How do I view predicted molecular weight, extinction coefficient (A280), absorbance (A280), isoelectric point, charge and the amino acid count for a protein sequence?
Open or Create a Protein Sequence
Import, Open or create a SnapGene protein file.
Switch to the Properties view.
Click the disclosure triangles to see details of predicted Properties.
Click the dropdown to calculate predicted charge at different pH values.
SnapGene uses the method of Grimsley et al, 2009 (https://www.ncbi.nlm.nih.gov/pubmed/19177368) to calculate Isoelectric point.
SnapGene uses the method of Pace et al, 1995 (https://pubmed.ncbi.nlm.nih.gov/8563639/) to calculate Extinction Coefficient (280 nm).
This calculation estimates the relative contribution to absorbance by Trptophan (Trp), Tyrosine (Tyr) and oxidised Cystine (Cys) residues present in the protein.
SnapGene reports three Extinction Coefficient values:
Extinction Coefficient: epsilon (280) (M-1 cm-1) = (nTrp*5500) + (nTyr*1490) + (nCys*62.5)
where nCys = the number of cystines in the protein sequence that are joined by a bond feature (i.e. known oxidised cystines only)
Fully Reduced: epsilon (280) (M-1 cm-1) = (nTrp*5500) + (nTyr*1490)
where nCys = 0 (The absorbance of reduced cystine is negligible at wavelength 280)
Fully Oxidised: epsilon (280) (M-1 cm-1) = (nTrp*5500) + (nTyr*1490) + (nCys*62.5)
where nCys = the total number of Cystines in the protein sequence (assumes all disulfide bonds have been oxidised)