JMDplots vignettes

Average oxidation state of carbon in proteins (2014)

This vignette runs the code to make the plots from the following paper:

Dick JM. 2014. Average oxidation state of carbon in proteins. Journal of the Royal Society Interface 11: 20131095. doi: 10.1098/rsif.2013.1095

This vignette was compiled on 2024-03-11 with JMDplots 1.2.19-11 and CHNOSZ 2.1.0-5.

library(JMDplots)

ZC of amino acids vs ZC of RNA codons and hydropathy index of amino acids (Figure 1)

aoscp1()

Histograms of ZC of all human proteins and human membrane proteins (Figure 2)

aoscp2()

Drawing of yeast cell color-coded with median ZC of proteins in different locations (Figure 3)

# first make the base plot, then add labels
aoscp3(TRUE)
aoscp3()

ZC and Eh ranges in yeast and ER-cytoplasm electron-transfer scheme (Figure 4)

aoscp4()

Average oxidation state of carbon in proteins from different organisms (Figure 5)

aoscp5()

ZC and Topt of different rubiscos and thermodynamic comparison (Figure 6)

aoscp6()