The amino acid lysine is incorporated into the nascent polypeptide chain during protein biosynthesis in response to two codons AAA and AAG—and represents approximately 5.7% of the residues of the proteins that have been characterized. The lysyl residue incorporated has a mass of 128.17 Da, a van der Waals volume of 135 A 3, and an accessible surface area of 211 A2. Lys residues are not changed very frequently during divergent evolution; they are interchanged in homologous proteins most frequently with arginine, asparagine, threonine, serine, and glutamine residues.
The side chain of Lys is a flexible hydrophobic chain of four methylene groups capped by an amino group:
The amino group ionizes with an intrinsic pKa value of about 11.1, so it is ionized under most physiological conditions. The ionized form is unreactive chemically, but there is always a finite fraction of nonionized amino groups, which are potent nucleophiles. Consequently, the amino groups of Lys residues readily undergo a typical wide variety of acylation, alkylation, arylation, and amidination reactions (see Amino Groups). These reactions can be used to measure the number of Lys residues in a protein (see Counting Residues and Trinitrobenzene Sulfonic Acid).
The ionized amino groups of Lys residues in protein structures are nearly always exposed to the solvent, with the entire side chain typically exposed to the solvent and flexible, when they have relaxation times in the nanosecond range. Of secondary structures, Lys residues occur most frequently in a-helices; they also favor the helical conformation in model peptides. Virtually no Lys residues are buried within the interiors of proteins. They are occasionally used to attach prosthetic groups to proteins, such as the Schiff Base attachment of pyridoxal phosphate to some enzymes. In an important post-translational modification, Lys residues of collagens in the sequence -Xaa-Lys-Gly- are hydroxylated on the d carbon by the enzyme lysyl 5-hydroxylase.
Proteinases frequently cleave polypeptide chains adjacent to Lys residues, as in the processing of pro-hormones, such as pro-insulin, at pairs of basic residues.
