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Next: [4] protein Up: CHNOSZ examples Previous: [1] buffer

[1] iprotein

## Don't show: data(thermo)
thermo$obigt: 1809 aqueous, 3368 total species
## End(Don't show) # search by name in thermo$protein ip1 <- iprotein("LYSC_CHICK") ip2 <- iprotein("LYSC", "CHICK") # these are the same stopifnot(all.equal(ip1, ip2)) # two organisms with the same protein name ip3 <- iprotein("MYG", c("HORSE", "PHYCA")) # their amino acid compositions ip2aa(ip3)
protein organism ref abbrv chains Ala Cys Asp Glu Phe Gly His Ile Lys Leu Met Asn Pro Gln Arg Ser 122 MYG HORSE BBA+03 P68082 1 15 0 8 13 7 15 11 9 19 17 2 2 4 6 2 5 7 MYG PHYCA BBA+03 P02185 1 17 0 7 14 6 11 12 9 19 18 2 1 4 5 4 6 Thr Val Trp Tyr 122 7 7 2 2 7 5 8 2 3
# their thermodynamic properties by group additivity aa2eos(ip2aa(ip3))
aa2eos: found MYG_HORSE (C769H1212N210O218S2, 153 residues) aa2eos: found MYG_PHYCA (C783H1240N216O216S2, 153 residues) name abbrv formula state ref1 ref2 date G H S Cp V 1 MYG_HORSE NA C769H1212N210O218S2 aq BBA+03 NA NA -5092861 -12598083 4977.26 8172.949 12568.77 2 MYG_PHYCA NA C783H1240N216O216S2 aq BBA+03 NA NA -4906543 -12549363 5060.59 8423.000 12845.90 a1.a a2.b a3.c a4.d c1.e c2.f omega.lambda z.T 1 3048.32 460.36 391.76 -512.56 9717.3 -785.6 -5.71 0 2 3098.26 490.84 518.43 -538.56 9957.6 -786.0 -6.87 0
# an example of an unrecognized protein name ip4 <- iprotein("MYGPHYCA")
iprotein: 1 protein not matched
stopifnot(is.na(ip4)) # manually adding a new protein # Human Gastric juice peptide 1 aa <- seq2aa("GAJU_HUMAN", "LAAGKVEDSD") ip <- add.protein(aa)
add.protein: added 1 new protein(s) to thermo$protein
stopifnot(protein.length(ip)==10) # the chemical formula of this peptide stopifnot(as.chemical.formula(protein.formula(ip))=="C41H69N11O18") # we can also calculate a formula without using add.protein as.chemical.formula(protein.formula(seq2aa("pentapeptide_test", "ANLSG")))
[1] "C18H32N6O8"
# read a fasta file, calculate H/C and O/C for all proteins # and averages by polypeptide chain, residue and mass ffile <- system.file("extdata/fasta/HTCC1062.faa.xz", package="CHNOSZ") aa <- read.fasta(ffile)
read.fasta: reading HTCC1062.faa.xz
pf <- as.data.frame(protein.formula(aa)) plot(pf$H/pf$C, pf$O/pf$C, pch=NA) points(pf$H/pf$C, pf$O/pf$C, pch=20, cex=0.5, col="grey") # average composition per polypeptide chain chainaa <- aasum(aa, average=TRUE) chainpf <- as.data.frame(protein.formula(chainaa)) points(chainpf$H/chainpf$C, chainpf$O/chainpf$C, pch=15, col="red") # average by amino acid residue pl <- protein.length(aa) resaa <- aasum(aa, abundance=pl, average=TRUE) respf <- as.data.frame(protein.formula(resaa)) points(respf$H/respf$C, respf$O/respf$C, pch=16, col="red") # average by mass pm <- mass(pf) massaa <- aasum(aa, abundance=pm, average=TRUE) masspf <- as.data.frame(protein.formula(massaa)) points(masspf$H/masspf$C, masspf$O/masspf$C, pch=17, col="red") # add a legend and title legend("topright", pch=c(20, 15, 16, 17), col=c("grey", rep("red", 3)), legend=c("protein", "chain average", "residue average", "mass average")) title(main=paste("O/C vs H/C for HTCC1062 proteins\n", "n =", nrow(aa)))

Image iprotein1

 


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Next: [4] protein Up: CHNOSZ examples Previous: [1] buffer