7
Comparison of the two polypeptide helices that occasionally occur in proteins with the commonly occurring a helix.
slide11

Stereo space-filling representation of the 6-stranded antiparallel b pleated sheet in jack bean concanavalin A as determined by crystal X-ray analysis.

slide12
Polypeptide chain folding in proteins illustrating the right-handed twist of b sheets: bovine carboxypeptidase A.
slide13

Polypeptide chain folding in proteins illustrating the right-handed twist of b sheets: chicken muscle triose phosphate isomerase. (b barrel)

slide19
The two-stranded coiled coil: view down the coil axis showing the interactions between the nonpolar edges of the a helices.
slide20

The two-stranded coiled coil: side view in which the polypeptide back bone is represented by skeletal (left) and space-filling (right) forms.

slide21
The amino acid sequence at the C-terminal end of the triple helical region of the bovine a1(I) collagen chain.
slide23

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.

slide24

X-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.

slide25

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.

electron density maps of proteins sperm whale myoglobin 2 4 angstrom resolution
Electron density maps of proteins (sperm whale myoglobin)(2.4 angstrom resolution)
slide30
Sections through the electron density map of diketopiperazine calculated at the indicated resolution.
slide31

The 2D proton NMR structures of proteins: a NOESY spectrum of a protein presented as a contour plot with two frequency axes w1 and w2.

slide32
The 2D proton NMR structures of proteins: NMR structure of a 64-residue polypeptide comprising the Src protein SH3 domain.
slide33
Representations of the X-ray structure of sperm whale myoglobin: the protein and its bound heme are drawn in stick form.
slide34

8 helices

Representations of the X-ray structure of sperm whale myoglobin: a diagram in which the protein is represented by its computer-generated Ca backbone.

slide35
Representations of the X-ray structure of sperm whale myoglobin: a computer-generated cartoon drawing.
the x ray structure of horse heart cytochrome c hydrophilic residues in green
The x-ray structure of horse heart cytochrome c. (hydrophilic residues in green)
slide40

H-helix

Representations of the x-ray structure of sperm whale myoglobin: a diagram in which the protein is represented by its computer-generated Ca backbone.

slide41

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

the h helix of sperm whale myoglobin a skeletal model orange nonpolar purple polar
The H helix of sperm whale myoglobin: a skeletal model.(orange = nonpolar; purple = polar)
one subunit of the enzyme glyceraldehyde 3 phosphate dehydrogenase from bacillus stearothermophilus

two domains

One subunit of the enzyme glyceraldehyde-3-phosphate dehydrogenase from Bacillus stearothermophilus.
slide52

X-ray structure of the C-terminal domain of bovine g-b crystallin: a topological diagram showing how its two Greek key motifs are arranged in a b barrel.

slide53
X-ray structure of the C-terminal domain of bovine g-b crystallin: the 83-residue peptide backbone displayed in ribbon form.
slide54
X-ray structure of the enzyme, peptide-N4-(N-acetyl-b-D-glucosaminyl)asparagine amidase F from Flavobacterium meningosepticum.
slide55
X-ray structure of the enzyme, peptide-N 4-(N-acetyl-b-D-glucosaminyl)asparagine amidase F from Flavobacterium meningosepticum.
the x ray structure of the 247 residue enzyme triose phosphate isomerase tim from chicken muscle
The X-ray structure of the 247-residue enzyme triose phosphate isomerase (TIM) from chicken muscle.
slide57
Topological diagrams of (a) carboxypeptidase A and (b) the N-terminal domain of glyceraldehyde-3-phosphate dehydrogenase.
slide58

X-ray structures of open b sheet-containing enzymes: dogfish lactate dehydrogenase, N-terminal domain (residues 20-163 of this 330-residue protein).

x ray structures of open b sheet containing enzymes porcine adenylate kinase 195 residues
X-ray structures of open b sheet-containing enzymes: porcine adenylate kinase (195 residues).
a grasp diagram of human growth hormone helps predict protein interactions with charged molecules

Graphical Representation

and Analysis of Surface

Properties

A GRASP diagram of human growth hormone (helps predict protein interactions with charged molecules)
melting temperature of rnase a as a function of the concentration of various salts

strengthen hydrophobic

interactions

Hofmeister series

chaotropic

Weaken hydrophobic

interactions

Melting temperature of RNase A as a function of the concentration of various salts.
slide69
Some possible symmetries of proteins with identical protomers. (a) Assemblies with the cyclic symmetries C2, C3, and C5.
slide70
Some possible symmetries of proteins with identical protomers. (b) Assemblies with the dihedral symmetries D2, D4, and D3.
slide71
Some possible symmetries of proteins with identical protomers. (c) Assemblies with T, O, and I symmetries.
x ray structure of glutamine synthetase from salmonella typhimurium view down 6 fold symmetry axis
X-ray structure of glutamine synthetase from Salmonella typhimurium - view down 6-fold symmetry axis
slide74
X-ray structure of glutamine synthetase from Salmonella typhimurium - view down one of the 2-fold symmetry axes