Protein secondary structures

criteria of proteins secondary structures

1. The bond lengths and bond angles should be distorted as little as possible.

   
   

2. No two atoms should approach one another more closely than is allowed by their van der Waals radii; thus, there are steric restrictions to rotations around the bonds that make up the peptide backbone.
   
   

3. The six atoms in the peptide amide group must remain coplanar with the associated α-carbons in the trans configuration. Only allowing the alpha carbons to rotate.
   
   

4. Some kind of noncovalent bonding is necessary to stabilize a regular folding. The most obvious possibility is hydrogen bonding between amide protons and carbonyl oxygens.

five main types of secondary structures?

• b Strand (antiparallel)

• b Strand (parallel)

• a helix

• 3-10 helix

• Polypeptide II helix.

How many polypeptide chains are required to form an a-helix versus a b-sheet?

a-helix: Requires only one continuous polypeptide chain, as the hydrogen bonds form within that single coiled strand.

b-sheet: Can be formed by one single chain folding back on itself (creating multiple segments), OR by two or more multiple separate polypeptide chains interacting next to each other.

What is the specific direction of rotation for a standard a-helix?

Right-handed rotation.

What defines the directionality of strands in a b-sheet?

The N-terminus to C-terminus (N to C) orientation.

What are the two ways b-strands can align next to each other based on their N-to-C direction?

Parallel (same direction) or Anti-parallel (opposite directions).

What type of chemical bond primarily stabilizes the structure of both a-helices and b-sheets?

Hydrogen bonds (between the backbone atoms).

In secondary structures like a-helices and b-sheets, where do the R-groups (side chains) point?

They stick outwards away from the core backbone.

What does it mean if a secondary structure is "amphiphilic" (or amphipathic)?

it means the structure has two distinct faces: one polar (hydrophilic) and one nonpolar (hydrophobic).

What is the spacing pattern of side chains required to create an amphiphilic a-helix?

Side chains of similar polarity occur every 3–4 residues. (This is because one full turn of the helix is about 3.6 residues, so this pattern stacks them on the same side).

the polar and nonpolar groups form opposite faces.

What is the spacing pattern of side chains required to create an amphiphilic b-strand?

Alternating polar and nonpolar side chains.

Why does an amphiphilic b-strand have alternating polarities?

Because R-groups on b-strand point in opposite directions (up, then down, then up) sequentially

What does a Ramachandran Plot map?

The allowable rotation angles of the polypeptide backbone.

The backbone rotations mapped on a Ramachandran plot occur around which specific atom?

The alpha carbon (a-carbon).

Why are the allowed rotation angles around the a-carbon so strict?

To prevent steric hindrance (preventing atoms from clashing into each other and maintaining proper distances).

What is steric hindrance in the context of a protein backbone?

When atoms are forced too close together, their electron clouds repel each other, preventing the structure from forming.

How do different secondary structures (like a-helices vs. b-sheets) relate to the Ramachandran plot?

Each distinct shape exhibits different allowable angles, meaning they cluster in different, specific regions on the plot.

Fibrous proteins

elongated and filamentous molecules with well-defined secondary structures. They usually play structural roles in the cell—they hold things together.

Fibrous proteins include the major proteins of skin and connective tissue, and of animal fibers like hair and silk.

The Keratins

Two important classes of fibrous proteins that have similar amino acid sequences and biological function are called α- and β-keratins.

α-keratins

are the major proteins of hair and fingernails, and comprise a major fraction of animal skin.

members of a broad group of intermediate filament proteins

intermediate filament proteins

play important structural roles in the nuclei, cytoplasm, and surfaces of many cell types.

All of the intermediate filament proteins are predominantly α-helical in structure

coiled-coil

two α-helices wrap around each other to make a superhelix.

β-keratins

The β-keratins are found mostly in birds and reptiles in structures like feathers and scales.

Fibroin

The β-sheet structure is most elegantly utilized in the fibers spun by silkworms and spiders

Almost half of its residues are glycine.

silkworm fibroin

contains long regions of stacked antiparallel β sheets, with the polypeptide chains running parallel to the fiber axis

The stacked sheets are held together by noncovalent interactions between the interdigitated side chains

fibers are very flexible because bonding between the sheets involves only the weak van der Waals interactions between the side chains, which provide little resistance to bending.

True

collagen is the most abundant single protein in most vertebrates.

true

tropocollagen

a triple helix of three polypeptide chains, each about 1000 residues in length

basic unit of the collagen fiber

why is tropocollagen every third residue must be a glycine?

Any side chain other than —H would be too bulky to fit within the tropocollagen triple helix.

Collagen fibers are built from triple helices of polypeptides rich in glycine and proline.

true

why is the left handed collagen helix favored?

it is favored by the presence of proline or hydroxyproline in the tropocollagen molecule.

A repetitive motif in the sequence is Gly–X–Y, where X is often proline and Y is proline or hydroxyproline.

Scurvy

is caused by vitamin C deficiency, which leads to failure to hydroxylate prolines and lysines in collagen.

Consequences are as might be expected: Lesions develop in skin and gums, and blood vessels weaken. The condition quickly improves with administration of vitamin C.

Toughness of collagen is due to?

the cross-linking of tropocollagen molecules to one another via a reaction involving lysine side chains.

Some of the lysine side chains are oxidized to aldehyde derivatives (allysine), which can then react with either a lysine residue, or with one another. Two allysine side chains react to produce a cross-link

as we age, the more cross-linked the Collagen

therefore more brittle, with age.