protein: 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)
  protein.residue(proteins)
  protein.info()

Arguments

protein

character, protein identifiers, or numeric, indices of protein (rownumbers of thermo$protein), or dataframe, protein compositions to sum into new protein.

organism

character, organism identifiers (required if protein is character), or physical state (optional if protein is numeric).

proteins

character, names of proteins.

online

logical, try an online search if the specified protein(s) are not found locally?

Value

If protein or organism contains an underscore, a row of the protein composition dataframe. Otherwise, if protein is numeric, a dataframe with calculated thermodynamic properties and parameters of the neutral protein, or if protein is character, an invisible return of numeric values (or NA for no match) representing rownumbers of thermo$protein that were matched to protein--organism identifiers.

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.

The user will generally specify a protein by submitting the name of one in the argument to a function like species or subcrt. 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 two character arguments are provided and neither one contains an underscore, a search in local and perhaps online data sources is initiated. For each protein--organism pair (the arguments should be the same length), the contents of thermo$proteins are searched for completely matching (both protein and organism) entries.

If no match is found in thermo$proteins, an online search is invoked, unless online is FALSE. (If online is NA, i.e., the default setting in thermo$opt$online, the user is prompted whether she or he wishes the search to be performed, and this response is stored in thermo$opt$online.) The function attempts a search of the SWISS-Prot database (Boeckmann et al., 2003). The search string in this case is formed by joining the corresponding elements of the two arguments with an intervening underscore character to make a name such as LYSC_CHICK. If the amino acid composition of the protein is successfully retrieved by the online searche, that composition is stored in thermo$proteins. For either local or online matches, the values returned by protein are the row numbers of the protein composition in thermo$proteins.

If protein is numeric, the compositional information found in that row(s) of thermo$proteins 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 $^{\circ}$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 refer to 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+ (see ionize).

If protein is character but organism is NULL, the function assumes that protein refers to the name of protein, that is searched for in thermo$proteins; if matches are found, the selected rows are returned. If organism looks like the name of a protein (it contains an underscore), the function assumes that protein contains the amino acid sequence and of a new protein, and the corresponding amino acid composition is added to thermo$protein, with the name given by organism. This allows for entry of protein compositions at the command line.

If protein is a data.frame, it is taken to be representative of 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 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 acids in each protein.

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 nominal carbon oxidation state.

Examples

Run this code

data(thermo)
  
  ### 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$protein
  iprotein <- protein('LYSC','CHICK')
  # calculate properties and parameters from group additivity	
  protein(iprotein)
  # a call to info() causes the protein properties to
  # be appended to thermo$obigt				
  info('LYSC_CHICK')
  # the second time it is faster				
  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'))
  # here, G in the Gibbs energy of a neutral protein, Z is the
  # charge of an ionized protein, G.Z is the Gibbs energy of the 
  # ionized protein, and Z.C is the nominal carbon oxidation state
  protein.info()
  
  ## Protein Data from Online Sources
  ## 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 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(-1/558,1/530),
    T=seq(0,350,length.out=15))
  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(-1/558,1/530),
    T=seq(0,350,length.out=15),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(160,-8,c2s(s2c(d,sep='=',move.sep=TRUE),sep='<n>'),cex=0.8)


  ### Metastability calculations

  ## sigma factors of E. coli as a function
  ## of logfO2 - logaNH3
  basis('CHNOS') 
  species(c('RPOE','RP32','RP54','RPOD'),'ECOLI')
  t <- affinity(NH3=c(-10,0),O2=c(-80,-75))
  diagram(t,balance='PBB',cex.axis=1.5)
  title(main=paste('Sigma factors of E. coli<n>',
    describe(thermo$basis[-c(3,5),])))
  
  ## subcellular homologs of yeast glutaredoxin
  ## as a function of logfO2 - logaH2O
  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),cex.axis=1.5)
  title(main=paste('Subcellular homologs of yeast glutaredoxin<n>',
    describe(thermo$basis[-c(2,5),])))


  ## surface-layer proteins from Methanococcus spp.:
  ## METVO (mesophile)
  ## METTL (thermophile)
  ## METJA (hyperthermophile)
  # 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),residue=TRUE,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>"))
  ## now, show the species richness 
  draw.diversity(d,"richness",logactmin=-4)
  title(main=paste("Surface-layer protein richness"))</n>

<references>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. <em>Nucleic Acids Res.</em>, 31, 365-370. <url>http://www.expasy.org</url>, 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. <em>Biogeosciences</em>, 3, 311-336.</references>

<keyword>misc</keyword></n></n></n></n>