charge {Peptides}

Compute the theoretical net charge of a protein sequence

Description

This function computes the net charge of a protein sequence based on the Henderson-Hasselbalch equation described by Moore, D. S. (1985). The net charge can be calculated at defined pH using one of the 9 pKa scales availables: Bjellqvist, Dawson, EMBOSS, Lehninger, Murray, Rodwell, Sillero, Solomon or Stryer.

Usage

charge(seq, pH = 7, pKscale = "Lehninger")

Arguments

seq

An amino-acids sequence

pH

A pH value

pKscale

A character string specifying the pKa scale to be used; must be one of "Bjellqvist", "Dawson", "EMBOSS", "Lehninger", "Murray", "Rodwell", "Sillero", "Solomon" or "Stryer"

Author(s)

Original by Daniel Osorio <[e-mail]>, C++ code optimized by Luis Pedro Coelho <[e-mail]>

References

Kiraga, J. (2008) Analysis and computer simulations of variability of isoelectric point of proteins in the proteomes. PhD thesis, University of Wroclaw, Poland.

Bjellqvist, B., Hughes, G.J., Pasquali, Ch., Paquet, N., Ravier, F., Sanchez, J.Ch., Frutige,r S., Hochstrasser D. (1993) The focusing positions of polypeptides in immobilized pH gradients can be predicted from their amino acid sequences. Electrophoresis, 14:1023-1031.

Dawson, R. M. C.; Elliot, D. C.; Elliot, W. H.; Jones, K. M. Data for biochemical research. Oxford University Press, 1989; p. 592.

EMBOSS data are from http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/iep.html.

Nelson, D. L.; Cox, M. M. Lehninger Principles of Biochemistry, Fourth Edition; W. H. Freeman, 2004; p. 1100.

Murray, R.K., Granner, D.K., Rodwell, V.W. (2006) Harper's illustrated Biochemistry. 27th edition. Published by The McGraw-Hill Companies.

Rodwell, J. Heterogeneity of component bands in isoelectric focusing patterns. Analytical Biochemistry, 1982, 119 (2), 440-449.

Sillero, A., Maldonado, A. (2006) Isoelectric point determination of proteins and other macromolecules: oscillating method. Comput Biol Med., 36:157-166.

Solomon, T.W.G. (1998) Fundamentals of Organic Chemistry, 5th edition. Published by Wiley.

Stryer L. (1999) Biochemia. czwarta edycja. Wydawnictwo Naukowe PWN.

Examples

# COMPARED TO EMBOSS PEPSTATS
# http://emboss.bioinformatics.nl/cgi-bin/emboss/pepstats
# SEQUENCE: FLPVLAGLTPSIVPKLVCLLTKKC
# Charge   = 3.0

charge(seq= "FLPVLAGLTPSIVPKLVCLLTKKC",pH= 7, pKscale= "Bjellqvist")
# [1] 2.737303
charge(seq= "FLPVLAGLTPSIVPKLVCLLTKKC",pH= 7, pKscale= "EMBOSS")
# [1] 2.914112
charge(seq= "FLPVLAGLTPSIVPKLVCLLTKKC",pH= 7, pKscale= "Murray")
# [1] 2.907541
charge(seq= "FLPVLAGLTPSIVPKLVCLLTKKC",pH= 7, pKscale= "Sillero")
# [1] 2.919812
charge(seq= "FLPVLAGLTPSIVPKLVCLLTKKC",pH= 7, pKscale= "Solomon")
# [1] 2.844406
charge(seq= "FLPVLAGLTPSIVPKLVCLLTKKC",pH= 7, pKscale= "Stryer")
# [1] 2.876504
charge(seq= "FLPVLAGLTPSIVPKLVCLLTKKC",pH= 7, pKscale= "Lehninger")
# [1] 2.87315
charge(seq= "FLPVLAGLTPSIVPKLVCLLTKKC",pH= 7, pKscale= "Dawson")
# [1] 2.844406
charge(seq= "FLPVLAGLTPSIVPKLVCLLTKKC",pH= 7, pKscale= "Rodwell")
# [1] 2.819755

# COMPARED TO YADAMP
# http://yadamp.unisa.it/showItem.aspx?yadampid=845&x=0,7055475
# SEQUENCE: FLPVLAGLTPSIVPKLVCLLTKKC
# CHARGE pH5: 3.00
# CHARGE pH7: 2.91
# CHARGE pH9: 1.09
charge(seq= "FLPVLAGLTPSIVPKLVCLLTKKC",pH= 5, pKscale= "EMBOSS")
# [1] 3.037398
charge(seq= "FLPVLAGLTPSIVPKLVCLLTKKC",pH= 7, pKscale= "EMBOSS")
# [1] 2.914112
charge(seq= "FLPVLAGLTPSIVPKLVCLLTKKC",pH= 9, pKscale= "EMBOSS")
# [1] 0.7184524

# JUST ONE COMMAND
charge(seq= "FLPVLAGLTPSIVPKLVCLLTKKC",pH= seq(from = 5,to = 9,by = 2), pKscale= "EMBOSS")
# [1] 3.0373984 2.9141123 0.7184524