charge {Peptides} | R Documentation |
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
.
charge(seq, pH = 7, pKscale = "Lehninger")
seq |
An amino-acids sequence |
pH |
A pH value |
pKscale |
A character string specifying the pKa scale to be used; must be one of |
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.
# 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