calc_metrics {chem16S}

Calculate chemical metrics from amino acid composition

Description

Calculates various chemical metrics from amino acid composition(s) of one or more proteins.

Usage

  calc_metrics(AAcomp, metrics = c("Zc", "nO2", "nH2O"))

Arguments

AAcomp

data frame of amino acid composition with column names being the 3-letter abbreviations of the amino acids (first letter uppercase)

metrics

character, chemical metrics to calculate

Details

The following metrics are available:

• Zc: Carbon oxidation state. Its value is calculated from elemental composition as described by Dick (2014).

• nO2: Stoichiometric oxidation state. nO2 and nH2O are calculated from theoretical formation reactions of proteins from the QEC basis species (glutamine, glutamic acid, cysteine, H₂O, and O₂) and are normalized by number of amino acid residues (see Dick et al., 2020).

• nH2O: Stoichiometric hydration state. See above; note that the contribution of terminal groups is not counted in the calculation of nH2O.

• GRAVY: Grand average of hydropathicity. Values of the hydropathy index for individual amino acids are from Kyte and Doolittle (1982).

• pI: Isoelectric point. The net charge for each ionizable group was pre-calculated from pH 0 to 14 at intervals of 0.01. The isoelectric point is found as the pH where the sum of charges of all groups in the protein is closest to zero. The pK values for the terminal groups and sidechains are taken from Bjellqvist et al. (1993) and Bjellqvist et al. (1994); note that the calculation does not implement position-specific adjustments described in the latter paper. The number of N- and C-terminal groups is taken to be one, unless a column for chains (number of polypeptide chains) is given in AAcomp.

• MW: Molecular weight. This is the per-residue molecular weight and doesn't include the contribution of terminal groups.

• length or Length: Protein length. This is the number of amino acid residues per protein.

• H/C, H_C, or HC: H/C ratio (not counting terminal H-OH groups of the protein backbone).

• N/C, N_C, or NC: N/C ratio.

• O/C, O_C, or OC: O/C ratio (not counting terminal H-OH groups of the protein backbone).

• S/C, S_C, or SC: S/C ratio.

Value

A data frame with the same number of rows as AAcomp and one column of numeric values for each of the metrics. An error is produced if any of the metrics is not available for calculation.

References

Bjellqvist B, Hughes GJ, Pasquali C, Paquet N, Ravier F, Sanchez J-C, Frutiger S, Hochstrasser D. 1993. The focusing positions of polypeptides in immobilized pH gradients can be predicted from their amino acid sequences. Electrophoresis 14: 1023–1031. doi:10.1002/elps.11501401163

Bjellqvist B, Basse B, Olsen E, Celis JE. 1994. Reference points for comparisons of two-dimensional maps of proteins from different human cell types defined in a pH scale where isoelectric points correlate with polypeptide compositions. Electrophoresis 15: 529–539. doi:10.1002/elps.1150150171

Dick JM. 2014. Average oxidation state of carbon in proteins. J. R. Soc. Interface 11: 20131095. doi:10.1098/rsif.2013.1095

Dick JM, Yu M, Tan J. 2020. Uncovering chemical signatures of salinity gradients through compositional analysis of protein sequences. Biogeosciences 17: 6145–6162. doi:10.5194/bg-17-6145-2020

Gasteiger E, Hoogland C, Gattiker A, Duvaud S, Wilkins MR, Appel RD, Bairoch A. 2005. Protein identification and analysis tools on the ExPASy server. In: Walker JM, editor. The Proteomics Protocols Handbook. Totowa, NJ: Humana Press. pp. 571–607. doi:10.1385/1-59259-890-0:571

Kyte J, Doolittle RF. 1982. A simple method for displaying the hydropathic character of a protein. J. Mol. Biol. 157: 105–132. doi:10.1016/0022-2836(82)90515-0

See Also

get_metrics

Examples

# Amino acid composition of alanylglycine
AG <- data.frame(Ala = 1, Gly = 1)
# Calculate default metrics
calc_metrics(AG)
# Calculate selected metrics
calc_metrics(AG, c("GRAVY", "pI"))