Untangling a protein's omega loops.

Untangling a protein's omega loops

The molecular backbones of globular proteins have an intricates structure. Segments of these chains may be coiled in the form of a helix or folded into parallel strands. The rest is sometimes classified as "random coil," but generally, it is neither random nor coiled. Recently, Jacquelyn F. Leszcynski and George D. Rose of Pennsylvania State University's Milton S. Hershey Medical Center in Hershey took a closer look at one group of random-coil segments often loosely described as "loops." Their systematic study reveals that compact loops, shaped like the Greek letter omega ([omega]), are common and may play an important role in the way protein molecules function. Their report appears in the Nov. 14 SCIENCE.

For their computer-aided survey of 67 proteins with known structures, the researchers established three criteria for defining omega loops. Such segments contain between 6 and 16 amino acids, they have no other regular structure, and the distance across the gap where the loop necks is less than 10 angstroms.

Leszczynski and Rose found 270 omega loops, abut four per protein molecule. Only six of the msallest proteins studied have no loops. Most of the loops are highly compact because loop side-chain atoms appear to pack tightly within the loop core. Nearly always, the loops sit at the molecule's surface.

These surface loops may be involved in processes like antibody binding or molecular recognition, the researchers say. If the loops function as integral units, they could be useful in bioengineering experiments that involve "clipping and swapping" protein segments. Such swapping processes may have occurred naturally as part of evolutionary change.