Predict the Topology of a Membrane Protein

2020-11-11

This demo shows how to estimate the location of the amino acids in a membrane protein. This package tmhmm uses the tool TMHMM to do so. The amino acids of a membrane protein are estimated to be either inside the cell (the cytosol side), outside of the cell (the surroundings of the cell) or in the transmembrane part.

library(tmhmm)

For this vignette to work, TMHMM must have been installed. TMHMM can be installed using install_tmhmm, but this does require a download link that must be requested from https://services.healthtech.dtu.dk/service.php?TMHMM-2.0.

install_tmhmm("https://services.healthtech.dtu.dk/download/28c408dc-ef5e-47ad-a284-66754bcd27f7")

The TMHMM installation is checked here, with the goal of producing a helpful error message:

check_tmhmm_installation()
#> /home/richel/.local/share/tmhmm-2.0c/bin/decodeanhmm.Linux_x86_64'
#>
#> Tip 1: from R, run 'tmhmm::install_tmhmm()'
#> Tip 2: request a download URL at the TMHMM request page at
#>
#> https://services.healthtech.dtu.dk/service.php?TMHMM-2.0

We need a FASTA file to work on:

fasta_filename <- system.file("extdata", "tmhmm.fasta", package = "tmhmm")
#> >5H2A_CRIGR you can have comments after the ID
#> MEILCEDNTSLSSIPNSLMQVDGDSGLYRNDFNSRDANSSDASNWTIDGENRTNLSFEGYLPPTCLSILHL
#> LPSKLCAVWIYLDVLFSTASIMHLCAISLDRYVAIQNPIHHSRFNSRTKAFLKIIAVWTISVGVSMPIPVF
#> PQSSLSSEKLFQRSIHREPGSYTGRRTMQSISNEQKACKVLGIVFFLFVVMWCPFFITNIMAVICKESCNE
#> HVIGALLNVFVWIGYLSSAVNPLVYTLFNKTYRSAFSRYIQCQYKENRKPLQLILVNTIPALAYKSSQLQA
#> GQNKDSKEDAEPTDNDCSMVTLGKQQSEETCTDNINTVNEKVSCV

Estimating the locations of the amino acids:

if (is_tmhmm_installed()) {
locatome <- run_tmhmm(fasta_filename)
cat(locatome, sep = "\n")
}

The legend of these locations:

Character Location
i Inside or cytosol-side
o Outside or surroundings-side
M Transmembrane