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A polyproline helix is a type of protein secondary structure which occurs in proteins comprising repeating proline residues. [1] A left-handed polyproline II helix (PPII, poly-Pro II, κ-helix [2]) is formed when sequential residues all adopt (φ,ψ) backbone dihedral angles of roughly (-75°, 150°) and have trans isomers of their peptide bonds.
The cyclic structure of proline's side chain locks the angle φ at approximately −65°. [19] Proline acts as a structural disruptor in the middle of regular secondary structure elements such as alpha helices and beta sheets; however, proline is commonly found as the first residue of an alpha helix and also in the edge strands of beta sheets.
Amino acids vary in their ability to form the various secondary structure elements. Proline and glycine are sometimes known as "helix breakers" because they disrupt the regularity of the α helical backbone conformation; however, both have unusual conformational abilities and are commonly found in turns.
Tandem repeats of short oligopeptides that are rich in glycine, proline, serine or threonine are capable of forming flexible structures that bind ligands under certain pH and temperature conditions. [6] Proline is a well-known alpha-helix breaker, however, amino acid repeats composed of proline may form poly-proline helices. [7]
The alpha helix is also commonly called a: Pauling–Corey–Branson α-helix (from the names of three scientists who described its structure); 3.6 13-helix because there are 3.6 amino acids in one ring, with 13 atoms being involved in the ring formed by the hydrogen bond (starting with amidic hydrogen and ending with carbonyl oxygen)
In 1954, Ramachandran & Kartha (13, 14) advanced a structure for the collagen triple helix on the basis of fiber diffraction data. It consists of a triple helix made of the repetitious amino acid sequence glycine-X-Y, where X and Y are frequently proline or hydroxyproline. [2] [3] Collagen folded into a triple helix is known as tropocollagen.
Hydroxyproline and proline play key roles for collagen stability. [4] They permit the sharp twisting of the collagen helix. [5] In the canonical collagen Xaa-Yaa-Gly triad (where Xaa and Yaa are any amino acid), a proline occupying the Yaa position is hydroxylated to give a Xaa-Hyp-Gly sequence.
A two-sided β-helix (right-handed) is found in some bacterial metalloproteases; its two loops are each six residues long and bind stabilizing calcium ions to maintain the integrity of the structure, using the backbone and the Asp side chain oxygens of a GGXGXD sequence motif. [20] This fold is called a β-roll in the SCOP classification.