Properties of Proteins

Description

Retrieve the amino acid compositions or thermodynamic properties and equations of state parameters of proteins.

Usage

  protein(protein,organism=NULL,online=thermo$opt$online,chains=1)
  protein.residue(proteins)
  protein.info(T=25)
  residue.info(T=25)

Arguments

Details

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. In CHNOSZ, the database of amino acid compositions of proteins is located at thermo$protein and is populated when the package loaded. See the help for thermo for more information.

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. If a protein name is submitted as a single argument to protein it is searched for in thermo$protein; if matches are found, the selected rows are returned. If protein and organism identifiers (e.g. LYSC and CHICK, respectively) are provided, the rownumbers of matches in thermo$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 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 to contain the compositions of one or more proteins that are summed to define a new protein whose amino acid composition is returned. In this case, the argument organism should contain the name of the new protein, e.g. PROTEIN_NEW.

The protein function modifies the database if organism is a valid name for a protein (it contains an underscore). The function assumes that protein contains the amino acid sequence of the new protein to be added to thermo$protein. The chains argument specifies the number of polypeptide chains that are in the molecule (0 for amino acid residues, 1 for amino acids and most proteins).

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 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.

Value

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.

References

Anderson, N. L. and Anderson, N. G. (2003) The human plasma proteome: History, character and diagnostic prospects (Vol. 1 (2002) 845-867). Molecular and Cellular Proteomics 2, 50. http://dx.doi.org/10.1074/mcp.A300001-MCP200

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

See Also

Functions info, subcrt, species and others accept protein names as species arguments. Properties of ionized proteins can be calculated using ionize (usually implicitly called as part of a calculation of affinity). Compositions of proteins beyond those in thermo$protein (including yeast and E. coli) are also provided in CHNOSZ; see get.protein for examples.

Examples

  
  ### 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) 

  ## 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 (this is it)
  # 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
  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)
  d <- describe(s$reaction,
    use.name=c(TRUE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE))
  text(170, -3, c2s(s2c(d,sep="="),sep="\n"), cex=0.8)

  ### Metastability calculations

  ## 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")
  a <- affinity(H2O=c(-10,0), O2=c(-85,-60))
  diagram(a, 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(a, 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")
  prot <- c("CYC","RNAS1","BPT1","ALBU","INS","PRIO")
  species(prot,"BOVIN")
  a <- affinity(T=c(0,200))
  d <- diagram(a, as.residue=TRUE, ylim=c(-2,0.5))
  # add some text labels
  text(40,data.frame(d$logact)[25,],prot)
  title(main="Relative stabilities of bovine proteins on glutathione buffer")

  ## relative metastabilities of plasma proteins,
  ## using chemical activities of H2 and O2
  # clean up basis species, species from previous example
  data(thermo)
  basis(c("CO2","NH3","H2S","H2","O2","H+"))
  basis("O2","aq")
  basis(c("CO2","NH3","H2S","H+"),c(-3,-3,-10,-7))
  f <- system.file("extdata/abundance/AA03.csv", package="CHNOSZ")
  pdata <- read.csv(f, as.is=TRUE)
  notna <- !is.na(pdata$name)
  pname <- pdata$name[notna]
  # take out insulin C peptide to show more proteins
  pname <- pname[!pname %in% "INS.C"]
  species(pname,"HUMAN")
  a <- affinity(H2=c(-20,0), O2=c(-80,-60))
  diagram(a)
  title(main="Human Plasma Proteins")
  # note that the darker colors go with higher abundances
  # as reported by Anderson and Anderson, 2003
  # add lines showing equilibrium activity of H2O
  species(delete=TRUE)
  species("H2O")
  logaH2 <- seq(-20,0,length.out=128)
  for(logaH2O in c(-5,0,5)) {
    species("H2O",logaH2O)
    a <- affinity(H2=logaH2)
    logaO2 <- diagram(a,what="O2",do.plot=FALSE)$logact[[1]]
    lines(logaH2,logaO2,lty=2)
    itext <- 72 + 5 * logaH2O
    lab <- paste("logaH2O =",logaH2O)
    text(logaH2[itext]+0.4,logaO2[itext],lab,srt=-64)
  }