pKaData: Sets of pKa values for Charged Amino Acids
In idpr: Profiling and Analyzing Intrinsically Disordered Proteins in R

Description Usage Format Additional Information Full Citations Source See Also

A dataset containing the various pKa accepted values for each charged amino acid residue. N- and C-terminus values are also included. See "IPC - Isoelectric Point Calculator" Kozlowski (2016) for information on variability in pKa Data sets. https://doi.org/10.1186/s13062-016-0159-9
Citations are also contained in the data frame for convenience. Please cite the specific pKa set source and/or Kozlowski (2016).

pKaData

a data frame with 10 rows and 16 variables.

AA: Amino acid residues as a single letter.
Residues are: Cys (C), Asp (D), Glu (E), His (H), Lys (K), Arg (R), and Tyr (Y).
N- and C-termini as NH2 and COOH, respectively. "citation" in the final row
EMBOSS: pKa Dataset from https://doi.org/10.1016/S0168-9525(00)02024-2
DTASelect: pKa Dataset from https://doi.org/10.1021/pr015504q
Solomons: pKa Dataset from: https://doi.org/10.1186/s13062-016-0159-9
pKa Dataset original source: ISBN: 978-1-118-87576-6
Sillero: pKa Dataset from https://doi.org/10.1016/0003-2697(89)90136-X
Rodwell: pKa Dataset from https://doi.org/10.1016/0003-2697(82)90611-X
Lehninger: pKa Dataset from ISBN-13: 978-1-4641-2611-6
Toseland: pKa Dataset from https://doi.org/10.1093/nar/gkj035
Thurlkill: pKa Dataset from https://doi.org/10.1110/ps.051840806
Nozaki: pKa Dataset from: https://doi.org/10.1110/ps.051840806
pKa Dataset original source: https://doi.org/10.1016/S0076-6879(67)11088-4
Dawson: pKa Dataset from: https://doi.org/10.1186/s13062-016-0159-9
pKa Dataset original source: ISBN: 9780198552994
Bjellqvist: pKa Dataset from: https://doi.org/10.1186/s13062-016-0159-9
pKa Dataset original source: https://doi.org/10.1002/elps.1150150171
ProMoST: pKa Dataset from https://doi.org/10.1093/nar/gkh356
IPC_protein: pKa Dataset from https://doi.org/10.1186/s13062-016-0159-9
IPC_peptide: pKa Dataset from https://doi.org/10.1186/s13062-016-0159-9
Vollhardt: pKa Dataset from ISBN-13: 978-1-4641-2027-5

Values for NH2 and COOH are averages of values provided within the Lehringer, ProMoST, and Volhardt datasets. Lehringer and Volhardt both are the Seventh edition. Lehringer varies from data presented in the IPC paper.
When values could not be sourced to the original source, values were taken from Kozlowski (2016), https://doi.org/10.1186/s13062-016-0159-9. Both Kozlowski (2016) and the original source DOI (where available) or ISBN are provided within the Format section of this documentation.

Dawson, Elliott, Elliott, & Jones, 2002; Halligan et al., 2004; Kozlowski, 2016; Nelson & Cox, 2017; Nozaki & Tanford, 1967; Rice, Longden, & Bleasby, 2000; Rodwell, 1982; Sillero & Ribeiro, 1989; Tabb, McDonald, & Yates, 2002; TG, 1992; Thurlkill, Grimsley, Scholtz, & Pace, 2006; Toseland, McSparron, Davies, & Flower, 2006; Vollhardt & Schore, 2014)
Dawson, R. M. C., Elliott, D. C., Elliott, W. H., & Jones, K. M. (2002). Data for biochemical research (Vol. 3): Clarendon Press.
Halligan, B. D., Ruotti, V., Jin, W., Laffoon, S., Twigger, S. N., & Dratz, E. A. (2004). ProMoST (Protein Modification Screening Tool): a web-based tool for mapping protein modifications on two-dimensional gels. Nucleic Acids Research, 32(Web Server issue), W638-W644. doi:10.1093/nar/gkh356
Kozlowski, L. P. (2016). IPC – Isoelectric Point Calculator. Biology Direct, 11(1), 55. doi:10.1186/s13062-016-0159-9
Nelson, D. L., & Cox, M. M. (2017). Lehninger Principles of Biochemistry (Seventh ed.). New York, NY: W. H. Freeman and Company.
Nozaki, Y., & Tanford, C. (1967). [84] Examination of titration behavior. In Methods in Enzymology (Vol. 11, pp. 715-734): Academic Press.
Rice, P., Longden, I., & Bleasby, A. (2000). EMBOSS: The European Molecular Biology Open Software Suite. Trends in Genetics, 16(6), 276-277. doi:10.1016/S0168-9525(00)02024-2
Rodwell, J. D. (1982). Heterogeneity of component bands in isoelectric focusing patterns. Analytical Biochemistry, 119(2), 440-449. doi:https://doi.org/10.1016/0003-2697(82)90611-X
Sillero, A., & Ribeiro, J. M. (1989). Isoelectric points of proteins: Theoretical determination. Analytical Biochemistry, 179(2), 319-325. doi:https://doi.org/10.1016/0003-2697(89)90136-X
Tabb, D. L., McDonald, W. H., & Yates, J. R. (2002). DTASelect and Contrast: Tools for Assembling and Comparing Protein Identifications from Shotgun Proteomics. Journal of Proteome Research, 1(1), 21-26. doi:10.1021/pr015504q
TG, S. (1992). Organic chemistry. USA: John Wiley & Sons.
Thurlkill, R. L., Grimsley, G. R., Scholtz, J. M., & Pace, C. N. (2006). pK values of the ionizable groups of proteins. Protein science : a publication of the Protein Society, 15(5), 1214-1218. doi:10.1110/ps.051840806
Toseland, C. P., McSparron, H., Davies, M. N., & Flower, D. R. (2006). PPD v1.0—an integrated, web-accessible database of experimentally determined protein pKa values. Nucleic Acids Research, 34(suppl_1), D199-D203. doi:10.1093/nar/gkj035
Vollhardt, P., & Schore, N. (2014). Organic Chemistry: Structure and Function (Seventh ed.). New York, NY: W. H. Freeman and Company.

Kozlowski, L. P. (2016). IPC – Isoelectric Point Calculator. Biology Direct, 11(1), 55. doi:10.1186/s13062-016-0159-9

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idpr documentation built on Dec. 26, 2020, 6 p.m.