data(thermo)
### Interaction with the 'protein'function
## Thermodynamic properties of proteins
# get the composition of a protein
protein("BPT1_BOVIN")
# retrieve the rownumber of a protein in thermo$protein
iprotein <- protein("LYSC","CHICK")
# calculate properties and parameters of aqueous protein
protein(iprotein)
# of crystalline protein
protein(iprotein,"cr")
# a call to info() causes the protein properties to
# be appended to thermo$obigt
info("LYSC_CHICK")
# thermodynamic properties can be calculated with subcrt()
subcrt("LYSC_CHICK")
### Table of properties of some proteins
basis("CHNOS+")
species(c("LYSC_CHICK","CYC_BOVIN","MYG_HORSE","RNAS1_BOVIN"))
protein.info()
# the following gives the per-residue composition (i.e. formation
# reaction cofficients) for the ionized proteins
residue.info()
## Protein Data from Online Sources
\dontrun{
## marked dontrun because it requires internet
# this asks to search SWISS-Prot
info("PRND_HUMAN")
# an online search can also be started from the
# "subcrt" function
subcrt("SPRN_HUMAN")
} ## end dontrun
## Inputting protein compositions
# make a new protein
protein("GGSGG","PROTEIN_TEST")
# a sequence can be pasted into the command line:
# type this
protein("
# then paste the sequence
# and end the command by typing
","PROTEIN_NEW")
# or use whatever name you want (with an underscore).
## Standard molal entropy of a protein reaction
basis("CHNOS")
# here we provide the reaction coefficients of the
# proteins (per protein backbone); 'subcrt' function calculates
# the coefficients of the basis species in the reaction
t <- subcrt(c("CSG_METTL","CSG_METJA"),c(-1/530,1/530),
T=seq(0,350,length.out=50))
thermo.plot.new(xlim=range(t$out$T),ylim=range(t$out$S),
xlab=axis.label("T"),ylab=axis.label("DS0r"))
lines(t$out$T,t$out$S)
# do it at high pressure as well
t <- subcrt(c("CSG_METTL","CSG_METJA"),c(-1/530,1/530),
T=seq(0,350,length.out=50),P=3000)
lines(t$out$T,t$out$S,lty=2)
# label the plot
title(main=paste("Standard molal entropy\n",
"P = Psat (solid), P = 3000 bar (dashed)"))
t$reaction$coeff <- round(t$reaction$coeff,3)
d <- describe(t$reaction,
use.name=c(TRUE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE))
text(170,-3,c2s(s2c(d,sep="="),sep="\n"),cex=0.8)
### Metastability calculations
## subcellular homologs of yeast glutaredoxin
## as a function of logfO2 - logaH2O, after Dick, 2009
basis("CHNOS+")
protein <- c("GLRX1","GLRX2","GLRX3","GLRX4","GLRX5")
loc <- c("(C)","(M)","(N)","(N)","(M)")
species(protein,"YEAST")
t <- affinity(H2O=c(-10,0),O2=c(-85,-60))
diagram(t,names=paste(protein,loc))
title(main=paste("Yeast glutaredoxins (black) and residues (blue)\n",
describe(thermo$basis[-c(2,5),])))
# note the difference when we set as.residue=TRUE to
# plot stability fields for the residue equivalents of the
# proteins instead of the proteins themselves ...
# the residue equivalent for one of the larger proteins appears
diagram(t,names=paste(protein,loc),as.residue=TRUE,
add=TRUE,col="blue")
## surface-layer proteins from Methanococcus and others:
## a speciation diagram for surface layer proteins
## as a function of oxygen fugacity after Dick, 2008
# make our protein list
organisms <- c("METSC","METJA","METFE","HALJP","METVO",
"METBU","ACEKI","BACST","BACLI","AERSA")
proteins <- c(rep("CSG",6),rep("SLAP",4))
proteins <- paste(proteins,organisms,sep="_")
# set some graphical parameters
lwd <- c(rep(3,6),rep(1,4))
lty <- c(1:6,1:4)
# load the basis species and proteins
basis("CHNOS+")
species(proteins)
# calculate affinities
a <- affinity(O2=c(-100,-65))
# make diagram
d <- diagram(a,ylim=c(-5,-1),legend.x=NULL,lwd=lwd,
ylab=as.expression(quote(log~italic(a[j]))),yline=1.7)
# label diagram
text(-80,-1.9,"METJA")
text(-74.5,-1.9,"METVO")
text(-69,-1.9,"HALJP")
text(-78,-2.85,"METBU",cex=0.8,srt=-22)
text(-79,-3.15,"ACEKI",cex=0.8,srt=-25)
text(-81,-3.3,"METSC",cex=0.8,srt=-25)
text(-87,-3.1,"METFE",cex=0.8,srt=-17)
text(-79,-4.3,"BACST",cex=0.8)
text(-85.5,-4.7,"AERSA",cex=0.8,srt=38)
text(-87,-4.25,"BACLI",cex=0.8,srt=30)
# add water line
abline(v=-83.1,lty=2)
title(main=paste("Surface-layer proteins",
"After Dick, 2008",sep="\n"))
## relative metastabilities 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,"GSH-GSSG",-7))
basis("CO2","gas")
species(c("CYC","RNAS1","BPT1","ALBU","INS","PRIO"),"BOVIN")
a <- affinity(T=c(0,200))
diagram(a,as.residue=TRUE,ylim=c(-2,0.5))
title(main="Relative metastabilities of bovine proteins")Run the code above in your browser using DataLab