Polypeptide loop structures

The binding of PALA to the R conformation of aspartate carbamoyl transferase. Arg 105 and His 134 are provided by one domain of a c subunit, and Arg 167 and Arg 229 by the other domain. Ser 80 and Lys 84 are part of a loop of protein from a different c subunit. The PALA is indicated by red. The wavy green lines indicate polypeptide backbone structure. 

Can a polypeptide chain fold into a regularly repeating structure In 1951, Linus Pauling and Robert Corey proposed two periodic structures called the a helix (alpha helix) and the p pleated sheet (beta pleated sheet). Subsequently, other structures such as the P turn and omega ( Q) loop were identified. Although not periodic, these common turn or loop structures are well defined and contribute with a helices and P sheets to form the final protein structure. 

Figure 1.29 Alternative cartoon depictions of proteins, (a) surface display structure of small metal rich protein cytochrome c (horse heart) (pdb Ihrc) showing Van der Waal s surface coloured for positive charge (blue) and for negative charge (red). Ball and stick representations of iron-porphyrin macrocycle (prosthetic group) are shown (red) for each subunit with central iron ion rendered as Van der Waals sphere (light blue) (b) CPK structure of cytochrome c in which all polypeptide atoms are rendered as Van der Waals spheres (purple). Porphryin and iron ion are shown as in Fig. 1.28 (c) schematic display structure (top view) of parallel a/p-protein triose phosphate isomerase (chicken muscle) (pdb Itim) with a-helix shown as cylinders (red), 8-strands as arrowed ribbons (light blue), loop structures (random coil) as rods (light grey) (d) schematic display structure (side view) of triose phosphate isomerase, otherwise as for (c).

Evidence supporting the presence of several zinc-stabilized polypeptide loops in TFIIIA came from the results of limited proteolytic digestion (Miller et al. 1985). This was corroborated by EXAFS (extended X-ray absorption fine structure) measurements on 7S RNP particles (Diakun et al. 

Loops are a class of secondary structure that reverse the direction of a polypeptide chain and are usually situated at the protein surface. Unlike a-helices and )6-sheets, loop structures have no regular patterns of dihedral angles and hydrogen bonds (Leszczynski and Rose, 1986 Fetrow, 1995). 

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