MIRRAGGE - Minimum Information Required for Reproducible AGGregation Experiments.

Pedro M Martins,Francisco Figueiredo,Susanna Navarro,Alexandra Silva,Sandra Macedo-Ribeiro,Michał Burdukiewicz,Zsuzsa Sárkány,Francisca Pinheiro,Zuzana Bednarikova,Salvador Ventura,Vytautas Smirnovas,Louise C Serpell,Cláudio M Gomes,Oxana V Galzitskaya,Pedro José Barbosa Pereira,Annalisa Pastore,Daniel E Otzen,Mantas Žiaunys ,Maria Filipa Pinto ,Zuzana Gažová ,Rostislav Škrabana

doi:10.3389/fnmol.2020.582488

Abstract

Reports on phase separation and amyloid formation for multiple proteins and aggregation-prone peptides are recurrently used to explore the molecular mechanisms associated with several human diseases. The information conveyed by these reports can be used directly in translational investigation, e.g., for the design of better drug screening strategies, or be compiled in databases for benchmarking novel aggregation-predicting algorithms. Given that minute protocol variations determine different outcomes of protein aggregation assays, there is a strong urge for standardized descriptions of the different types of aggregates and the detailed methods used in their production. In an attempt to address this need, we assembled the Minimum Information Required for Reproducible Aggregation Experiments (MIRRAGGE) guidelines, considering first-principles and the established literature on protein self-assembly and aggregation. This consensus information aims to cover the major and subtle determinants of experimental reproducibility while avoiding excessive technical details that are of limited practical interest for non-specialized users. The MIRRAGGE table (template available in Supplementary Information) is useful as a guide for the design of new studies and as a checklist during submission of experimental reports for publication. Full disclosure of relevant information also enables other researchers to reproduce results correctly and facilitates systematic data deposition into curated databases.

Highlights

Aggregation of misfolded proteins and peptides is associated with common and rare neurodegenerative disorders and with amyloidoses (Aguzzi and O’Connor, 2010; Chiti and Dobson, 2017; Benson et al, 2018)
Protein self-assembly is a complex process that might result in the formation of amorphous aggregates, different oligomers or amyloid fibrils, heterogeneous species that often coexist during the aggregation process
We focus on the study of amyloid fibril formation, which can be addressed from the structural and the kinetic point of view

Summary

Introduction

Aggregation of misfolded proteins and peptides is associated with common and rare neurodegenerative disorders and with amyloidoses (Aguzzi and O’Connor, 2010; Chiti and Dobson, 2017; Benson et al, 2018). Classical neuropathological hallmarks such as neurofibrillary tangles in Alzheimer’s disease (AD), Lewy bodies in Parkinson’s disease (PD), or inclusion bodies in Huntington’s disease, have as main constituent characteristic polypeptides aggregated in the form of insoluble highly-ordered structures named amyloid fibrils (Westermark et al, 2007; Gremer et al, 2017). Occurring microcrystals are used by living cells for protein storage, protection and stabilization (Schönherr et al, 2018), whereas in crystallopathies such as eosinophilic inflammation, protein crystals have been reported as promising drug targets (Persson et al, 2019)

Objectives

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Methods