Can Polyproline form a triple helix?

In the middle of the 50s, the structure of the fibrous protein collagen has been determined, and found to contain a left-handed triple-helical structure (Phi= -75 , Psi= 155 , n= -3.3). This structure is called polyproline II (PPII) helix.

What does a Ramachandran diagram tell us about protein structure?

The Ramachandran plot is a plot of the torsional angles – phi (φ)and psi (ψ) – of the residues (amino acids) contained in a peptide. By making a Ramachandran plot, protein structural scientists can determine which torsional angles are permitted and can obtain insight into the structure of peptides.

What does Ramachandran plot show?

The Ramachandran plot shows the statistical distribution of the combinations of the backbone dihedral angles ϕ and ψ. In theory, the allowed regions of the Ramachandran plot show which values of the Phi/Psi angles are possible for an amino acid, X, in a ala-X-ala tripeptide (Ramachandran et al., 1963).

Where is proline in Ramachandran plot?

Proline has restrictions in phi-psi space that arise from the 5-membered ring. Phi is restricted to approxamatly -60 by the ring and psi angles fall into two groupings near -45 and +135 in the helical and sheet regions of the Ramachandran plot.

Why is collagen a triple helix?

The Basic Structural Unit of Collagen Is a Triple Helix Because its abundance in tendon-rich tissue such as rat tail makes the fibrous type I collagen easy to isolate, it was the first to be characterized.

How does a π Helix differ from an α-helix?

The amino acids in a standard π-helix are arranged in a right-handed helical structure. group of the amino acid five residues earlier; this repeated i + 5 → i hydrogen bonding defines a π-helix. Similar structures include the 310 helix (i + 3 → i hydrogen bonding) and the α-helix (i + 4 → i hydrogen bonding).

When would you use a Ramachandran plot?

A Ramachandran plot can be used in two somewhat different ways. One is to show in theory which values, or conformations, of the ψ and φ angles are possible for an amino-acid residue in a protein (as at top right).

Who discovered Ramachandran plot?

Gopalasamudram Narayanan Ramachandran
Gopalasamudram Narayanan Ramachandran, or G.N. Ramachandran, FRS (8 October 1922 – 7 April 2001) was an Indian physicist who was known for his work that led to his creation of the Ramachandran plot for understanding peptide structure. He was the first to propose a triple-helical model for the structure of collagen.

Why is proline Ramachandran plot so small?

Its van der Waals radius is smaller and is thus less restricted. Proline, on the other hand has a 5-membered ring as a side chain. Therefore it is much more restricted than the other amino acids and allows for only a limited number of ψ and φ. Gly is the least restricted, Pro is the most restricted.

What angle is phi?

Typical values are phi = -140 degrees and psi = 130 degrees.

Can glycine be in an alpha helix?

All the amino acids are found in α-helices, but glycine and proline are uncommon, as they destabilize the α-helix.

How is the Ramachandran plot different from the proline plot?

In contrast, the Ramachandran plot for proline, with its 5-membered-ring side chain connecting Cα to backbone N, shows a limited number of possible combinations of ψ and φ (see Pro plot in gallery ). The residue preceding proline (“pre-proline”) also has limited combinations compared to the general case.

How is a left handed polyproline helix formed?

A left-handed polyproline II helix ( PPII, poly-Pro II) is formed when sequential residues all adopt (φ,ψ) backbone dihedral angles of roughly (-75°, 150°) and have trans isomers of their peptide bonds. This PPII conformation is also common in proteins and polypeptides with other amino acids apart from proline.

Which is an analog of the polyproline helix?

The analog of the poly-Pro II helix in poly-glycine is called the poly-Gly II helix. Some proteins, such as the antifreeze protein of Hypogastrura harveyi consist of bundles of glycine-rich polyproline II helices.

How is a Ramachandran plot generated from PCNA?

For instance, the small strip of allowed values along the lower-left edge of the plot are a continuation of the large, extended-chain region at upper left. A Ramachandran plot generated from human PCNA, a trimeric DNA clamp protein that contains both β-sheet and α-helix ( PDB ID 1AXC).