JMDplots vignettes

Energy release during protein synthesis at ultramafic-hosted hydrothermal systems (2021)

This vignette runs the code to make the plots from the following paper:

Dick JM, Shock EL. 2021. The release of energy during protein synthesis at ultramafic-hosted submarine hydrothermal ecosystems. Journal of Geophysical Research: Biogeosciences 126(11): e2021JG006436. doi: 10.1029/2021JG006436

Click here for full-text access to a view-only version of the paper.

This vignette was compiled on 2024-03-11 with JMDplots 1.2.19-11 and CHNOSZ 2.1.0-5.

library(JMDplots)

Affinities for methanogenesis and amino acid synthesis (Figure 1)

mjenergy1()

Calculations shown in this and other figures use activities of CH4, CO2, NH4+, H2S, H2, and H+ from the mixing models of Shock and Canovas (2010).

ZC of amino acids vs frequency in the Mj proteome (Figure 2)

mjenergy2()

Affinities of overall synthesis of proteins in the Mj proteome (Figure 3)

mjenergy3()

Calculate affinity for amino acid synthesis and polymerization

calc_affinity()
## [1] "Affinity for synthesis of 530 amino acids: 37.8 MJ/mol"
## [1] "Affinity for polymerization to form CSG_METJA: -20.4 MJ/mol"
## [1] "Affinity for synthesis of CSG_METJA (non-ionized): 17.4 MJ/mol"
## [1] "Affinity for synthesis of CSG_METJA (ionized): 19.7 MJ/mol"

References

Shock EL, Canovas P. 2010. The potential for abiotic organic synthesis and biosynthesis at seafloor hydrothermal systems. Geofluids 10(1-2): 161–192. doi: 10.1111/j.1468-8123.2010.00277.x