Examples of Calculations for Proteins

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Description

This page contains some examples of using the functions in CHNOSZ to calculate thermodynamic properties and relative stabilities of proteins.

See Also

For accessing, updating, and downloading amino acid compositions of proteins, see iprotein. For getting chemical formulas and stoichiometric coefficients in reactions of proteins, see protein.info. For more examples of metastable equilibrium calculations for proteins, see read.expr, more.aa, ionize.aa, and apc for reaction-path calculations.

Examples

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## thermodynamic properties and activity diagrams
prot4 <- c("LYSC_CHICK", "BPT1_BOVIN", "CYC_BOVIN", "MYG_PHYCA")
# aqueous protein properties (nonionized)
subcrt(prot4, T=seq(0, 200, 10))$out
# T-logfO2 activity diagram
basis("CHNOS")
species(prot4)
a <- affinity(T=c(0, 200), O2=c(-80, -40))
diagram(a)

## one way to calculate the standard Gibbs energy of a 
## reaction to form an ionized protein at 100 degrees and pH 8
basis("CHNOS+")   # do this to auto-balance the formation reaction
Gr.nonionized <- subcrt("LYSC_CHICK", 1, T=100)$out$G
basis("pH", 8)
pinfo <- protein.info("LYSC_CHICK", round.it=FALSE, T=100)
Gr.ionization <- pinfo$G.Z - pinfo$G
# standard Gibbs energy of the reaction
# in cal/mol ionized protein:
Gr.ionized <- Gr.nonionized + Gr.ionization
# in cal/mol ionized residue:
Gr.ionized_residue <- Gr.ionized/protein.length("LYSC_CHICK")

## 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
s <- subcrt(c("CSG_METTL","CSG_METJA"), c(-1/530,1/530),
  T=seq(0, 350, length.out=50))
thermo.plot.new(xlim=range(s$out$T), ylim=range(s$out$S),
  xlab=axis.label("T"), ylab=axis.label("DS0r"))
lines(s$out$T, s$out$S)
# do it at high pressure as well
s <- subcrt(c("CSG_METTL","CSG_METJA"), c(-1/530,1/530),
  T=seq(0,350,length.out=50), P=3000)
lines(s$out$T, s$out$S, lty=2)
# label the plot
title(main=paste("Standard molal entropy\n",
  "P = Psat (solid), P = 3000 bar (dashed)"))
s$reaction$coeff <- round(s$reaction$coeff, 3)
dsr <- describe.reaction(s$reaction, iname=c(1,2))
text(170, -3, dsr, cex=0.8)


### Equilibrium activity diagrams

## surface-layer proteins from Methanococcus and others
## as a function of oxygen fugacity, after Dick, 2008, Fig. 5b
# use old properties of [Met] to reproduce this example
data(thermo)
add.obigt()
# 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), legend.x=NA, names=organisms)
# 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
data(thermo)

## 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 <- rep("red", length(prot))
col[ZC > 0] <- "blue"
e <- equilibrate(a, normalize=TRUE)
d <- diagram(e, col=col, legend.x=NA)
title(main="Bovine proteins, GSH/GSSG redox buffer")

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