MELD-accelerated molecular dynamics help determine amyloid fibril structures

Abstract

It is challenging to determine the structures of protein fibrils such as amyloids. In principle, Molecular Dynamics (MD) modeling can aid experiments, but normal MD has been impractical for these large multi-molecules. Here, we show that MELD accelerated MD (MELD x MD) can give amyloid structures from limited data. Five long-chain fibril structures are accurately predicted from NMR and Solid State NMR (SSNMR) data. Ten short-chain fibril structures are accurately predicted from more limited restraints information derived from the knowledge of strand directions. Although the present study only tests against structure predictions – which are the most detailed form of validation currently available – the main promise of this physical approach is ultimately in going beyond structures to also give mechanical properties, conformational ensembles, and relative stabilities.