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[2] ionize.aa

## Don't show: data(thermo)
thermo$obigt: 1809 aqueous, 3368 total species
## End(Don't show) ## Charge of LYSC_CHICK as a function of pH and T # After Fig. 10 of Dick et al., 2006 # the rownumber of the protein in thermo$protein ip <- iprotein("LYSC_CHICK") # its amino acid composition aa <- ip2aa(ip) # additive charges of unfolded protein at 25, 100, 150 degrees C # as a function of pH pH <- seq(0, 14, 0.1) Z.25 <- ionize.aa(aa, T=25, pH=pH)
subcrt: 18 species at 298.15 K and 1 bar (wet)
plot(pH, Z.25[, 1], type="l", xlab="pH", ylab="net charge (Z)") lines(pH, ionize.aa(aa, T=100, pH=pH)[, 1], col="red")
subcrt: 18 species at 373.15 K and 1.01 bar (wet)
lines(pH, ionize.aa(aa, T=150, pH=pH)[, 1], col="orange")
subcrt: 18 species at 423.15 K and 4.76 bar (wet)
text(c(12, 10, 9), c(-15, -16, -18), labels=paste("T=", c(25, 100, 150), sep="")) # suppress ionization of cysteine as if it was oxidized # (to form non-ionizable cystine disulfide bonds) lines(pH, ionize.aa(aa, T=25, pH=pH, suppress.Cys=TRUE)[, 1], lty=2)
subcrt: 18 species at 298.15 K and 1 bar (wet)
text(12, -7, "T=25, oxidized") # add experimental points RT71 <- read.csv(system.file("extdata/cpetc/RT71.csv", package="CHNOSZ")) points(RT71$pH, RT71$Z) legend("topright", pch=1, legend="Roxby and Tanford, 1971") title(main=paste("Ionization of unfolded LYSC_CHICK\n", "After Dick et al., 2006"))

Image ionizeaa1

 

## Heat capacity of LYSC_CHICK as a function of T pH <- c(5, 9, 3) T <- seq(0, 100) # Cp of non-ionized protein Cp.nonion <- subcrt("LYSC_CHICK", T=T)$out[[1]]$Cp
aa2eos: found LYSC_CHICK (C613H959N193O185S10, 129 residues) subcrt: 1 species at 101 values of T and P (wet)
plot(T, Cp.nonion, xlab=axis.label("T"), type="l", ylab=axis.label("Cp"), ylim=c(5000, 8000)) # Cp of ionization and ionized protein aa <- ip2aa("LYSC_CHICK") for(pH in c(5, 9, 3)) { Cp.ionized <- Cp.nonion + ionize.aa(aa, "Cp", T=T, pH=pH)[, 1] lines(T, Cp.ionized, lty=2) text(80, Cp.ionized[70], paste("pH =",pH) ) }
subcrt: 18 species at 101 values of T and P (wet) subcrt: 18 species at 101 values of T and P (wet) subcrt: 18 species at 101 values of T and P (wet)
# Makhatadze and Privalov's group contributions T <- c(5, 25, 50, 75, 100, 125) points(T, convert(MP90.cp("LYSC_CHICK", T), "cal")) # Privalov and Makhatadze's experimental values e <- read.csv(system.file("extdata/cpetc/PM90.csv", package="CHNOSZ")) e <- e[e$protein=="LYSC_CHICK",] points(e$T, convert(e$Cp, "cal"), pch=16) legend("bottomright", pch=c(16, 1, NA, NA), lty=c(NA, NA, 1, 2), legend=c("PM90 experiment", "MP90 groups", "DLH06 groups no ion", "DLH06 groups ionized")) title("Heat capacity of unfolded LYSC_CHICK")

Image ionizeaa2

 


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Next: more.aa Up: CHNOSZ examples Previous: [4] protein