I am working on MD simulation project aiming potential drug discovery. I took mutants of a certain group and modelled protein structures with and without transit peptide sequences. My one aim is to see whether there is any structural, physiological or functional changes for the presence of transit peptide sequence. In Acinetobacter baumannii, with/without transit peptide ,what is the functional and structural difference occur due to mutation?
Dear Mannu Bardhan Paul ,
You can go through the following papers to get the answer of this question:
1. Article Ω76: A designed antimicrobial peptide to combat carbapenem- ...
2. Article Pan-Drug Resistant Acinetobacter baumannii, but Not Other St...
I hope this will be helpful to you.
Dear Mannu Bardhan Paul ,
If I understand your question correctly you wonder whether signal sequences affect folding of the mature part of precursor proteins.
It is good to realize that proteins are exported across the inner membrane by different pathways. Either by the Sec pathway or by the twin-arginine translocation (TAT) pathway. Specific Sec- and TAT-dependent signal peptides target unfolded or folded proteins, respectively. There are also some proteins lacking any apparent targeting signal by the so-called non-classical secretion pathway.
See for example:
Renuka Kudva, Kärt Denks, Patrick Kuhn, Andreas Vogt, Matthias Müller, Hans-Georg Koch, Protein translocation across the inner membrane of Gram-negative bacteria: the Sec and Tat dependent protein transport pathways, Research in Microbiology, Volume 164, Issue 6, 2013, Pages 505-534, ISSN 0923-2508, https://doi.org/10.1016/j.resmic.2013.03.016 (see enclosed file).
Indeed, there are indications that signal sequences affect the stability and folding of the precursor (or better the mature part of the precursor):
Beena, K., Udgaonkar, J. B., & Varadarajan, R. (2004). Effect of signal peptide on the stability and folding kinetics of maltose binding protein. Biochemistry, 43(12), 3608-3619.
Prajapati, R. S., Indu, S., & Varadarajan, R. (2007). Identification and thermodynamic characterization of molten globule states of periplasmic binding proteins. Biochemistry, 46(36), 10339-10352.
Singh, P., Sharma, L., Kulothungan, S. R., Adkar, B. V., Prajapati, R. S., Ali, P. S. S., ... & Varadarajan, R. (2013). Effect of signal peptide on stability and folding of Escherichia coli thioredoxin. PloS one, 8(5), e63442.
Hope this helps you a bit further. Best regards.
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