canprot-package {canprot}

Chemical analysis of proteins

Description

Chemical metrics of proteins are important for understanding biomolecular adaptation to environments. canprot computes chemical metrics of proteins from their amino acid compositions.

Details

• read_fasta – start here to read amino acid compositions from FASTA files.

• metrics – use these functions to calculate chemical metrics from amino acid compositions.

Chemical metrics include carbon oxidation state (Z_C) stoichiometric oxidation and hydration state (n_O2 and n_H2O) as described in Dick et al. (2020). Other variables that can be calculated are protein length, average molecular weight of amino acid residues, grand average of hydropathy (GRAVY), and isoelectric point (pI).

Differential expression datasets that were in the package up to version 1.1.2, mainly for the paper by Dick (2021), have been moved to JMDplots.

Three demos are available:

• demo("thermophiles"): Specific entropy vs Z_C for methanogen genomes and Nitrososphaeria MAGs. Amino acid compositions and optimal growth temperatures for methanogens were obtained from Dick et al. (2023). Accession numbers and data for Nitrososphaeria MAGs were taken from Tables S1 and S3 Luo et al. (2024) and are saved in ‘extdata/aa/nitrososphaeria_MAGs.csv’. Sequences of MAGs were downloaded from NCBI and processed to obtain amino acid compositions using the script in ‘extdata/aa/prepare.R’

• demo("locations"): Z_C and pI for human proteins with different subcellular locations. The localization data was taken from Thul et al. (2017) and is stored in ‘extdata/protein/TAW+17_Table_S6_Validated.csv’.

• demo("redoxins"): Z_C vs the midpoint reduction potentials of ferredoxin and thioredoxin in spinach and glutaredoxin and thioredoxin in E. coli. The sequences were obtained from UniProt and is stored in ‘extdata/fasta/redoxin.fasta’. The reduction potential data was taken from Åslund et al. (1997) and Hirasawa et al. (1999) and is stored in ‘extdata/fasta/redoxin.csv’. This file also lists UniProt IDs and start and stop positions for the protein chains excluding initiator methionines and signal peptides.

References

Åslund F, Berndt KD, Holmgren A. 1997. Redox potentials of glutaredoxins and other thiol-disulfide oxidoreductases of the thioredoxin superfamily determined by direct protein-protein redox equilibria. Journal of Biological Chemistry 272(49): 30780–30786. doi:10.1074/jbc.272.49.30780

Dick JM. 2021. Water as a reactant in the differential expression of proteins in cancer. Computational and Systems Oncology 1(1): e1007. doi:10.1002/cso2.1007

Dick JM, Yu M, Tan J. 2020. Uncovering chemical signatures of salinity gradients through compositional analysis of protein sequences. Biogeosciences 17(23): 6145–6162. doi:10.5194/bg-17-6145-2020

Dick JM, Boyer GM, Canovas PA, Shock EL. 2023. Using thermodynamics to obtain geochemical information from genomes. Geobiology 21(2): 262–273. doi:10.1111/gbi.12532

Hirasawa M, Schürmann P, Jacquot J-P, Manieri W, Jacquot P, Keryer E, Hartman FC, Knaff DB. 1999. Oxidation-reduction properties of chloroplast thioredoxins, ferredoxin:thioredoxin reductase, and thioredoxin f-regulated enzymes. Biochemistry 38(16): 5200–5205. doi:10.1021/bi982783v

Luo Z-H, Li Q, Xie Y-G, Lv A-P, Qi Y-L, Li M-M, Qu Y-N, Liu Z-T, Li Y-X, Rao Y-Z, et al. 2024 Jan. Temperature, pH, and oxygen availability contributed to the functional differentiation of ancient Nitrososphaeria. The ISME Journal 18(1): wrad031. doi:10.1093/ismejo/wrad031

Thul PJ, Åkesson L, Wiking M, Mahdessian D, Geladaki A, Blal HA, Alm T, Asplund A, Björk L, Breckels LM, et al. 2017. A subcellular map of the human proteome. Science 356(6340): eaal3321. doi:10.1126/science.aal3321