Cell penetrating peptides.
Cell penetrating peptides (CPPs) are a class of short amino acid sequences which are sufficient for crossing cell membranes and delivering themselves along with any attached cargo into the cytoplasm of cells. They were branded CPPs recently, while the term "protein transduction domain" (PTD) was used in the early days of their study, when the necessary sequences were being isolated from native proteins with cell-penetrating activity (notably, HIV-1 Tat).
Most of the scientific literature I have found on CPPs focuses on their potential relevance for targeted drug delivery, and mostly discusses the delivery of proteins and nanoparticles via fusion of CPPs to the N-terminus of the target protein. The only Stack Exchange question & answer on CPPs also points to a discussion of N-terminal fusion of CPPs to a cargo peptide. However, research on cell penetrating peptides has come a long way since the 2005 article referenced in that post.
The 2012 Milletti review highlights that there has been a dramatic increase in the number of different classes of cell penetrating peptides, including hydrophobic CPPs, primary amphipathic CPPs, alpha-helical amphipathic CPPs, beta sheet amphipathic CPPs, and proline-rich CPPs, among others. And that is just between 2005 and 2012! The Milletti 2012 article also covers some CPPs isolated from other viruses.
I have not been able to find a review of similar detail written since, although I'm sure much progress has been made in the field.
Although it is not my main question, I would appreciate any citations for more recent reviews which go into detail on the molecular mechanism of cell penetration for one or more classes of CPPs - especially a review of the function of PTDs in their native proteins.
I have only begun to research CPPs and PTDs in their native proteins and in the drug-delivery setting because it became apparent that a protein I am studying for an undergraduate thesis may have an internal PTD which is essential for its function. I am no expert on the topic and I would appreciate information on CPPs/PTDs including further synonyms for CPPs/PTDs to aid in my literature search - especially synonyms specific to native proteins with CPP-like functions.
What are the secondary structure requirements for cell-penetrating peptides?
My question is whether the previously described positively charged CPPs and/or the new classes of CPPs described in Milletti 2012 are only functional as N-terminal fusions, or whether they typically function efficiently when they are incorporated within an internal loop (in terms of primary sequence, but still exposed to the solvent). The 2005 article cited in the previous Stack Exchange question on this topic stated that the CPP derived from HIV-1 Tat is based on residues 47-57, which are internal residues of the 86 amino acid protein - a protein which has cell-penetrating activity in its native role in HIV-1 infection.
Therefore, my question is not whether or not this ever occurs - it clearly does - but to what extent do CPPs isolated from internal sequences of native proteins have CPP-like functions in their native proteins?
The system I am studying for my thesis is a virus, so any information specifically on CPPs and PTDs function in the native proteins of viruses would be particularly useful.
Jones, S. W., Christison, R., Bundell, K., Voyce, C. J., Brockbank, S. M. V., Newham, P., & Lindsay, M. A. (2005). Characterisation of cell-penetrating peptide-mediated peptide delivery. British Journal of Pharmacology, 145(8), 1093–1102. http://doi.org/10.1038/sj.bjp.0706279
Milletti, F. (2012). Review: Cell-penetrating peptides: classes, origin, and current landscape. Drug Discovery Today, 17850-860. doi:10.1016/j.drudis.2012.03.002
Vivès, E., Brodin, P., & Lebleu, B. (1997). A truncated HIV-1 Tat protein basic domain rapidly translocates through the plasma membrane and accumulates in the cell nucleus. The Journal Of Biological Chemistry, 272(25), 16010-16017.
If anyone interested in answering this question is not an expert, the best resource I can currently provide for a list of CPPs derived from natural proteins (besides the Milletti 2012 article above) is:
Hallbrink, M., Kilk, K., Elmquist, A., Lundberg, P., Lindgren, M., Jiang, Y., & ... Langel, U. (n.d). Prediction of cell-penetrating peptides. International Journal Of Peptide Research And Therapeutics, 11(4), 249-259.
I will be continuing to research this topic for my thesis, so if you're interested in answering this question but require more information, feel free to comment asking for specific information that would help.