aaaq: Amino acid group additivity
In jedick/JMDplots: Plots from Papers by Jeffrey M. Dick

aaaq	R Documentation

Amino acid group additivity

Description

Plots from the paper by Dick et al. (2006).

Usage

  aaaq4(pdf = FALSE)
  aaaq10(pdf = FALSE)
  aaaq13(pdf = FALSE)

Arguments

pdf

logical, make a PDF file?

Details

This table gives a brief description of each function.

`aaaq4`	\pKa of sidechain and amino acid backbone groups
`aaaq10`	Net charge of proteins as a function of pH and \T
`aaaq13`	Eh-pH diagram for extracellular alpha-amylases

Files in extdata/aaaq

BKM60_Fig7.csv: Eh-pH values for normal, wet and waterlogged soils from Fig. 7 of Baas Becking et al. (1960).
NT67.csv: Hydrogen ion titration curve for unfolded ribonuclease (‘⁠RNAS1_BOVN⁠’) from Nozaki and Tanford (1967).
RT71.csv: Hydrogen ion titration curve for unfolded lysozyme (‘⁠LYSC_CHICK⁠’) from Roxby and Tanford (1971).
WG00.csv: Hydrogen ion titration curve for unfolded staphylococcal nuclease (‘⁠NUC_STAAU⁠’) from Whitten and García-Morena E. (2000).

References

Baas Becking LGM, Kaplan IR and Moore D (1960) Limits of the natural environment in terms of pH and oxidation-reduction potentials. Journal of Geology 68, 243–284. https://www.jstor.org/stable/30059218

Dick JM, LaRowe DE and 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, 311–336. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.5194/bg-3-311-2006")}

Nozaki Y and Tanford C (1967) Proteins as random coils. II. Hydrogen ion titration curve of ribonuclease in 6 M guanidine hydrochloride J. Amer. Chem. Soc. 89, 742–749. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1021/ja00980a003")}

Roxby R and Tanford C (1971) Hydrogen ion titration curve of lysozyme in 6 M guanidine hydrochloride. Biochemistry 10, 3348–3352. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1021/bi00794a005")}

Whitten ST and García-Morena E. B (2000) pH dependence of stability of staphylococcal nuclease: Evidence of substantial electrostatic interactions in the denatured state. Biochemistry 39, 14292–14304. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1021/bi001015c")}