# Notes

This page describes the technical details of our Peptide Property Calculator.

## Calculating the molecular weight

The molecular weight *M* of a peptide may be estimated by calculating

where *N _{i}* are the number, and

*M*the average

_{i}*residue*molecular weights, of the amino acids.

*M*+

_{N}*M*are added to the total in order to account for the termini: H at the N-terminus and OH at the C-terminus. Of course, if the termini are modified, these additions are replaced by those of the modifiers.

_{C}The resulting molecular weight depends on what values the algorithm uses. Innovagen's Peptide Property Calculator uses the following values:

A, Ala | 71.0788 | C, Cys | 103.1448 | D, Asp | 115.0886 | E, Glu | 129.1155 |

F, Phe | 147.1766 | G, Gly | 57.052 | H, His | 137.1412 | I, Ile | 113.1595 |

K, Lys | 128.1742 | L, Leu | 113.1595 | M, Met | 131.1986 | N, Asn | 114.1039 |

P, Pro | 97.1167 | Q, Gln | 128.1308 | R, Arg | 156.1876 | S, Ser | 87.0782 |

T, Thr | 101.1051 | V, Val | 99.1326 | W, Trp | 186.2133 | Y, Tyr | 163.1760 |

H | 1.0079 | OH | 17.0073 | pS, pSer | 167.0581 | ||

Ac | 43.0452 | NH2 | 16.0226 | pT, pThr | 181.0850 | ||

Biotin | 227.3013 | pY, pTyr | 243.1559 |

## Calculating the net charge

The net charge *Z* of a peptide at a certain pH can be estimated
by calculating

where *N _{i}* are the number, and pKa

*the pKa values, of the N-terminus and the side chains of Arginine, Lysine, and Histidine. The*

_{i}*j*-index pertain to the C-terminus and the Aspartic Acid, Glutamic Acid, Cysteine, Tyrosine amino acids.

Innovagen's Peptide Property Calculator calculates the net charge for all pH values of 0.1 to 14 in increments of 0.1, and plots these producing a titration curve.

This algorithm has its limitations:

- The residues are assumed to be independent of each other.
- N- and C-terminii have fixed pKa values, except modified terminii which are ignored.
- Modified residues, eg (pS) are ignored.
- Cysteines are assumed not to take part in disulfide bridges, i.e. they may contribute to the charge.

Finally, the resulting net charge depends on what pKa values the algorithm uses. Innovagen's Peptide Property Calculator uses the following values:

(NH2-) | 9.69 | (-COOH) | 2.34 |

K, Lys | 10.5 | D, Asp | 3.86 |

R, Arg | 12.4 | E, Glu | 4.25 |

H, His | 6.00 | C, Cys | 8.33 |

Y, Tyr | 10.0 | ||

A. Lehninger |

## Calculating the isoelectric point, pI

The isoelectric point, pI, is the pH at which the net charge of the peptide is zero. Innovagen's Peptide Property Calculator first calculates the net charge for pH 7.0. If the charge is > 0 the next pH to check is 7 + 3.5, if the charge is < 0 then pH 7 - 3.5 is checked. This is repeated, using increments/decrements half the size of the previous, until the charge found equals 0, or is sufficiently close to 0.

## Hydrophilicity

Innovagen's Peptide Property Calculator plots the hydrophilicty for each amino acid in the peptide sequence in a bar graph. The average hydrophilicity is calculated and the ratio of hydrophilic residues to total number of amino acids is reported. The results depend on what index is used. Innovagen's Peptide Property Calculator uses the following values:

A, Ala | -0.5 | C, Cys | -1 | D, Asp | 3 | E, Glu | 3 |

F, Phe | -2.5 | G, Gly | 0 | H, His | -0.5 | I, Ile | -1.8 |

K, Lys | 3 | L, Leu | -1.8 | M, Met | -1.3 | N, Asn | 0.2 |

P, Pro | 0 | Q, Gln | 0.2 | R, Arg | 3 | S, Ser | 0.3 |

T, Thr | -0.4 | V, Val | -1.5 | W, Trp | -3.4 | Y, Tyr | -2.3 |

Hopp & Woods |