[1] yeast.aa

## Don't show: data(thermo)
thermo$obigt: 1911 aqueous, 3588 total species
## End(Don't show) # the first few names in UniProt for "aminotransferase yeast" genes <- c("AATC", "ARO8", "BCA1", "AMPL", "BCA2", "ARO9") # the corresponding ORF names ORF <- c("YLR027C", "YGL202W", "YHR208W", "YKL103C", "YJR148W", "YHR137W") # we only match two of them by gene name, but all by ORF name aa <- yeast.aa(genes)
yeast.aa: AATC BCA1 AMPL BCA2 were not matched
aa <- yeast.aa(ORF) # what are their formulas and average oxidation states of carbon protein.formula(aa)
C H N O S YLR027C_Sce 2074 3239 557 606 12 YGL202W_Sce 2560 3930 652 751 10 YHR208W_Sce 1971 3090 526 568 11 YKL103C_Sce 2564 3992 682 773 11 YJR148W_Sce 1874 2935 491 552 14 YHR137W_Sce 2644 4071 677 786 19
ZC(protein.formula(aa))
[1] -0.1600771 -0.1765625 -0.1796043 -0.1474259 -0.1760939 -0.1626324
## potential fields for overall protein compositions ## transcriptionally induced and repressed in aerobic ## and anaerobic carbon limitation ## (experiments of Tai et al., 2005) # the activities of ammonium and sulfate used here # are similar to the non-growth-limiting concentrations # used by Boer et al., 2003 basis(c("glucose", "H2O", "NH4+", "hydrogen", "SO4-2", "H+"), c(-1, 0, -1.3, 999, -1.4, -7))
C H N O S Z ispecies logact state C6H12O6 6 12 0 6 0 0 1646 -1.0 aq H2O 0 2 0 1 0 0 1 0.0 liq NH4+ 0 4 1 0 0 1 18 -1.3 aq H2 0 2 0 0 0 0 3309 999.0 gas SO4-2 0 0 0 4 1 -2 24 -1.4 aq H+ 0 1 0 0 0 1 3 -7.0 aq
# the names of the experiments in TBD+05.csv expt <- c("Clim.aerobic.down", "Clim.aerobic.up", "Clim.anaerobic.down", "Clim.anaerobic.up") file <- system.file("extdata/abundance/TBD+05.csv", package="CHNOSZ") dat <- read.csv(file, as.is=TRUE) # yeast.aa: get the amino acid compositions # aasum: average them together for(thisexpt in expt) { p <- dat$protein[dat[, thisexpt]] aa <- yeast.aa(p) aa <- aasum(aa, average=TRUE, protein=thisexpt) add.protein(aa) }
add.protein: added 1 new protein(s) to thermo$protein add.protein: added 1 new protein(s) to thermo$protein add.protein: added 1 new protein(s) to thermo$protein add.protein: added 1 new protein(s) to thermo$protein
species(expt, "Sce")
C6H12O6 H2O NH4+ H2 SO4-2 H+ ispecies logact state name 1 384.4827 -1692.895 606.875 254.4785 16.729 -573.417 3589 -3 aq Clim.aerobic.down_Sce 2 366.5690 -1597.538 590.469 218.6205 14.931 -560.607 3590 -3 aq Clim.aerobic.up_Sce 3 408.3423 -1771.524 659.199 241.9095 16.988 -625.223 3591 -3 aq Clim.anaerobic.down_Sce 4 233.6048 -1029.086 378.486 154.5135 10.600 -357.286 3592 -3 aq Clim.anaerobic.up_Sce
a <- affinity(C6H12O6=c(-30, 0), H2=c(-20, 0))
energy.args: temperature is 25 C energy.args: pressure is Psat energy.args: variable 1 is log_a(C6H12O6) at 128 values from -30 to 0 energy.args: variable 2 is log_f(H2) at 128 values from -20 to 0 subcrt: 10 species at 298.15 K and 1 bar (wet) subcrt: 18 species at 298.15 K and 1 bar (wet)
d <- diagram(a, normalize=TRUE, fill=NULL)
balance: from protein length diagram: plotting A/(2.303RT) / n.balance (maximum affinity method for 2-D diagrams) diagram: using 'normalize' in calculation of predominant species
title(main=paste("Formation potential of proteins associated with\n", "transcriptional response to carbon limitation in yeast")) # the affinity of formation favors the proteins upregulated # by carbon limitation at low chemical potentials of C6H12O6 ... stopifnot(c(d$predominant[1,1], d$predominant[1,128])==grep("up", expt)) # ... and favors proteins downregulated by aerobic conditions # at high hydrogen fugacities stopifnot(c(d$predominant[128, 128], d$predominant[128, 1])==grep("down", expt))

Image yeastaa1

 

## overall oxidation state of proteins exclusively localized ## to cytoplasm of S. cerevisiae with/without abundance weighting y <- yeastgfp("cytoplasm") aa <- yeast.aa(y$protein)
yeast.aa: YJL017W was not matched
aaavg <- aasum(aa, average=TRUE)
aasum: dropped 1 proteins with NA composition and/or abundance
ZC(protein.formula(aaavg))
[1] -0.1293854
# the average composition weighted by abundance waaavg <- aasum(aa, abundance=y$abundance, average=TRUE)
aasum: dropped 75 proteins with NA composition and/or abundance
ZC(protein.formula(waaavg))
[1] -0.1488026