protein.info: Summaries of Thermodynamic Properties of Proteins

Description Usage Arguments Details References Examples

Description

Protein information, length, chemical formula, thermodynamic properties by group additivity, reaction coefficients of basis species, and metastable equilibrium example calculation.

Usage

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  pinfo(protein, organism=NULL, residue=FALSE, regexp=FALSE)
  protein.length(protein, organism = NULL)
  protein.formula(protein, organism = NULL, residue = FALSE)
  protein.obigt(protein, organism = NULL, state=get("thermo")$opt$state)
  protein.basis(protein, T = 25, normalize = FALSE)
  protein.equil(protein, T=25, loga.protein = 0, digits = 4)

Arguments

protein

character, names of proteins; numeric, species index of proteins; data frame; amino acid composition of proteins

organism

character, names of organisms

residue

logical, return per-residue values (those of the proteins divided by their lengths)?

regexp

logical, find matches using regular expressions?

normalize

logical, return per-residue values (those of the proteins divided by their lengths)?

state

character, physical state

T

numeric, temperature in °C

loga.protein

numeric, decimal logarithms of reference activities of proteins

digits

integer, number of significant digits (see signif)

Details

For character protein, pinfo returns the rownumber(s) of thermo$protein that match the protein names. The names can be supplied in the single protein argument (with an underscore, denoting protein_organism) or as pairs of proteins and organisms. NA is returned for any unmatched proteins, including those for which no organism is given or that do not have an underscore in protein.

Alternatively, if regexp is TRUE, the protein argument is used as a pattern (regular expression); rownumbers of all matches of thermo$protein$protein to this pattern are returned. When using regexp, the organism can optionally be provided to return only those entries that also match thermo$protein$organism.

For numeric protein, pinfo returns the corresponding row(s) of thermo$protein. Set residue to TRUE to return the per-residue composition (i.e. amino acid composition of the protein divided by total number of residues).

For dataframe protein, pinfo returns it unchanged, except for possibly the per-residue calculation.

The following functions accept any specification of protein(s) described above for pinfo:

protein.length returns the lengths (number of amino acids) of the proteins.

protein.formula returns a stoichiometrix matrix representing the chemical formulas of the proteins that can be pased to e.g. mass or ZC. The amino acid compositions are multiplied by the output of group.formulas to generate the result.

protein.obigt calculates the thermodynamic properties and equations-of-state parameters for the completely nonionized proteins using group additivity with parameters taken from Dick et al., 2006 (aqueous proteins) and LaRowe and Dick, 2012 (crystalline proteins and revised aqueous methionine sidechain group). The return value is a data frame in the same format as thermo$obigt. state indicates the physical state for the parameters used in the calculation (aq or cr).

The following functions also depend on an existing definition of the basis species:

protein.basis calculates the numbers of the basis species (i.e. opposite of the coefficients in the formation reactions) that can be combined to form the composition of each of the proteins. The basis species must be present in thermo$basis, and if H+ is among the basis species, the ionization states of the proteins are included. The ionization state of the protein is calculated at the pH defined in thermo$basis and at the temperature specified by the T argument. If normalize is TRUE, the coefficients on the basis species are divided by the lengths of the proteins.

protein.equil produces a series of messages showing step-by-step a calculation of the chemical activities of proteins in metastable equilibrium. For the first protein, it shows the standard Gibbs energies of the reaction to form the nonionized protein from the basis species and of the ionization reaction of the protein (if H+ is in the basis), then the standard Gibbs energy/RT of the reaction to form the (possibly ionized) protein per residue. The per-residue values of logQstar and Astar/RT are also shown for the first protein. Equilibrium calculations are then performed, only if more than one protein is specified. This calculation applies the Boltzmann distribution to the calculation of the equilibrium degrees of formation of the residue equivalents of the proteins, then converts them to activities of proteins taking account of loga.protein and protein length. If the protein argument is numeric (indicating rownumbers in thermo$protein), the values of Astar/RT are compared with the output of affinity, and those of the equilibrium degrees of formation of the residues and the chemical activities of the proteins with the output of diagram. If the values in any of these tests are are not all.equal an error is produced indicating a bug.

References

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. https://doi.org/10.5194/bg-3-311-2006

LaRowe, D. E. and Dick, J. M. (2012) Calculation of the standard molal thermodynamic properties of crystalline peptides. Geochim. Cosmochim. Acta 80, 70–91. https://doi.org/10.1016/j.gca.2011.11.041

Dick, J. M. (2014) Average oxidation state of carbon in proteins. J. R. Soc. Interface 11, 20131095. https://doi.org/10.1098/rsif.2013.1095

Examples

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# search by name in thermo$protein
ip1 <- pinfo("LYSC_CHICK")
ip2 <- pinfo("LYSC", "CHICK")
# these are the same
stopifnot(all.equal(ip1, ip2))
# two organisms with the same protein name
ip3 <- pinfo("MYG", c("HORSE", "PHYCA"))
# their amino acid compositions
pinfo(ip3)
# their thermodynamic properties by group additivity
protein.obigt(ip3)

# an example of an unrecognized protein name
ip4 <- pinfo("MYGPHYCA")
stopifnot(is.na(ip4))

## example for chicken lysozyme C
# index in thermo$protein
ip <- pinfo("LYSC_CHICK")
# amino acid composition
pinfo(ip)
# length and chemical formula
protein.length(ip)
protein.formula(ip)
# group additivity for thermodynamic properties and HKF equation-of-state
# parameters of non-ionized protein
protein.obigt(ip)
# calculation of standard thermodynamic properties
# (subcrt uses the species name, not ip)
subcrt("LYSC_CHICK")
# affinity calculation, protein identified by ip
basis("CHNOS+")
affinity(iprotein=ip)
# affinity calculation, protein loaded as a species
species("LYSC_CHICK")
affinity()
# NB: subcrt() only shows the properties of the non-ionized
# protein, but affinity() uses the properties of the ionized
# protein if the basis species have H+

## these are all the same
protein.formula("P53_PIG")
protein.formula(pinfo("P53_PIG"))
protein.formula(pinfo(pinfo("P53_PIG")))

## using protein.formula: average oxidation state of 
## carbon of proteins from different organisms (Dick, 2014)
# get amino acid compositions of microbial proteins 
# generated from the RefSeq database 
file <- system.file("extdata/refseq/protein_refseq.csv.xz", package="CHNOSZ")
ip <- add.protein(read.csv(file, as.is=TRUE))
# only use those organisms with a certain
# number of sequenced bases
ip <- ip[as.numeric(thermo$protein$abbrv[ip]) > 50000]
pf <- protein.formula(thermo$protein[ip, ])
zc <- ZC(pf)
# the organism names we search for
# "" matches all organisms
terms <- c("Natr", "Halo", "Rhodo", "Acido", "Methylo",
  "Chloro", "Nitro", "Desulfo", "Geo", "Methano",
  "Thermo", "Pyro", "Sulfo", "Buchner", "")
tps <- thermo$protein$ref[ip]
plot(0, 0, xlim=c(1, 15), ylim=c(-0.3, -0.05), pch="",
  ylab=expression(italic(Z)[C]),
  xlab="", xaxt="n", mar=c(6, 3, 1, 1))
for(i in 1:length(terms)) {
  it <- grep(terms[i], tps)
  zct <- zc[it]
  points(jitter(rep(i, length(zct))), zct, pch=20)
}
terms[15] <- paste("all", length(ip))
axis(1, 1:15, terms, las=2)
title(main=paste("Average oxidation state of carbon in proteins",
  "by taxID in NCBI RefSeq (after Dick, 2014)", sep="\n"))


# using pinfo() with regexp=TRUE:
# plot ZC and nH2O/residue of HOX proteins
# basis species: glutamine-glutamic acid-cysteine-O2-H2O
basis("QEC")
# device setup
par(mfrow=c(2, 2))
# a red-blue scale from 1-13
col <- ZC.col(1:13)
# axis labels
ZClab <- axis.label("ZC")
nH2Olab <- expression(bar(italic(n))[H[2]*O])
# loop over HOX gene clusters
for(cluster in c("A", "B", "C", "D")) {
  # get protein indices
  pattern <- paste0("^HX", cluster)
  ip <- pinfo(pattern, "HUMAN", regexp=TRUE)
  # calculate ZC and nH2O/residue
  thisZC <- ZC(protein.formula(ip))
  thisH2O <- protein.basis(ip)[, "H2O"] / protein.length(ip)
  # plot lines
  plot(thisZC, thisH2O, type="l", xlab=ZClab, ylab=nH2Olab)
  # the number of the HOX gene
  pname <- pinfo(ip)$protein
  nHOX <- as.numeric(gsub("[A-Za-z]*", "", pname))
  # plot colored points
  points(thisZC, thisH2O, pch=19, col=col[nHOX], cex=3.5)
  points(thisZC, thisH2O, pch=19, col="white", cex=2.5)
  # plot the number of the HOX gene
  text(thisZC, thisH2O, nHOX)
  # add title
  title(main=paste0("HOX", cluster))
}

CHNOSZ documentation built on May 25, 2017, 3:01 a.m.

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