canprot-package {canprot}R Documentation

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

Chemical metrics include carbon oxidation state (ZC) stoichiometric oxidation and hydration state (nO2 and nH2O) 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:

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


[Package canprot version 2.0.0 Index]