JMDplots vignettes

Amino acid group additivity (2006)

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

Dick JM, LaRowe DE, Helgeson HC. 2006. Temperature, pressure, and electrochemical constraints on protein speciation: Group additivity calculation of the standard molal thermodynamic properties of ionized unfolded proteins. Biogeosciences 3(3): 311–-336. doi: 10.5194/bg-3-311-2006

These plots have been modified from the original figures to add a neutral pH line to Figure 4 and a legend and colored labels to Figure 13.

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

library(JMDplots)

pKa of sidechain and amino acid backbone groups (Figure 4)

aaaq4()

Net charge of proteins as a function of pH and T (Figure 10)

aaaq10()

Experimental data are from Roxby and Tanford (1971), Nozaki and Tanford (1967), and Whitten and García-Moreno E. (2000).

Eh-pH diagram for extracellular α-amylases (Figure 13)

This plot, showing the relative stabilities of extracellular α-amylases from two organisms on an Eh-pH diagram, is based on Fig. 13 of Dick et al. (2006). Points are added for Eh-pH values from soils (Baas Becking et al., 1960) and hot springs in Yellowstone (Spear et al., 2005) and Iceland (Stefánsson and Arnórsson, 2002). Note that the symbols for Yellowstone and Iceland were incorrectly swapped in the original figure caption.

aaaq13()

References

Baas Becking LGM, Kaplan IR, Moore D. 1960. Limits of the natural environment in terms of pH and oxidation-reduction potentials. The Journal of Geology 68(3): 243–284. doi: 10.1086/626659

Nozaki Y, Tanford C. 1967. Proteins as random coils. II. Hydrogen ion titration curve of ribonuclease in 6 m guanidine hydrochloride. Journal of the American Chemical Society 89(4): 742–749. doi: 10.1021/ja00980a003

Roxby R, Tanford C. 1971. Hydrogen ion titration curve of lysozyme in 6 m guanidine hydrochloride. Biochemistry 10(18): 3348–3352. doi: 10.1021/bi00794a005

Spear JR, Walker JJ, McCollom TM, Pace NR. 2005. Hydrogen and bioenergetics in the Yellowstone geothermal ecosystem. Proceedings of the National Academy of Sciences 102(7): 2555–2560. doi: 10.1073/pnas.0409574102

Stefánsson A, Arnórsson S. 2002. Gas pressures and redox reactions in geothermal fluids in Iceland. Chemical Geology 190: 251–271. doi: 10.1016/S0009-2541(02)00119-5

Whitten ST, García-Moreno E. B. 2000. pH dependence of stability of staphylococcal nuclease: Evidence of substantial electrostatic interactions in the denatured state. Biochemistry 39(46): 14292–14304. doi: 10.1021/bi001015c