Net Charge

Net charge is an arithmetic property, not a fixed one: it is the total of all charges a peptide carries at a stated pH. Four side chains do most of the work. Aspartate and glutamate are deprotonated and negative above roughly pH 4; lysine and arginine are protonated and positive well past pH 10; histidine sits near 6 and is therefore partly charged at blood pH, which is what makes it a useful buffering residue. Add the positive N-terminal amine and the negative C-terminal carboxylate and you have the sum. When positives and negatives cancel exactly, the molecule is a zwitterion with a net charge of zero, and the pH at which that happens is the isoelectric point.

The consequences are concrete. Cationic antimicrobial peptides and defensins typically carry a net charge in the range of plus four to plus six, and that surplus is what draws them to the anionic phospholipids and lipopolysaccharide of bacterial surfaces rather than to the zwitterionic outer leaflet of a mammalian cell. Cell-penetrating sequences derived from HIV TAT rely on a dense arginine cluster for the same electrostatic reason. In the laboratory, charge is what ion-exchange chromatography separates on, and a C-terminal amide is a routine way to add one unit of positive charge to a design.

Practically, charge is the first thing to check when a peptide will not dissolve or will not behave on a column. Solubility is at its worst near the isoelectric point, and moving the buffer pH a unit or two away from it often fixes the problem outright.

The error to watch is quoting a charge without a pH, or quoting the charge of a bare sequence while ignoring modifications. Acetylating the N-terminus removes a positive charge, amidating the C-terminus removes a negative one, and a phosphate or a fatty diacid adds negative charge that the letters in the sequence do not show.