How to calculate the inner diameter of peptide nano-tubes made up of peptide? I have seen that people can find the diameter by 3D reconstruction of CRYO-TEM, which is a very specialized technique [1]. Is there any other way to estimate the inner diameter of nano-tubes of dimension less than 10 nm?
1. Zhang R, et al. (2009) Interprotofilament interactions between Alzheimer’s Abeta1-42 peptides in amyloid fibrils revealed by cryoEM. Proc Natl Acad Sci USA 106(12): 4653–4658
Negative staining of the tubes in 1% aqueous uranyl acetate or 1% phosphotungstic acid might do the job.
First, how are the peptides oriented in the nanotubes? Are the nanotubes made from unique peptides? (I would guess so.) What is the sequence of the peptides making up the nanotubes? From these information alone, you can calculate the structural parameters of the nanotube because structural parameters of any peptide can be calculated from the amino acid structural parameters, which have long been well-established.
Dear @ Vicente, my sample is made up of a homopolymer of the dipeptide. Do You think we can still calculate the diameter? Please share some article, if you have where people used the structural parameters of the dipeptide to calculate the diameter of the nanotube. I am not sharing the sequence because there is a lot of dipeptides. You can take the example of FF.
How are the peptides oriented with respect to the axis of the nanotubes? If you have cryo-EM access, you can indirectly measure the diameters of the nanotubes by the following process:
In your cryo-EM experiments, include one or two standard molecules whose structural parameters are well-known. By comparing the structural parameters (as measured from the cryo-EM pictures) of your peptide nanotubes with those of the standards, you can, just by using ratios and proportions, calculate the structural parameters of your peptide nanotubes. Make sure you have enough redundancy in your measurements, then take the average(s).
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