How is protein molecular weight calculated?
The molecular weight of a protein is calculated by adding up the molecular weights of the amino acids, per standard calculations.
In Benchling, the following molecular weights are assigned to amino acids:
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A: 89.09
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B: 132.65
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C: 121.15
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D: 133.1
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E: 147.13
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F: 165.19
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G: 75.07
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H: 155.16
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I: 131.17
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J: 131.2
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K: 146.19
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L: 131.17
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M: 149.21
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N: 132.12
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O: 255.31
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P: 115.13
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Q: 146.15
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R: 174.2
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S: 105.09
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T: 119.12
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U: 168.06
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V: 117.15
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W: 204.23
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X: 143.7
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Y: 181.19
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Z: 146.75
Notes
We have lightly modified constants from biopython, to match results from expasy. These are the average isotopic masses, as opposed to the monoisotopic mass. See http://www.ionsource.com/tutorial/isotopes/slide8.htm.
Molecular weights for B and Z are non-standard and were reverse engineered from
http://web.expasy.org/protparam/.
How is a protein's isoelectric point (pI) calculated?
The pI (isoelectric point) refers to the pH at which the net charge of a protein is zero. We calculate the theoretical pI by using the pKa's of amino acids and summing the net charge across the protein at a given pH, searching with our algorithm for the pH at which the net charge is zero.
How is a protein's extinction coefficient calculated?
The extinction coefficient is calculated by per standard calculations using Beer's Law, via an algorithm from http://biojava.org/.
How is a protein's instability index calculated?
Per ProtParam, "a protein whose instability index is smaller than 40 is predicted as stable, a value above 40 predicts that the protein may be unstable."
To calculate this, we use the same algorithm as biojava. You can see the specifics here.
Where do amino acid hydrophobicity values come from?
Molecular weights for J and X were taken from Geneious.
The hydrophobicities given are the "Scaled" values from computational log(P) determinations by the "Small Fragment Approach" (see "Development of Hydrophobicity Parameters to Analyze Proteins Which Bear Post- or Cotranslational Modifications" Black, S.D. and Mould, D.R. (1991) Anal. Biochem. 193, 72-82).
The equation used to scale raw log(P) values to the scaled values given is as follows: Scaled Parameters = (Raw Parameters + 2.061)/4.484.
The work above is summarized here.