Prediction of Transmembrane Regions, Cholesterol, and Ganglioside Binding Sites in Amyloid-Forming Proteins Indicate Potential for Amyloid Pore Formation

Abstract

Besides amyloid fibrils, amyloid pores (APs) represent another mechanism of amyloid induced toxicity. Since hypothesis put forward by Arispe and collegues in 1993 that amyloid-beta makes ion-conducting channels and that Alzheimer's disease may be due to the toxic effect of these channels, many studies have confirmed that APs are formed by prefibrillar oligomers of amyloidogenic proteins and are a common source of cytotoxicity. The mechanism of pore formation is still not well-understood and the structure and imaging of APs in living cells remains an open issue. To get closer to understand AP formation we used predictive methods to assess the propensity of a set of 30 amyloid-forming proteins (AFPs) to form transmembrane channels. A range of amino-acid sequence tools were applied to predict AP domains of AFPs, and provided context on future experiments that are needed in order to contribute toward a deeper understanding of amyloid toxicity. In a set of 30 AFPs we predicted their amyloidogenic propensity, presence of transmembrane (TM) regions, and cholesterol (CBM) and ganglioside binding motifs (GBM), to which the oligomers likely bind. Noteworthy, all pathological AFPs share the presence of TM, CBM, and GBM regions, whereas the functional amyloids seem to show just one of these regions. For comparative purposes, we also analyzed a few examples of amyloid proteins that behave as biologically non-relevant AFPs. Based on the known experimental data on the β-amyloid and α-synuclein pore formation, we suggest that many AFPs have the potential for pore formation. Oligomerization and α-TM helix to β-TM strands transition on lipid rafts seem to be the common key events.

Cholesterol as a key player in amyloid β-mediated toxicity in Alzheimer’s disease

“…Amyloid β peptides have been shown to oligomerize into ion-permeable transmembrane pores of varying structure, composition, and permeability. Aβ42 oligomers are known to adopt a β-sheet-rich structure in the presence of membrane lipids and self-organize into transmembrane channels permeable to calcium ions, which can cause cell death (Prangkio et al, 2012 ; Arbor et al, 2016 ; Serra-Batiste et al, 2016 ; Lee et al, 2017 ; Julien et al, 2018 ; Ciudad et al, 2020 ; Ruiz-Arias et al, 2020 ; Venko et al, 2021 ).…”

“…The Aβ-membrane interaction begins with the formation of electrostatic interactions of the basic amyloid residues with the negative charge of sialic acid on gangliosides, whereupon the peptide inserts into the hydrophobic zone of the bilayer with the help of cholesterol molecules. Then, Ca 2+ -permeable pore formation may occur (Lin et al, 2008 ; Di Scala et al, 2016 ; Venko et al, 2021 ). In another study, Aβ monomers bound to raft-like dipalmitoyl-PC:Chol:GM1 membranes and were incorporated into the bilayer only when both GM1 and cholesterol were present.…”

Coexisting Ordered and Disordered Membrane Phases Have Distinct Modes of Interaction with Disease-Associated Oligomers

“…Another important and less-understood aspect of lipid interaction is the depth of insertion of the oligomers into the lipid bilayers. In this context, we note that one suggested mechanism of amyloid toxicity is the formation of unregulated ion channels in the membrane, ,,, and the process of the formation of ion channels was found to be dependent on local membrane organization . Such channel formation would require insertion of the oligomers into the membrane.…”

Structural Studies Providing Insights into Production and Conformational Behavior of Amyloid-β Peptide Associated with Alzheimer’s Disease Development

“…Exposure to oligomeric Aβ was shown to cause an increase in calcium flow across the membrane [ 120 ] inhibited by submillimolar concentrations of Zn 2+ and Cu 2+ ions [ 121 ]. According to some reports, the channel-like structures formed by Aβ oligomers [ 122 , 123 , 124 ] can influence the electrical potential of the neurons [ 125 ], and short-term memory impairments induced by Aβ oligomers can be caused by an increase in the local concentration of Zn 2+ in the presynaptic region [ 126 ]. Electrophysiological measurements revealed that Aβ 1–42 peptides can form at least three different types of ion channels differing in permeability, whereas Aβ 1–40 peptides form no ion channels [ 127 ].…”