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ionize(affinity = NULL, other = NULL)affinity if proteins are among the species of interest, H+ is in the basis, and thermo$opt$ionize is TRUE. This function can also be used from the top level to calculate the ionization state and ionization contributions to thermodynamic properties other than the chemical affinity (see examples below). The ionization model used by this function takes account of the ionization constants of amino acid sidechain groups and the terminal groups in proteins as a function of temperature and pressure calculated using the properties and parameters taken from Dick et al., 2006. ionize responds to different argument configurations. affinity and other both refer to the list contained in the values element of the output of affinity. If both these arguments are missing, species is called to load the ionizable sidechain and backbone groups of proteins into the global species list. If other is missing, the function calculates and outputs the affinities of formation of the ionized proteins. If other is present, it contains the values of other properties, for example Cp, for which ionization values are calculated. Finally, if other is identical to affinity, the function outputs the calculated net charges (overall ionization states) of the proteins. Note that ionize only computes values for proteins; those for other species are returned unaltered in the output.
Makhatadze, G. I. and Privalov, P. L., 1990. Heat capacity of proteins. 1. Partial molar heat capacity of individual amino acid residues in aqueous solution: Hydration effect. J. Mol. Biol., 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. J. Mol. Biol., 213, 385-391.
protein.info and residue.info use this function to display ionization states of proteins.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]],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
",
"Experimental points at 25 degC from Roxby and Tanford, 1971"),
cex.main=0.9)
# forget our changes to thermo$obigt for next examples
data(thermo)
## Heat capacity of LYSC_CHICK as a function of T
basis("CHNOS+"); species("LYSC_CHICK")
pH <- c(5,9,3); T <- c(0,100,25)
T.values <- seq(T[1],T[2],length.out=T[3])
# add the ionizable groups
ionize()
a <- affinity(pH=pH,T=T)
# values for non-ionized protein
c <- affinity(pH=pH,T=T,property="Cp.species")
plot(T.values,c$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$Cp,"cal"),pch=16)
title(main=paste("Calc'd heat capacity of LYSC_CHICK:",
"non/ionized(solid/dashed);
",
"Makhatadze+Privalov 1990 (open, calc; filled, expt)"),
cex.main=0.9)
### Metastability calculations using 'ionize'
## Eh-pH diagrams for intra/extracellular proteins
organism <- c("PYRFU","ECOLI","YEAST")
intracellular <- c("AMPM","AMPM","AMPM1")
extracellular <- c("O08452","AMY1","PST1")
basis("CHNOSe") # for Eh we need electrons
mycol <- c("red","green","blue")
for(i in 1:3) {
species(delete=TRUE)
species(c(intracellular[i],extracellular[i]),organism[i])
if(i == 1) add <- FALSE else add <- TRUE
t <- affinity(pH=c(0,14),Eh=c(-1,0))
diagram(t,add=add,color=NULL,names=species()$name,
col=mycol[i],col.names=mycol[i])
}
title(main=paste("Intracellular (AMPM) and extracellular proteins\n",
describe(thermo$basis[1:4,])))
## Buffer + ionization: Metastablilities of
## thiol peroxidases from model bactera
## (ECOLI, BACSU mesophile; AQUAE thermophile,
## THIDA acidophile, BACHD alkaliphile)
basis("CHNOS+")
organisms <- c("ECOLI","AQUAE","BACSU","BACHD","THIDA")
species("TPX",organisms)
# create a buffer with our proteins in it
mod.buffer("TPX",paste("TPX",organisms,sep="_"))
# set up the buffered activities
basis(c("CO2","H2O","NH3","O2"),"TPX")
t <- affinity(return.buffer=TRUE,T=50)
basis(c("CO2","H2O","NH3","O2"),as.numeric(t[1:4]))
t <- affinity(pH=c(0,14,200),T=c(25,80,200))
diagram(t,color=NULL)
title(main=paste("Thiol peroxidases from bacteria\n",
describe(thermo$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, i.e.
# 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",residue=FALSE)
title(main=paste("Sigma factors in E. coli\n",
describe(thermo$basis[-6,],T=NULL)),cex.main=0.95)Run the code above in your browser using DataLab