In literature interaction of Amyloid beta peptide with membrane sometimes attributed to the fragments (22-35) or (16-22). As they are the transmembrane components of the peptide. Assuming that, I am wondering about biological relevance of these fragments compare to the whole peptide (1-40, 1-42)?
Well, I just read an article where binding to the biomimetic membrane of six fragments [Aβ(1-11), Aβ(1-28), (10-26), Aβ(12-24), Aβ(16-22) and Aβ(22-35)] were studied {Yates et al, jmb 2013, 425, 1915}. Indeed, fragments binding is not the same as the whole peptide.
I should may be rephrase my question and ask about a shortest amyloid peptide, may be between 10 and 25 amino acids. Before, I was working with antimicrobial peptide what has only 11 residues. Currently searching for an analogs within amyloids.
It is difficult to find a short Abeta sequence that will reproduce its behavior accurately. For example Abeta1-40 and Abeta1-42 are only two amino acids apart but behave very differently in some contexts.
If you are looking for a shorter, biologically relevant Abeta peptide you may want to look at the p3 fragment (Abeta17-42). It occurs naturally, is one of the major components of preamyloid plaques in Down's patients, and is neurotoxic. It also has the interesting property of forming oligomers but not forming amyloid fibers.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2851998/
http://www.ncbi.nlm.nih.gov/pubmed/8969231
If you are working with membrane disruption by Abeta you may want to look at this paper:
https://www.researchgate.net/publication/230796871_Two-Step_Mechanism_of_Membrane_Disruption_by_A_through_Membrane_Fragmentation_and_Pore_Formation
For general information on amyloids you want to look at this thread and join the project associated with it:
https://www.researchgate.net/post/Amyloid_protocols_project
Article Two-Step Mechanism of Membrane Disruption by Aβ through Memb...
May I ask rhetoric question? Why amyloid peptides are amyloid? They look quite similar in respect to antimicrobial peptides, even share some properties, like for instance it is highlighted here:
http://www.ncbi.nlm.nih.gov/pubmed/23649542
Are there more reasons then ability to form fibril?
Some differences between amyloids and AMPS regarding membrane disruption:
1. Amyloids almost always require oligomer assembly to be active, while AMPs are at least partially active as monomers
2. Fiber dependent membrane disruption appears to be a general mechanism for amyloid membrane disruption that is not found in AMPs. See for example the two step mechanism paper above and http://www.pnas.org/content/109/50/20455.full
Note that the two steps can be blocked independently https://www.researchgate.net/publication/49798682_Biphasic_effects_of_insulin_on_islet_amyloid_polypeptide_membrane_disruption?ev=prf_pub
3. Amyloids are generally more hydrophobic than AMPs with fewer positively charged residues
However, some AMPs are also amyloidogneic: http://www.ncbi.nlm.nih.gov/pubmed/22308196 It is also suggested that some amyloid peptides like Abeta may be AMPs.
* Note that the Protein Science paper you listed above suggests the toroidal pore mechanism, a common pore formation for AMPs, is also responsible for early pore formation by amyloids. We measured the lipid flip-flop rate for IAPP and found no lipid flip-flop before fiber formation. This suggests (but does not prove) that toroidal pores do not form with IAPP at least since lipid movement from one bilayer to the other other would seem to be a requirement for a toroidal pore.
https://www.researchgate.net/publication/230840494_Phosphatidylethanolamine_enhances_amyloid_fiber-dependent_membrane_fragmentation?ev=prf_pub
Article Biphasic Effects of Insulin on Islet Amyloid Polypeptide Mem...
Article Phosphatidylethanolamine Enhances Amyloid Fiber-Dependent Me...
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