Protein Properties :
- Isoelectric point (pI) is a pH in which net charge of protein is zero. In case of proteins isoelectric point mostly depends on seven charged amino acids: glutamate (δ-carboxyl group), aspartate (ß-carboxyl group), cysteine (thiol group), tyrosine (phenol group), histidine (imidazole side chains), lysine (ε-ammonium group) and arginine (guanidinium group). Additonally, one should take into account charge of protein terminal groups (NH2 i COOH). Each of them has its unique acid dissociation constant referred to as pK.
Moreover, net charge of the protein is in tight relation with the solution (buffer) pH. Keeping in mind this we can use Henderson-Hasselbach equation to calculate protein charge in certain pH:
 Lawrence J. Henderson (01 May 1908). "Concerning the relationship between the strength of acids and their capacity to preserve neutrality" (Abstract). Am. J. Physiol. 21 (4): 173–179. http://ajplegacy.physiology.org/cgi/content/abstract/21/4/465-s.
 Hasselbalch, K. A. (1917). "Die Berechnung der Wasserstoffzahl des Blutes aus der freien und gebundenen Kohlensäure desselben, und die Sauerstoffbindung des Blutes als Funktion der Wasserstoffzahl". Biochemische Zeitschrift 78: 112–144.
 Po, Henry N.; Senozan, N. M. (2001). "Henderson–Hasselbalch Equation: Its History and Limitations". J. Chem. Educ. 78: 1499–1503.
 de Levie, Robert. (2003). "The Henderson–Hasselbalch Equation: Its History and Limitations". J. Chem. Educ. 80: 146.
 de Levie, Robert (2002). "The Henderson Approximation and the Mass Action Law of Guldberg and Waage". The Chemical Educator 7: 132–135. doi:10.1007/s00897020562a.
- PIPE predicts protein solubility assuming the protein is being overexpressed in Escherichia coli.
 R.G. Harrison. 2000. Expression of soluble heterologous proteins via fusion with NusA protein. inNovations. 11:4-7. PDF file
 Davis, G.D., Elisee, C., Newham, D.M. and R.G. Harrison. 1999. New fusion protein systems designed to give soluble expression in Escherichia coli. Biotechnol. Bioeng. 65(4):382-8. PubMed Abstract
 Wilkinson, D.L. and R.G. Harrison. 1991. Predicting the solubility of recombinant proteins in Escherichia coli. Bio/Technology. 9: 443-448. PubMed Abstract
- The half-life is a prediction of the time it takes for half of the amount of protein in a cell to disappear after its synthesis in the cell. ProtParam relies on the "N-end rule", which relates the half-life of a protein to the identity of its N-terminal residue; the prediction is given for 3 model organisms (human, yeast and E.coli). The N-end rule originated from the observations that the identity of the N-terminal residue of a protein plays an important role in determining its stability in vivo. The rule was established from experiments that explored the metabolic fate of artificial beta-galactosidase proteins with different N-terminal amino acids engineered by site-directed mutagenesis. The beta-gal proteins thus designed have strikingly different half-lives in vivo, from more than 100 hours to less than 2 minutes, depending on the nature of the amino acid at the amino terminus and on the experimental model (yeast in vivo; mammalian reticulocytes in vitro, Escherichia coli in vivo). In addition, it has been shown that in eukaryotes, the association of a destabilizing N-terminal residue and of an internal lysine targets the protein to ubiquitin-mediated proteolytic degradation. Note that the program gives an estimation of the protein half-life and is not applicable for N-terminally modified proteins.
Table of the amino acids and the corresponding half-life
|Amino Acid||Mammalian||Yeast||E. coli
|Ala||4.4 hour||>20 hour||>10 hour
|Arg||1 hour||2 min||2 min
|Asn||1.4 hour||3 min||>10 hour
|Asp||1.1 hour||3 min||>10 hour
|Cys||1.2 hour||>20 hour||>10 hour
|Gln||0.8 hour||10 min||>10 hour
|Glu||1 hour||30 min||>10 hour
|Gly||30 hour||>20 hour||>10 hour
|His||3.5 hour||10 min||>10 hour
|Ile||20 hour||30 min||>10 hour
|Leu||5.5 hour||3 min||2 min
|Lys||1.3 hour||3 min||2 min
|Met||30 hour||>20 hour||>10 hour
|Phe||1.1 hour||3 min||2 min
|Pro||>20 hour||>20 hour||?
|Ser||1.9 hour||>20 hour||>10 hour
|Thr||7.2 hour||>20 hour||>10 hour
|Trp||2.8 hour||3 min||2 min
|Tyr||2.8 hour||10 min||2 min
|Val||100 hour||>20 hour||>10 hour
 Bachmair, A., Finley, D. and Varshavsky, A. (1986) In vivo half-life of a protein is a function of its amino-terminal residue. Science 234, 179-186. [PubMed: 3018930]
 Gonda, D.K., Bachmair, A., Wunning, I., Tobias, J.W., Lane, W.S. and Varshavsky, A. J. (1989) Universality and structure of the N-end rule. J. Biol. Chem. 264, 16700-16712. [PubMed: 2506181]
 Tobias, J.W., Shrader, T.E., Rocap, G. and Varshavsky, A. (1991) The N-end rule in bacteria. Science 254, 1374-1377. [PubMed: 1962196]
 Ciechanover, A. and Schwartz, A.L. (1989) How are substrates recognized by the ubiquitin-mediated proteolytic system? Trends Biochem. Sci. 14, 483-488. [PubMed: 2696178]
 Varshavsky, A. (1997) The N-end rule pathway of protein degradation. Genes Cells 2, 13-28. [PubMed: 9112437]
- The extinction coefficient indicates how much light a protein absorbs at a certain wavelength. It is useful to have an estimation of this coefficient for following a protein which a spectrophotometer when purifying it.
It has been shown that it is possible to estimate the molar extinction coefficient of a protein from knowledge of its amino acid composition. From the molar extinction coefficient of tyrosine, tryptophan and cystine (cysteine does not absorb appreciably at wavelengths >260 nm, while cystine does) at a given wavelength, the extinction coefficient of the native protein in water can be computed using the following equation:
E1 = Numb(Tyr)*Ext(Tyr) + Numb(Trp)*Ext(Trp) Numb(Cystine)*Ext(Cystine)
E2 = Numb(Tyr)*Ext(Tyr) + Numb(Trp)*Ext(Trp)
where (for proteins in water measured at 280 nm)
Ext(Tyr) = 1490, Ext(Trp) = 5500, Ext(Cystine) = 125;
Two values are produced based on the above equations, both for proteins measured in water at 280 nm. The first one shows the computed value based on the assumption that all cysteine residues appear as half cystines, and the second one assuming that no cysteine appears as half cystine. Experience shows that the computation is quite reliable for proteins containing Trp residues, however there may be more than 10% error for proteins without Trp residues.
Note: Cystine is the amino acid formed when of a pair of cysteine molecules are joined by a disulfide bond.
 Pace, C.N., Vajdos, F., Fee, L., Grimsley, G., and Gray, T. (1995) How to measure and predict the molar absorption coefficient of a protein. Protein Sci. 11, 2411-2423. [PubMed: 8563639]
 Edelhoch, H. (1967) Spectroscopic determination of tryptophan and tyrosine in proteins. Biochemistry 6, 1948-1954. [PubMed: 6049437]
 Gill, S.C. and von Hippel, P.H. (1989) Calculation of protein extinction coefficients from amino acid sequence data. Anal. Biochem. 182:319-326(1989). [PubMed: 2610349]
The aliphatic index of a protein is defined as the relative volume occupied by aliphatic side chains (alanine, valine, isoleucine, and leucine). It may be regarded as a positive factor for the increase of thermostability of globular proteins
The aliphatic index of a protein is calculated according to the following formula :
Aliphatic index = X(Ala) + a * X(Val) + b * ( X(Ile) + X(Leu) )
*The coefficients a and b are the relative volume of valine side chain (a = 2.9)
and of Leu/Ile side chains (b = 3.9) to the side chain of alanine.
 Ikai A.J. Biochem. 88:1895-1898(1980). [PubMed: 7462184]
- The Grand average of hydropathicity (GRAVY) of the linear polypeptide sequence is calculated as the sum of hydropathy values of all amino acids, divided by the number of residues in the sequence. Increasing positive score indicates greater hydrophobicity. The calculation is based on the Kyte-Doolittle scale.
A simple method for displaying the hydropathic character of a protein.
 Kyte, J. and Doolittle, R.F. (1982) A simple method for displaying the hydropathic character of a protein. J. Mol. Biol. 157, 105-132. [PubMed: 7108955]