Molecule of the Month: Amyloids

Proteins have evolved to fold into a functional shape, or in cases where a flexible tether is needed, to remain consistently unfolded. In some cases, however, proteins aggregate to form unwanted structures, which can have dangerous consequences. The amyloid-beta precursor protein is a perfect example. In its normal form, it is a membrane-bound protein with folded regions connected by flexible tethers. But if the protein chain is broken, some of the resulting peptides aggregate into long fibrils, termed "amyloids," that can gum up the proper working of cells.

When these fibrils are studied by x-ray diffraction, they show a distinctive pattern, termed the "cross-beta pattern." This is caused by the way that the many small peptides in the fibril stack upon one another, forming individual beta strands that hydrogen bond with their neighbors to form a huge, extended beta sheet. This results in a very sturdy structure that rivals the strength of steel or spider silk.

When these fibrils are formed in the brain, they contribute to the development of Alzheimer's disease. The amyloid fibril shown here, PDB entry 2m4j , was isolated from a patient with Alzheimer's disease and shows how many small peptides stack to form a three-fold-symmetric fibril. Some amyloid structures are also infectious. Prion diseases, such as mad cow disease or kuru, can be caused when the amyloid form of a protein is eaten. The amyloids then act as a template to nucleate the misfolding and aggregation of normal proteins in the body, leading to the formation of many more amyloid fibrils.

Since amyloid structures are so large and fibrillar, they have been difficult to study by traditional structure determination methods. Several approaches have been taken. Scientists have cut the amyloid proteins into even smaller pieces, which are able to form crystals. For instance, the crystallographic structure shown on the left (PDB entry 3nhc ) is a peptide with six amino acids from a human prion protein. These types of structures have been used to discover the many different ways that amyloid proteins stack into an extended beta sheet. Hybrid methods, which combine several experimental techniques, have been used to determine many structures, including a yeast prion (center, PDB entry 2kj3 ), a fragment of transthyretin (right, PDB entry 3zpk ), and the amyloid-beta structure shown above. In these structures, solid state NMR is used to determine local conformational features, beta-sheet structure, and long range contacts between atoms. Electron microscopy is used to determine the overall dimensions of the fibril and the number of subunits. Finally, molecular modeling is used to find structures that are consistent with this data.