protein {CHNOSZ} | R Documentation |
Retrieve the amino acid compositions or thermodynamic properties and equations of state parameters of proteins.
protein(protein,organism=NULL,online=thermo$opt$online) protein.residue(proteins) protein.info(T=25) residue.info(T=25)
protein |
character, names of proteins, protein identifiers, or amino acid sequences, or numeric, indices of proteins (rownumbers of thermo$protein ), or dataframe, protein compositions to sum into new protein. |
organism |
character, organism identifiers, or physical state. |
proteins |
character, names of proteins. |
online |
logical, try an online search if the specified protein(s) are not found locally? |
T |
numeric, temperature in units specified by nuts . |
protein
is a function to query the protein database and to perform group additivity calculations of the standard molal thermodynamic properties and equations of state parameters of proteins. To distinguish names of proteins from those of other species, protein names in CHNOSZ have an underscore ("_") somewhere in their name, as in LYSC_CHICK. The user will generally include a protein in calculations by submitting the name of one in the arguments to a function like species
or subcrt
.
If a protein name is submitted as a single argument to protein
it is searched in thermo$proteins
; if matches are found, the selected rows are returned. If protein and organism identifiers (e.g. LYSC and CHICK, respectively) are provided, the rownumbers of matches in thermo$protein
are returned.
If no match is found in thermo$protein
, an online search is invoked, unless online
is FALSE. (If online
is NA, the default value of thermo$opt$online
, the user is prompted whether the online search should be performed, and this response is stored in thermo$opt$online
.) The function attempts a search of the SWISS-Prot database (Boeckmann et al., 2003). If the amino acid composition of the protein is successfully retrieved by the online search, that composition is stored in thermo$protein
.
If organism
looks like the name of a protein (it contains an underscore), the function assumes that protein
contains the amino acid sequence of a new protein, and the corresponding amino acid composition is added to thermo$protein
, with the name given by organism
. This allows for entry of protein compositions at the command line.
If protein
is numeric, the compositional information found in that row(s) of thermo$protein
is combined with sidechain and backbone group contributions to generate the standard molal thermodynamic properties and equations of state parameters of the proteins at 25 degree C and 1 bar (Dick et al., 2006), and a dataframe of these values returned. The physical state of the proteins in this calculation is controlled by the value of organism
(aq or cr; NULL
defaults to aq). Note that the properties of aqueous (and crystalline) proteins calculated in this step are hypothetically completely nonionized proteins; the contributions by ionization to the chemical affinities of formation reactions of aqueous proteins can be calculated during execution of affinity
if the basis species contain H+.
If protein
is a data.frame
, it is taken contain the compositions of one or more proteins that are summed to make a new protein. In this case, the argument organism
should contain the name of the new protein, e.g. PROTEIN_NEW.
protein.residue
generates average amino acid residue compositions of proteins. It takes the name(s) of one or more proteins (e.g. LYSC_CHICK), retrieves their amino acid compositions from thermo$protein
, and divides by the total number of amino acid residues in each of the proteins.
protein.info
is a utility to tabulate some properties of proteins. A dataframe is returned containing for each protein that is among the species
of interest, the name of the protein, its length, formula, and values of the standard molal Gibbs energy of the neutral protein, net charge, standard molal Gibbs energy of the ionized protein, and average oxidation number of carbon. The value of T
indicates the temperature at which to calculate the Gibbs energies and net charge. Net charge and standard molal Gibbs energy of the ionized protein become NA if H+ is not among the basis species. The values are rounded at a set number of digits for convenient display, and the values of Gibbs energy are in kcal/mol.
residue.info
calculates the per-residue makeup of the proteins that have been loaded using species
. This amounts to dividing the reaction coefficients in thermo$species
by the length of the protein, but also takes into account the ionization state of the protein if H+ is one of the basis species. As with protein.info
, the ionization state of the protein is calculated at the pH defined in thermo$basis
and at the temperature specified by the T
argument.
If protein
is one or more protein names, the matching row(s) of thermo$protein
. If protein
and organism
are protein and organisms identifiers, rownumbers of thermo$protein
. If protein
is numeric, a dataframe with calculated thermodynamic properties and parameters of the neutral protein.
Boeckmann, B., Bairoch, A., Apweiler, R., Blatter, M.-C., Estreicher, A., Gasteiger, E., Martin, M. J., Michoud, K., Donovan, C., Phan, I., Pilbout, S. and Schneider, M., 2003. The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res., 31, 365-370. http://www.expasy.org, accessed on 2007-12-19.
Dick, J. M., LaRowe, D. E. and Helgeson, H. C., 2006. Temperature, pressure, and electrochemical constraints on protein speciation: Group additivity calculation of the standard molal thermodynamic properties of ionized unfolded proteins. Biogeosciences, 3, 311-336. http://www.biogeosciences.net/3/311/2006/bg-3-311-2006.html
Dick, J. M., 2008. Calculation of the relative metastabilities of proteins using the CHNOSZ software package. Geochem. Trans., 9:10. http://dx.doi.org/10.1186/1467-4866-9-10
get.protein
for retrieving compositions of proteins in yeast and E. coli, including those identified in stress response experiments.
### Interaction with the 'protein'function ## Thermodynamic properties of proteins # get the composition of a protein protein("BPT1_BOVIN") # retrieve the rownumber of a protein in thermo$protein iprotein <- protein("LYSC","CHICK") # calculate properties and parameters of aqueous protein protein(iprotein) # of crystalline protein protein(iprotein,"cr") # a call to info() causes the protein properties to # be appended to thermo$obigt info("LYSC_CHICK") # thermodynamic properties can be calculated with subcrt() subcrt("LYSC_CHICK") ### Table of properties of some proteins basis("CHNOS+") species(c("LYSC_CHICK","CYC_BOVIN","MYG_HORSE","RNAS1_BOVIN")) protein.info() # the following gives the per-residue composition (i.e. formation # reaction cofficients) for the ionized proteins residue.info() ## Protein Data from Online Sources ## Not run: ## marked dontrun because it requires internet # this asks to search SWISS-Prot info("PRND_HUMAN") # an online search can also be started from the # "subcrt" function subcrt("SPRN_HUMAN") ## End(Not run) ## end dontrun ## Inputting protein compositions # make a new protein protein("GGSGG","PROTEIN_TEST") # a sequence can be pasted into the command line: # type this protein(" # then paste the sequence # and end the command by typing ","PROTEIN_NEW") # or use whatever name you want (with an underscore). ## 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 t <- subcrt(c("CSG_METTL","CSG_METJA"),c(-1/530,1/530), T=seq(0,350,length.out=50)) thermo.plot.new(xlim=range(t$out$T),ylim=range(t$out$S), xlab=axis.label("T"),ylab=axis.label("DS0r")) lines(t$out$T,t$out$S) # do it at high pressure as well t <- subcrt(c("CSG_METTL","CSG_METJA"),c(-1/530,1/530), T=seq(0,350,length.out=50),P=3000) lines(t$out$T,t$out$S,lty=2) # label the plot title(main=paste("Standard molal entropy\n", "P = Psat (solid), P = 3000 bar (dashed)")) t$reaction$coeff <- round(t$reaction$coeff,3) d <- describe(t$reaction, use.name=c(TRUE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE)) text(170,-3,c2s(s2c(d,sep="=",move.sep=TRUE),sep="\n"),cex=0.8) ### Metastability calculations ### these examples can be run using longex("protein") ## Not run: ## subcellular homologs of yeast glutaredoxin ## as a function of logfO2 - logaH2O, after Dick, 2009 basis("CHNOS+") protein <- c("GLRX1","GLRX2","GLRX3","GLRX4","GLRX5") loc <- c("(C)","(M)","(N)","(N)","(M)") species(protein,"YEAST") t <- affinity(H2O=c(-10,0),O2=c(-85,-60)) diagram(t,names=paste(protein,loc)) title(main=paste("Yeast glutaredoxins (black) and residues (blue)\n", describe(thermo$basis[-c(2,5),]))) # note the difference when we set as.residue=TRUE to # plot stability fields for the residue equivalents of the # proteins instead of the proteins themselves ... # the residue equivalent for one of the larger proteins appears diagram(t,names=paste(protein,loc),as.residue=TRUE, add=TRUE,col="blue") ## surface-layer proteins from Methanococcus and others: ## a speciation diagram for surface layer proteins ## as a function of oxygen fugacity after Dick, 2008 # make our protein list organisms <- c("METSC","METJA","METFE","HALJP","METVO", "METBU","ACEKI","BACST","BACLI","AERSA") proteins <- c(rep("CSG",6),rep("SLAP",4)) proteins <- paste(proteins,organisms,sep="_") # set some graphical parameters lwd <- c(rep(3,6),rep(1,4)) lty <- c(1:6,1:4) # load the basis species and proteins basis("CHNOS+") species(proteins) # calculate affinities a <- affinity(O2=c(-100,-65)) # make diagram d <- diagram(a,ylim=c(-5,-1),legend.x=NULL,lwd=lwd, ylab=as.expression(quote(log~italic(a[j]))),yline=1.7) # label diagram text(-80,-1.9,"METJA") text(-74.5,-1.9,"METVO") text(-69,-1.9,"HALJP") text(-78,-2.85,"METBU",cex=0.8,srt=-22) text(-79,-3.15,"ACEKI",cex=0.8,srt=-25) text(-81,-3.3,"METSC",cex=0.8,srt=-25) text(-87,-3.1,"METFE",cex=0.8,srt=-17) text(-79,-4.3,"BACST",cex=0.8) text(-85.5,-4.7,"AERSA",cex=0.8,srt=38) text(-87,-4.25,"BACLI",cex=0.8,srt=30) # add water line abline(v=-83.1,lty=2) title(main=paste("Surface-layer proteins", "After Dick, 2008",sep="\n")) ## relative metastabilities 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,"GSH-GSSG",-7)) basis("CO2","gas") species(c("CYC","RNAS1","BPT1","ALBU","INS","PRIO"),"BOVIN") a <- affinity(T=c(0,200)) diagram(a,as.residue=TRUE,ylim=c(-2,0.5)) title(main="Bovine proteins") ## End(Not run)