The Ramachandran diagram. - PowerPoint PPT Presentation

The ramachandran diagram l.jpg
Download
1 / 79

  • 727 Views
  • Updated On :
  • Presentation posted in: Pets / Animals

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.

I am the owner, or an agent authorized to act on behalf of the owner, of the copyrighted work described.

Download Presentation

The Ramachandran diagram.

An Image/Link below is provided (as is) to download presentation

Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author.While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server.


- - - - - - - - - - - - - - - - - - - - - - - - - - E N D - - - - - - - - - - - - - - - - - - - - - - - - - -

Presentation Transcript


The ramachandran diagram l.jpg

The Ramachandran diagram.


Allowed phi and psi torsion angles in proteins l.jpg

Allowed phi and psi torsion angles in proteins.


The ramachandran diagram of gly residues in a polypeptide chain l.jpg

The Ramachandran diagram of Gly residues in a polypeptide chain.


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


Slide5 l.jpg

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


The hydrogen bonding pattern of several polypeptide helices l.jpg

The hydrogen bonding pattern of several polypeptide helices.


Slide7 l.jpg

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 pleated sheet: antiparallel orientation


B pleated sheets parallel orientation l.jpg

b pleated sheets: parallel orientation


A two stranded b antiparallel pleated sheet drawn to emphasize its pleated appearance l.jpg

A two-stranded b antiparallel pleated sheet drawn to emphasize its pleated appearance.


Slide11 l.jpg

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 l.jpg

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


Slide13 l.jpg

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

out-of-plane

crossovers

Connections between adjacent polypeptide strands in b pleated sheets.


Origin of a right handed crossover connection l.jpg

Origin of a right-handed crossover connection.


Reverse turns in polypeptide chains l.jpg

Reverse turns in polypeptide chains.


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 a keratin.


Slide19 l.jpg

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


Slide20 l.jpg

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


Slide21 l.jpg

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.


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 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 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)(2.4 angstrom resolution)


Slide30 l.jpg

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


Slide31 l.jpg

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 l.jpg

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


Slide33 l.jpg

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

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.


Human carbonic anhydrase l.jpg

Human carbonic anhydrase.


The x ray structure of horse heart cytochrome c hydrophobic residues in red l.jpg

The x-ray structure of horse heart cytochrome 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 c. (hydrophilic residues in green)


Slide40 l.jpg

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 l.jpg

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 l.jpg

The H helix of sperm whale myoglobin: a skeletal model.(orange = nonpolar; purple = polar)


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

orange = nonpolar

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

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

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


Schematic diagrams of supersecondary structures l.jpg

aa

bab

b-hairpin

Schematic diagrams of supersecondary structures.


Schematic diagrams of supersecondary structures47 l.jpg

Greek key motif

Schematic diagrams of supersecondary structures.


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

directionality of helices

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

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


X ray structure of the immunoglobulin fold l.jpg

stacked 4-stranded and

3-stranded antiparallel

b-sheets

X-ray structure of the immunoglobulin fold.


X ray structure of retinol binding protein l.jpg

Up-down b-barrel

X-ray structure of retinol binding protein.


Slide52 l.jpg

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 l.jpg

X-ray structure of the C-terminal domain of bovine g-b crystallin: the 83-residue peptide backbone displayed in ribbon form.


Slide54 l.jpg

X-ray structure of the enzyme, peptide-N4-(N-acetyl-b-D-glucosaminyl)asparagine amidase F from Flavobacterium meningosepticum.


Slide55 l.jpg

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 l.jpg

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


Slide57 l.jpg

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


Slide58 l.jpg

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 l.jpg

X-ray structures of open b sheet-containing enzymes: porcine adenylate kinase (195 residues).


Doubly wound sheets l.jpg

Doubly wound sheets.


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

Graphical 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


Hydropathic index plot for bovine chymotrypsinogen l.jpg

Hydropathic index plot for bovine chymotrypsinogen.


Protein denaturation curve l.jpg

Protein denaturation curve


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

strengthen hydrophobic

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.


The quaternary structure of hemoglobin l.jpg

The quaternary structure of hemoglobin


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.


A dimer of transthyretin as viewed down its twofold axis red lenticular symbol l.jpg

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


X ray structure of glutamine synthetase from salmonella typhimurium view down 6 fold symmetry axis l.jpg

X-ray structure of glutamine synthetase from Salmonella typhimurium - view down 6-fold symmetry axis


Slide74 l.jpg

X-ray structure of glutamine synthetase from 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

A helical structure composed of a single kind of subunit.


Chemical cross linking agents l.jpg

Chemicalcross-linking agents.


Structural bioinformatics websites urls l.jpg

Structural Bioinformatics Websites (URLs)


Structural bioinformatics websites urls78 l.jpg

Structural Bioinformatics Websites (URLs)


Structural bioinformatics websites urls79 l.jpg

Structural Bioinformatics Websites (URLs)


  • Login