protein {CHNOSZ} | R Documentation |
This page contains some examples of using the functions in CHNOSZ to calculate thermodynamic properties of and make diagrams for proteins.
## Standard molal entropy of a protein reaction basis("CHNOS") # here we provide the reaction coefficients of the # proteins (per protein backbone); subcrt() calculates # the coefficients of the basis species in the reaction s <- subcrt(c("CSG_METTL", "CSG_METJA"), c(-1/530, 1/530), T=seq(0, 350, length.out=50)) # note: this uses the properties of the nonionized proteins ## logfO2-pH potential diagram # with a charged basis, we calculate properties of ionized proteins basis("CHNOS+") file <- system.file("extdata/protein/DS11.csv", package = "CHNOSZ") aa <- read.csv(file, as.is=TRUE) aa <- aa[grep("transferase", aa$protein), ] ip <- add.protein(aa) a <- affinity(pH=c(0, 14), O2=c(-64, -61), T=75, iprotein=ip) diagram(a) title(main="Sequences for transferase at Bison Pool") ## surface-layer proteins from Methanococcus and others ## as a function of oxygen fugacity, after Dick, 2008, Fig. 5b # to reproduce the calculations in the paper, # use superseded data for [Met], [Gly] and [UPBB] reset() add.obigt("OldAA") # make our protein list organisms <- c("METSC", "METJA", "METFE", "HALJP", "METVO", "METBU", "ACEKI", "GEOSE", "BACLI", "AERSA") proteins <- c(rep("CSG", 6), rep("SLAP", 4)) proteins <- paste(proteins, organisms, sep="_") # load the basis species and proteins basis("CHNOS+") species(proteins) # calculate affinities; we go to lower logfO2 than Dick, 2008 # and find an interesting convergence of stabilities there a <- affinity(O2=c(-100, -65)) # try normalize=FALSE to make Fig. 5a in the paper e <- equilibrate(a, normalize=TRUE) d <- diagram(e, ylim=c(-5, -1), names=organisms, format.names=FALSE) # add water stability line abline(v=-83.1, lty=2) title(main="Surface-layer proteins, after Dick, 2008") # checking the geometry of the diagram # most preominant along the x-axis stopifnot(organisms[unique(which.pmax(e$loga.equil))] == c("METFE", "METJA", "METVO", "HALJP")) # stability order close to logfO2=-83.1 stopifnot(order(as.data.frame(e$loga.equil)[62,], decreasing=TRUE)==c(2, 6, 7, 5, 3, 1, 9, 8, 10, 4)) # reset thermodynamic database reset() ## relative stabilities of bovine proteins ## as a function of temperature along a glutathione redox buffer mod.buffer("GSH-GSSG", c("GSH","GSSG"), logact=c(-3, -7)) basis(c("CO2", "H2O", "NH4+", "SO4-2", "H2", "H+"), c(-1, 0, -4, -4, 999, -7)) basis("H2", "GSH-GSSG") basis("CO2", "gas") prot <- c("CYC", "RNAS1", "BPT1", "ALBU", "INS", "PRIO") species(prot, "BOVIN") a <- affinity(T=c(0, 200)) # set line colors according to oxidation state of carbon ZC <- ZC(species()$ispecies) col <- ZC.col(ZC) e <- equilibrate(a, normalize=TRUE) d <- diagram(e, col=col, lwd=3) title(main="Bovine proteins, GSH/GSSG redox buffer")