Conformational preferences of non-polar amino acid residues: An additional factor in amyloid formation

Abstract

Amyloid consists of β-sheet polymers and is associated with disease and with functional assemblies. Amyloid-forming proteins differ widely in native structures and sequences. We describe here how conformational preferences of non-polar amino acid residues can affect amyloid formation. The most non-polar residues promote either β-strands (Val, Ile, Phe, and Cys, VIFC) or α-helices (Leu, Ala, and Met, LAM), while the most polar residues promote only α-helices. For 12 proteins associated with disease, the localizations of the amyloid core regions are known. Eleven of these contain segments that are biased for VIFC, but essentially lack segments that are biased for LAM. For the amyloid β-peptide associated with Alzheimer’s disease and an amyloidogenic fragment of the prion protein, observed effects of mutations support that VIFC bias favors formation of β-sheet aggregates and amyloid, while LAM bias prevents it. VIFC and LAM profiles combine information on secondary structure propensities and polarity, and add a simple criterion to the prediction of amyloidogenic regions.

Introduction

Amyloid consists of polypeptides that have turned into insoluble β-sheet fibrils and is associated with about 30 human diseases, e.g. Alzheimer’s disease (amyloid β-peptide, Aβ), Creutzfeldt–Jakob disease (prion protein, PrP), and systemic amyloidosis (lysozyme) [1], [2]. The most common human amyloid is formed from a fragment of lactadherin, medin, which is found in the aortic wall of virtually all above age sixty [3]. Amyloid can be formed from wildtype, non-processed protein, but in some cases mutations or proteolytic cleavages are required to make the protein amyloidogenic [4]. Amyloid is not only associated with disease but so-called functional amyloid can generate, for example, bacterial pili and human pigment binding templates, or regulate translation in yeast [5], [6]. Amyloid fibrils derived from the yeast prion protein Sup35 are formed by self-complementary side-chain interactions in steric zippers, showing that fibril formation is sequence-dependent [7]. Similar types of steric zippers have been found in fibrils derived from Aβ, PrP and other amyloidogenic regions [8].

The human proteome harbors many proteins that are prone to aggregate and to form self-complementary steric zippers, the “amylome” [9], [10], but apparently only a small fraction of these actually forms amyloid. Regions prone to aggregate or form steric zippers are often buried, flanked by charged residues or twisted, making them less likely to form intermolecular β-sheets [10], [11]. However, it is not clear what distinguishes truly amyloidogenic proteins from other proteins in the amylome. This has motivated the search for factors that determine amyloid formation, and several algorithms that predict amyloidogenic regions are available. For example, the Waltz algorithm combines polarities, α-helix and β-strand propensities with charge of amino acid residues, and takes into account sequence dependency to identify regions prone to form amyloid fibrils [12]. In an attempt to further elucidate determinants of amyloid formation we have here investigated the conformational preferences of non-polar amino acid residues and their distribution in amyloid-forming proteins.