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.