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Membrane proteins

| posted 11 Mar, 2021 17:53
My students love calling membrane proteins this semester for some reason. What do I advise them to do with proteins that have two or more good TM domains (using at least 2 different programs) but no phagesdb BLAST membrane protein calls. So far, I've been explaining that hydrophobic helices can be internal to proteins as well as serve as TM domains. I've told them they need more evidence than 2 or more good TM domains predicted to make a membrane protein call. Am I giving them good advice or should I be more liberal in calling membrane protein?
| posted 12 Mar, 2021 18:47
Your question about false positives is an interesting one. I had always assumed the algorithms were specifically designed to distinguish the differences between membrane domains and simple hydrophobic helices. So I went back to the 2001 paper for TMHMM (doi:10.1006/jmbi.2000.4315). The intro in the paper has a really good discussion on the early methods used to distinguish just that issue. There is also a whole section of the paper on this issue. Bottom line is there are other structures and length requirements that help in the determination which helps distinguish a "real" transmembrane domain. Might even be worth pointing out this paper to students who are interested, if only to read the intro.

As for the issue of false positives with TM-HMM, according to the paper, the algorithm has a specificity of around 99% if there is not a leader peptide, so I think the protocol as defined is a pretty good one and further support from BLAST is not required.

But this issue that a leader peptide reduces the quality of the results is very interesting. Maybe the SEA-phages protocol should be amended if a leader peptide is predicted. That is really a good question for a faculty workshop I think.
Edited 12 Mar, 2021 18:52
| posted 12 Mar, 2021 18:49
Thanks Chris! I will definitely work through that paper with my students.
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