A number of amino acid residues are subject to methylation, catalyzed by methyltransferases using S-adenosylmethionine as the methyl donor (1). In carboxyl methylation of glutamate, aspartate, or carboxyl-terminal residues, the methylation is reversible. In methylation of sulfur or nitrogen atoms, it is probably not reversed during normal metabolism. In the former, the methylation may play a role in signal transduction, or it may be connected with protein rejuvenation. In the latter, methylation is probably related to specific structures of proteins that enable them to function better (2, 3). Four distinct types of carboxyl methylation are known.
1. Glutamate Residues
The first is that of specific glutamate side-chains on chemoreceptors mediating chemotaxis in bacteria (Fig. 1). Increased methylation increases the activity of the CheA kinase that governs the behavior. The purpose of the receptors is to regulate the CheA kinase. For example, in E. coli, reduction of CheA activity caused by addition of attractant is compensated for by receptor methylation so that the stimulus is only short-lived (4) (see Chemotaxis).
Figure 1. Methylation reactions on glutamate residues within the chemotaxis receptors in bacteria. The methylation reaction is catalyzed by CheR, and demethylation by CheB. Upon loss of its methyl group, the S-adenyosyl methionine (AdoMet) is converted to S-adenosyl homocysteine (AdoHcy).
2. C-Terminal Residues
The second type involves methylesterification in eukaryotic cells of C-terminal residues, specifically leucine and isoprenylcysteine. Protein phosphatase 2A dephosphorylates a number of phosphorylated, regulated enzymes, and it is regulated by methylation of its C-terminal leucine residue. Following the addition of a C15-farnesyl or a C20-geranylgeranyl group to the side-chain and usually the cleavage of the three terminal amino acids (see Prenylation), certain cysteine residues now become candidates for carboxyl methylation (Fig. 2). Certain fungal mating type factors, ras proteins, analogous small G proteins, and the g-subunits of large G-proteins are some of the proteins regulated by methylation. The assembly and disassembly of nuclear lamins may be regulated by methylation Even eukaryotic chemotaxis and platelet aggregation may involve reversible protein methylation (3).
Figure 2. Reactions involved in the process of C-terminal methylation of cysteine residues in eukaryotic cells. The C-ter the target protein are shown at the top in the one-letter code. FPP is farnesyl diphosphate, and GGPP is geranylgeranyl d transfer to the protein releases pyrophosphate (PP;). The methyl donor is S-adenosylmethionine (AdoMet), which is relet adenosylhomocysteine (AdoHcy).
3. Basic Residues
Protein methylation also facilitates "permanent" structural changes in proteins to allow them to function even better. Methylation of lysine residues to mono-, di-, or trimethyl-lysine is common in bacteria and eukaryotic cells. Examples include bacterial flagellins, ribosomal proteins, histones, rhodopsin and calmodulin. Calmodulin plays a role in controlling many enzymes, and transgenic plants that have unmethylated calmodulin produce poor seed. Trimethyl-lysine has a fixed positive charge and remains charged even in a hydrophobic environment.
Arginine residues can be mono- or dimethylated. Examples include myelin basic proteins, myosin, heat shock proteins, and proteins of the nucleus and ribosomes. It is common to find these among RNA-binding proteins, possibly because arginine methylation might disrupt certain hydrogen bonds that would occur between the protein and the nucleic acid (2).
Histidine, also a basic residue, is methylated in actin, myosin, histones, and rhodopsin, but beyond the possibility of furthering interactions with particular proteins, the purpose has not been discerned in any of the cases. One related example is the further metabolism of a particular histidine residue in ribosomal elongation factor EF-2 that is subject to ADP-ribosylation by diphtheria toxin. This histidine residue is metabolized to diphthamide in a process involving trimethylation of the a-amino group. Yeast unable by mutation to make this change grow more slowly. Finally, a particular amide nitrogen on an asparagine residue in certain phycocyanins and phycoerythrins, involved in photosynthesis in cyanobacteria and red algae, may be methylated, possibly to enhance efficiency of energy transfer to the light-harvesting complex (2).
4. Isomerized Aspartate Residues
As proteins "age," L-aspartyl residues become isomerized to L-isoaspartyl residues or racemized to D-aspartyl residues. Then these residues may become methylated, and their spontaneous demethylation sometimes restores the original L-isomer. Repeated cycles eventually restore the native protein (Fig. 3) (2).
Figure 3. Isomerization of an aspartate residue and its reversal using methylation. The succinimide intermediate can be generated by deamidation of an asparagine residue.
