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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 l.jpg

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


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



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


B pleated sheet antiparallel orientation l.jpg
b occur in proteins with the commonly occurring pleated sheet: antiparallel orientation


B pleated sheets parallel orientation l.jpg
b occur in proteins with the commonly occurring pleated sheets: parallel orientation


A two stranded b antiparallel pleated sheet drawn to emphasize its pleated appearance l.jpg
A two-stranded occur in proteins with the commonly occurring b antiparallel pleated sheet drawn to emphasize its pleated appearance.


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


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


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


Connections between adjacent polypeptide strands in b pleated sheets l.jpg

hairpin right-handed twist of

out-of-plane

crossovers

Connections between adjacent polypeptide strands in b pleated sheets.




Space filling representation of an loop comprising residues 40 to 54 of cytochrome c l.jpg
Space-filling representation of an Ω loop comprising residues 40 to 54 of cytochrome c.


The structure of a keratin l.jpg
The structure of residues 40 to 54 of cytochrome a keratin.


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


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


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


The triple helix of collagen l.jpg
The triple helix of collagen. helical region of the bovine


Slide23 l.jpg

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 l.jpg

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 l.jpg

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.


A biosynthetic pathway for cross linking lys hyl and his side chains in collagen l.jpg
A biosynthetic pathway for (Pro-Hyp-Gly)cross-linking Lys, Hyl, and His side chains in collagen.


X ray diffraction photograph of a single crystal of sperm whale myoglobin l.jpg
X-Ray diffraction photograph of a single crystal of (Pro-Hyp-Gly)sperm whale myoglobin.


Electron density maps of proteins heme of sperm whale myoglobin 2 angstrom resolution l.jpg
Electron density maps of proteins (heme of sperm whale myoglobin) (2 angstrom resolution)


Electron density maps of proteins sperm whale myoglobin 2 4 angstrom resolution l.jpg
Electron density maps of proteins (sperm whale myoglobin) myoglobin) (2 angstrom resolution)(2.4 angstrom resolution)


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Sections through the electron density map of diketopiperazine calculated at the indicated resolution.


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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.


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The 2D proton NMR structures of proteins: NMR structure of a 64-residue polypeptide comprising the Src protein SH3 domain.


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Representations of the X-ray structure of sperm whale myoglobin: the protein and its bound heme are drawn in stick form.


Slide34 l.jpg

8 helices myoglobin: the protein and its bound heme are drawn in stick form.

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 l.jpg
Representations of the X-ray structure of sperm whale myoglobin: a computer-generated cartoon drawing.


The x ray structure of jack bean protein concanavalin a l.jpg
The X-ray structure of jack bean protein concanavalin A. myoglobin: a computer-generated cartoon drawing.


Human carbonic anhydrase l.jpg
Human carbonic anhydrase. myoglobin: a computer-generated cartoon drawing.


The x ray structure of horse heart cytochrome c hydrophobic residues in red l.jpg
The x-ray structure of horse heart cytochrome myoglobin: a computer-generated cartoon drawing.c. (hydrophobic residues in red)


The x ray structure of horse heart cytochrome c hydrophilic residues in green l.jpg
The x-ray structure of horse heart cytochrome myoglobin: a computer-generated cartoon drawing.c. (hydrophilic residues in green)


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H-helix myoglobin: a computer-generated cartoon drawing.

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 l.jpg

The H helix of sperm whale myoglobin. ( myoglobin: a computer-generated cartoon drawing.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 l.jpg
The H helix of sperm whale myoglobin: a skeletal model. myoglobin: a computer-generated cartoon drawing.(orange = nonpolar; purple = polar)


The h helix of sperm whale myoglobin a space filling model l.jpg

orange = nonpolar myoglobin: a computer-generated cartoon drawing.

purple = polar

The H helix of sperm whale myoglobin: a space-filling model.


A space filling model of an antiparallel b sheet from concanavalin a l.jpg

red = nonpolar myoglobin: a computer-generated cartoon drawing.

purple = polar

A space-filling model of an antiparallel b sheet from concanavalin A.


One subunit of the enzyme glyceraldehyde 3 phosphate dehydrogenase from bacillus stearothermophilus l.jpg

two domains myoglobin: a computer-generated cartoon drawing.

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


Schematic diagrams of supersecondary structures l.jpg

aa myoglobin: a computer-generated cartoon drawing.

bab

b-hairpin

Schematic diagrams of supersecondary structures.


Schematic diagrams of supersecondary structures47 l.jpg

Greek key motif myoglobin: a computer-generated cartoon drawing.

Schematic diagrams of supersecondary structures.


X ray structures of 4 helix bundle proteins e coli cytochrome b 562 l.jpg

directionality of helices myoglobin: a computer-generated cartoon drawing.

X-ray structures of 4-helix bundle proteins: E. coli cytochrome b562.


X ray structures of 4 helix bundle proteins human growth hormone l.jpg

directionality of helices myoglobin: a computer-generated cartoon drawing.

X-ray structures of 4-helix bundle proteins: human growth hormone.


X ray structure of the immunoglobulin fold l.jpg

stacked 4-stranded and myoglobin: a computer-generated cartoon drawing.

3-stranded antiparallel

b-sheets

X-ray structure of the immunoglobulin fold.


X ray structure of retinol binding protein l.jpg

Up-down myoglobin: a computer-generated cartoon drawing.b-barrel

X-ray structure of retinol binding protein.


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


Slide53 l.jpg
X-ray structure of the C-terminal domain of bovine myoglobin: a computer-generated cartoon drawing.g-b crystallin: the 83-residue peptide backbone displayed in ribbon form.


Slide54 l.jpg
X-ray structure of the enzyme, peptide- myoglobin: a computer-generated cartoon drawing.N4-(N-acetyl-b-D-glucosaminyl)asparagine amidase F from Flavobacterium meningosepticum.


Slide55 l.jpg
X-ray structure of the enzyme, peptide- myoglobin: a computer-generated cartoon drawing.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 l.jpg
The X-ray structure of the 247-residue enzyme triose phosphate isomerase (TIM) from chicken muscle.


Slide57 l.jpg
Topological diagrams of ( phosphate isomerase (TIM) from chicken muscle.a) carboxypeptidase A and (b) the N-terminal domain of glyceraldehyde-3-phosphate dehydrogenase.


Slide58 l.jpg

X-ray structures of open phosphate isomerase (TIM) from chicken muscle.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 l.jpg
X-ray structures of open phosphate isomerase (TIM) from chicken muscle.b sheet-containing enzymes: porcine adenylate kinase (195 residues).


Doubly wound sheets l.jpg
Doubly wound sheets. phosphate isomerase (TIM) from chicken muscle.


A grasp diagram of human growth hormone helps predict protein interactions with charged molecules l.jpg

G phosphate isomerase (TIM) from chicken muscle.raphical Representation

and Analysis of Surface

Properties

A GRASP diagram of human growth hormone (helps predict protein interactions with charged molecules)


Thermodynamic changes for transferring hydrocarbons from water to nonpolar solvents at 25 c l.jpg
Thermodynamic changes for transferring hydrocarbons from water to nonpolar solvents at 25°C.


Hydropathy scale for amino acid side chains l.jpg
Hydropathy Scale for Amino Acid Side Chains water to nonpolar solvents at 25°C.


Hydropathic index plot for bovine chymotrypsinogen l.jpg
Hydropathic index plot for bovine chymotrypsinogen. water to nonpolar solvents at 25°C.


Protein denaturation curve l.jpg
Protein denaturation water to nonpolar solvents at 25°C.curve


Melting temperature of rnase a as a function of the concentration of various salts l.jpg

strengthen hydrophobic water to nonpolar solvents at 25°C.

interactions

Hofmeister series

chaotropic

Weaken hydrophobic

interactions

Melting temperature of RNase A as a function of the concentration of various salts.


Slide67 l.jpg

The structural hierarchy in proteins. water to nonpolar solvents at 25°C.


The quaternary structure of hemoglobin l.jpg
The quaternary structure of hemoglobin water to nonpolar solvents at 25°C.


Slide69 l.jpg
Some possible symmetries of proteins with identical protomers. (a) Assemblies with the cyclic symmetries C2, C3, and C5.


Slide70 l.jpg
Some possible symmetries of proteins with identical protomers. (b) Assemblies with the dihedral symmetries D2, D4, and D3.


Slide71 l.jpg
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 l.jpg
X-ray structure of glutamine synthetase from protomers. (Salmonella typhimurium - view down 6-fold symmetry axis


Slide74 l.jpg
X-ray structure of glutamine synthetase from protomers. (Salmonella typhimurium - view down one of the 2-fold symmetry axes


A helical structure composed of a single kind of subunit l.jpg

actin, tubulin protomers. (

A helical structure composed of a single kind of subunit.


Chemical cross linking agents l.jpg
Chemical protomers. (cross-linking agents.





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