Peptide properties
Property | Definition | Biological Significance | How to Calculate |
---|---|---|---|
Molecular Weight | Total mass of a peptide measured in Daltons (Da). | Indicates the size of a peptide; important for mass spectrometry and chromatography. | Sum the average mass of each amino acid residue (exclude water for peptide bonds: −18.015 Da per bond). |
Isoelectric Point (pI) | pH at which the peptide carries no net electrical charge. | Important for protein purification and solubility (proteins are least soluble at pI). | Estimate by iteratively adjusting pH until positive and negative charges on the peptide are equal. |
Hydrophobicity (GRAVY) | Grand Average of Hydropathy index. Average hydrophobicity value of amino acids. | Affects solubility, folding, and membrane interaction of peptides. | Add hydropathy index for each residue (Kyte-Doolittle scale), divide by number of residues. |
Net Charge | Net electrical charge of a peptide at pH 7.0. | Affects interaction with membranes, other molecules, and electrophoresis behaviour. | Sum charges of side chains and termini using Henderson-Hasselbalch equation at pH 7.0. |
Aromaticity | Proportion of aromatic residues (F, Y, W) in the sequence. | Linked to UV absorbance and protein stability. | (Number of F, Y, W residues) / (Total residues). |
Aliphatic Index | Relative volume of aliphatic side chains (A, V, I, L) in the sequence. | Positively correlated with thermostability of globular proteins. | AI = (Ala%) + (Val%× 2.9) + ((Ile% + Leu%) × 3.9), where residue% = percentage of residue in the sequence. |
Hydrophobic Moment | A measure of amphipathicity, reflecting the distribution of hydrophobic residues in a helix or sheet. | Indicates membrane-binding potential and secondary structure polarity. | Vector sum of hydrophobicity values using Eisenberg scale, assuming α-helix or β-sheet geometry. |
Solubility | An empirical score based on residue-wise solubility contribution. | Predicts peptide solubility; higher scores suggest better aqueous solubility. | Sum of amino acid solubility scores (e.g., A: 1.0, R: 2.5, etc.), averaged over sequence length. |
Instability | Predicts the stability of a protein in vitro based on dipeptide composition. | Values > 40 suggest instability; < 40 suggest stable proteins or peptides. | Computed from dipeptide instability weights using the Guruprasad et al. method. |
Extinction Coefficient | Absorbance of a peptide at 280 nm, usually in water. | Used to estimate protein concentration using UV spectroscopy. | ε = (nY × 1490) + (nW × 5500), where n = number of residues. |