Automated Fibril Structure Calculation in Xplor-NIH

Abstract

Amyloid fibrils are protein assemblies that are pathologically linked to neurodegenerative diseases. Structures of these fibrils can aid in development of highly specific ligands for diagnostic imaging and therapeutics. Solid-state NMR (SSNMR) has been a leading technology for solving fibril structures; however, most protocols require manual analysis of extensive spectral data, presenting a major bottleneck in structure determination. Existing automation routines fall short for symmetric multimeric assemblies like amyloids due to high cross peak degeneracy and the need to account for multiple protein subunits. Here, we employ the PASD protocol in conjunction with strict symmetry in the XPLOR-NIH structure determination software on a previously determined structure of an α-synuclein (Asyn) amyloid fibril implicated in Parkinson Disease. The automated protocol generated a structure of comparable, if not superior, quality in just a few days of computational time, eliminating one of the major bottlenecks towards solving complicated structures by SSNMR.

Keywords: Automated assignment, automated structure calculation, α-synuclein, fibril, PASD, protofilament, solid-state NMR, strict-symmetry, XPLOR-NIH, Parkinson Disease