Automated fibril structure calculations in Xplor-NIH

Abstract

Amyloid fibrils are protein assemblies that are pathologically linked to neurodegenerative diseases. Fibril structures can aid development of highly specific ligands for diagnostic imaging and therapeutics. Solid-state NMR (SSNMR) is a viable approach to solving fibril structures; however, most SSNMR protocols require manual analysis of extensive spectral data, presenting a major bottleneck to determining structures. Standard 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 probabilistic assignment for structure determination protocol in conjunction with strict; symmetry in Xplor-NIH structure determination software, demonstrating the methodology using data from a previous structure of an α-synuclein (Asyn) fibril implicated in Parkinson disease. The automated protocol generated a structure of comparable, if not superior, quality in a few days of computational time, reducing the manual effort required; to solve amyloid structures by SSNMR.

Keywords: PASD; Parkinson disease; Xplor-NIH; automated assignment; automated structure calculation; fibril; protofilament; solid-state NMR; strict-symmetry; α-synuclein.