data(thermo)
### Direct Interaction with 'ionize'
## Charge of LYSC_CHICK as a function of pH and T
# After Fig. 10 of Dick et al., 2006
basis(c('CO2','H2O','NH3','H2S','O2','H+'),rep(999,6))
species('LYSC_CHICK')
# add the ionizable groups
ionize()
# get the affinities and charges (along equal temperature increments ...)
T <- c(25,150,6); pH <- c(0,14,50)
x <- affinity(pH=pH,T=T)
z <- ionize(x$values,x$values)
# plot charges at the temperatures we're interested in
plot(z[[1]][1,],x=seq(0,14,length.out=50),type='l',xlab='pH',
ylab='net charge (Z)') # 25 deg C
lines(z[[1]][4,],x=seq(0,14,length.out=50),col='red') # 100 deg C
lines(z[[1]][6,],x=seq(0,14,length.out=50),col='orange') # 150 deg C
text(x=c(12,10,9),y=c(-15,-16,-18),labels=paste('T=',c(25,100,150),sep=''))
# if cysteine is oxidized (to cystine disulfide bonds) it may not ionize.
# suppress its ionization by upping energy of the ionized group
mod.obigt('[Cys-]',G=999999)
x <- affinity(pH=pH,T=25)
z <- ionize(x$values,x$values)
lines(z[[1]][1,],x=seq(0,14,length.out=50),lty=2)
text(x=12,y=-7,'T=25, oxidized')
# add experimental points
points(thermo$expt$RT71$pH,thermo$expt$RT71$Z)
title(main=paste('Ionization of unfolded LYSC_CHICK<n>',
'Experimental points at 25 degC from Roxby and Tanford, 1971'),
cex.main=0.9)
# forget our changes to 'thermo'
data(thermo)
## Heat capacity of LYSC_CHICK as a function of T
basis('CHNOS+'); species('LYSC_CHICK')
pH <- c(5,9,3); T <- c(0,100,25)
T.values <- seq(T[1],T[2],length.out=T[3])
# add the ionizable groups
ionize()
a <- affinity(pH=pH,T=T)
# values for non-ionized protein
c <- affinity(pH=pH,T=T,property='Cp.species')
plot(T.values,c$values[[1]][,1],
xlab=axis.label('T'),ylab=axis.label('Cp'),
ylim=c(5000,8000),type='l',mgp=c(2.2,0.2,0))
# values for ionized protein
cp <- ionize(a$values,c$values)
for(i in 1:3) {
lines(seq(T[1],T[2],length.out=T[3]),cp[[1]][,i],lty=2)
text(80,cp[[1]][,i][21],paste('pH=',pH[i],sep=''))
}
# Makhatadze and Privalov's group contributions
T.MP <- c(5,25,50,75,100,125)
points(T.MP,convert(MP90.cp(T.MP,'LYSC_CHICK'),'cal'))
# Privalov and Makhatadze's experimental values
e <- thermo$expt$PM90
e <- e[e$protein=='LYSC_CHICK',]
points(e$T,convert(e$Cp,'cal'),pch=16)
title(main=paste('Calc'd heat capacity of LYSC_CHICK:',
'non/ionized(solid/dashed);<n>',
'Makhatadze+Privalov 1990 (open, calc; filled, expt)'),
cex.main=0.9)
### Metastability calculations using 'ionize'
## fO2-pH diagram for methionine aminopeptidases
organism <- c('PYRFU','ECOLI','YEAST')
intracellular <- c('AMPM','AMPM','AMPM1')
basis('CHNOS+')
basis('H2O',-10)
species(intracellular,organism)
diagram(affinity(pH=c(0,14),O2=c(-80,-75)),cex.axis=1.5)
title(main=paste('Methionine aminopeptidases<n>',
describe(thermo$basis[1:4,])))
## Eh-pH diagrams for intra/extracellular proteins
organism <- c('PYRFU','ECOLI','YEAST')
intracellular <- c('AMPM','AMPM','AMPM1')
extracellular <- c('O08452','AMY1','PST1')
basis('CHNOSe') # for Eh we need electrons
mycol <- c('red','green','blue')
for(i in 1:3) {
species(delete=TRUE)
species(c(intracellular[i],extracellular[i]),organism[i])
if(i == 1) add <- FALSE else add <- TRUE
t <- affinity(pH=c(0,14),Eh=c(-1,0))
diagram(t,add=add,color=NULL,names=species()$name,
col=mycol[i],col.names=mycol[i])
}
title(main=paste('Intracellular (AMPM) and extracellular proteins<n>',
describe(thermo$basis[1:4,])))
## Buffer + ionization: Metastablilities of
## thiol peroxidases from model bactera
## (ECOLI, BACSU mesophile; AQUAE thermophile,
## THIDA acidophile, BACHD alkaliphile)
basis('CHNOS+')
organisms <- c('ECOLI','AQUAE','BACSU','BACHD','THIDA')
species('TPX',organisms)
# create a buffer with our proteins in it
mod.buffer('TPX',paste('TPX',organisms,sep='_'))
# set up the buffered activities
basis(c('CO2','H2O','NH3','O2'),'TPX')
t <- affinity(return.buffer=TRUE,T=50)
basis(c('CO2','H2O','NH3','O2'),as.numeric(t[1:4]))
t <- affinity(pH=c(0,14),T=c(0,100))
diagram(t,color=NULL)
title(main=paste('Thiol peroxidases from bacteria<n>',
describe(thermo$basis[-6,],T=NULL)),cex.main=0.9)
## Buffer + ionization: Metastable assemblage
## for E. coli sigma factors on a T-pH diagram
# (sigma factors 24, 32, 38, 54, 70, or
# RpoE, RpoH, RpoS, RpoN, RpoD)
proteins <- c('RPOE','RP32','RPOS','RP54','RPOD')
basis('CHNOS+')
basis('pH',7.4)
# define and set the buffer
change('_sigma',paste(proteins,'ECOLI',sep='_'))
basis(c('CO2','NH3','H2S','O2'),'sigma')
logact <- affinity(return.buffer=TRUE,T=25)
# Set the activities of the basis species to constants
# corresponding to the buffer, and diagram the relative
# stabilities as a function of T and pH
basis(c('CO2','NH3','H2S','O2'),as.numeric(logact))
species(paste(proteins,'ECOLI',sep='_'))
a <- affinity(pH=c(5,10),T=c(10,40))
diagram(a,balance='PBB')
title(main=paste('Sigma factors in E. coli<n>',
describe(thermo$basis[-6,],T=NULL)))</n>
<references>Dick, J. M., LaRowe, D. E. and Helgeson, H. C., 2006. Temperature, pressure, and electrochemical constraints on protein speciation: Group additivity calculation of the standard molal thermodynamic properties of ionized unfolded proteins. <em>Biogeosciences</em>, 3, 311-336.
Makhatadze, G. I. and Privalov, P. L., 1990. Heat capacity of proteins. I. Partial molar heat capacity of individual amino acid residues in aqueous solution: Hydration efect. <em>J. Mol. Biol.</em>, 213, 375-384.
Privalov, P. L. and Makhatadze, G. I., 1990. Heat capacity of proteins. II. Partial molar heat capacity of the unfolded polypeptide chain of proteins: Protein unfolding effects. <em>J. Mol. Biol.</em>, 213, 385-391.</references>
<keyword>misc</keyword></n></n></n></n></n>Run the code above in your browser using DataLab