Structure of amyloid fibrils. A computational analysis

Abstract

Amyloid fibrils are misfolded proteins related to several different diseases, such as Alzheimer’s and Parkinson’s disease. The aims of the report are to computationally analyze significant patterns and distributions of certain amino acids in the structure of amyloid fibrils. The direction relative to the fibril core is investigated for the charged amino acids and those present in bends. Amino acids in the amyloid fibrils tend to stack upon each other, these stacks are identified for the amino acids containing aromatic rings and the tilt of the aromatic rings are calculated relative to the axis of the fibril. The result from the analysis of the bends does not show significant patterns exclusive to amyloid fibrils, while the analysis of the charged amino acids indicates that they tend to face outwards relative to the fibril core. The tilt of the aromatic rings tends to be distributed around 55°. The results are consistent with previous findings and provide some information which could be of use when predicting the structure of amyloid fibrils.