HKMTs

Dotl proteins and S ET H KMTs illustrate how methyl transfer to a protein Lys side-chain can be done with different structural scaffolding and unrelated local active site spatial arrangements. To date, Dotl proteins are the only nonSET HKMTs and further work and structures are needed to understand the mechanism of methylation of Lys-79, a histone core residue. 

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In addition to histone deacetylation, histone lysine methylation can also lead to gene silencing which is not blocked by the HDAC inhibitors [6, 51], Several lines of evidence have suggested a connection between cancer and histone lysine methyltrans-ferases (HKMTs) [52], HKMTs catalyze the transfer of methyl group(s) from the cofactor. S -adenosyI-methionine (AdoMet) to some specific lysine residues in the N-terminal histone tails [53, 54], With one exception of Dotl [55], all known HKMTs contain the SET domain which represents a novel structural fold [53, 56], Among SET-domain HKMTs, SET7/9 is one of the best characterized experimentally. It is a... 

Histone lysine (K) methyltransferase (HKMTs) may lead to mono, di- and trimethy-lation of the E-amino group and the extent of modification at a specific site controls the recruitment of the effector proteins. Two unequally populated folds are presently known the SET domain-containing family and the Dotl family (for a recent review, see Ref. [70])... 

In vitro catalytic data have been obtained for only a few of the characterized SET domain containing proteins. These data are summarized in Fig. 5. Most of the examined HKMTs have optimal methyl transferase activity between a pH of 8 and 10. The mechanism for methyl group attachment to lysine residues is illustrated in Fig. 6. 

Lysine 9 of histone H3 is the target of many SET-domain-containing enzymes (Fig. 2). Most of the HKMTs that methylate this residue belong to the Su(var)3-9 family. In Drosophila and humans, methylation of this lysine provides a binding site for the chromo domain of heterochromatin protein 1 (HP1 Aagaard et al., 2000 Loyola et al., 2001). Work done in Drosophila has demonstrated that the interaction of HP1 and methylated... 

Fig. 1 Top Reaction mechanism for the methylation of the Lysine side chain of histone by 5-adenosyhnethionine using HKMT as the catalyst Middle The three cluster models used. Stars indicate fixed atoms in the coordinate-locking scheme. Bottom Potential energy profiles (kcal/mol). Results for various values of the dielectric constant are shown in different colors. Reproduced with permission from [24]...

We turn now to histone lysine methyltransferase (HKMT) which catalyzes the methylation of the N-terminal histone tail of chromatin using the 5-adenosyl-methionine (SAM) cofactor as the methylating agent (see Fig. 1). 

This is clearly a more complex reaction than that of HKMT just described. Of the seven steps shown in the movie all but one involve conformational changes of the enzyme that are more in the domain of Molecular Mechanics than in that of quantum chemistry (we are studying these conformational steps, but they are not the topic of the present chapter). The sole exception is step 4, catalytic incorporation, which actually involves a multistep mechanism of chemical reactions. This is where theory and computation have to step in to help elucidate the mechanism. The first steps of the process involve the construction of cluster models for the calculation of relevant portions of the potential energy surface corresponding to proposed reaction steps. Several key choices have to be made for which reactions to consider. 

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