In jedick/canprot: Chemical Analysis of Proteins

library(canprot)
library(CHNOSZ)
oldopt <- options(width = 80)

Zc <- "<i>Z</i><sub>C</sub>"

The canprot package calculates chemical metrics of proteins from amino acid compositions. This vignette was compiled on r Sys.Date() with canprot version r packageDescription("canprot")$Version.

Next vignette: Introduction to canprot

canprot demo #1: Thermophiles

Run the demo using demo("thermophiles"). For this demo, just the output is shown below.

The canprot functions used are:

calc_metrics(): Calculates metrics named in an argument. The metrics calculated here are:
S0g: standard specific entropy
Zc: carbon oxidation state
cplab: This is not a function, but an object that has formatted text labels for each metric.
add_hull(): Adds a convex hull around data points

knitr::read_chunk("../demo/thermophiles.R")

The data are from @DBCS23 for methanogen genomes (amino acid composition and optimal growth temperature) and from @LLX+24 for Nitrososphaeria MAGs (genome assemblies and habitat and respiration types). The plots reveal that proteins tend to have higher specific entropy in thermophilic genomes and MAGs from thermal habitats compared to mesophilic genomes and MAGs from nonthermal habitats, for a given carbon oxidation state. This implies that, after correcting for Z_C, proteins in thermophiles have a more negative derivative of the standard Gibbs energy per gram of protein with respect to temperature.

canprot demo #2: Subcellular locations

Run the demo using demo("locations"). The code and output of the demo are shown below.

The canprot functions used are:

human_aa(): Gets amino acid compositions of human proteins from UniProt IDs
plength(): Calculates protein length (this line is commented out)
Zc(): Calculates carbon oxidation state
pI(): Calculates isoelectric point
add_cld(): Adds compact letter display to a boxplot

knitr::read_chunk("../demo/locations.R")

The plots show carbon oxidation state (r Zc) and isoelectric point (pI) for human proteins in different subcellular locations. The localization data is from Table S6 of @TAW+17, filtered to include proteins that have both a validated location and only one predicted location.

canprot demo #3: Redoxins

Run the demo using demo("redoxins"). For this demo, just the output is shown below.

The canprot functions used are:

read_fasta(): Reads a FASTA sequence file and returns amino acid compositions of proteins. Additional processing is performed by using the following arguments:
type to read header lines
iseq to read specific sequences
start and stop to read segments of the sequences
Zc(): Calculates carbon oxidation state

knitr::read_chunk("../demo/redoxins.R")

This is an exploratory analysis for hypothesis generation about evolutionary links between midpoint reduction potential and r Zc of proteins. The reduction potential data was taken from @ABH97 and @HSJ+99 for E. coli and spinach proteins, respectively. This plot is modified from Fig. 5 of this preprint; the figure did not appear in the published paper.