Structural studies of carbonic anhydrase isozymes

The studies contained in this thesis provide insights into structure/function relationships of the carbonic anhydrase isozymes. The X-ray crystallographic structure of wild-type CAV has complemented the kinetic studies investigating the unique proton transfer pathway in this mitochondrial isozyme. The crystal structures of CA-inhibitor complexes have allowed visualization of the binding modes of these inhibitors in the CAII and CAV active sites and have provided a foundation for understanding their high affinity binding. Additionally, these studies provide a starting point for the design of isozyme-specific inhibitors. The major conclusions drawn from this thesis are as follows: (1) The tetrahedrally-coordinated zinc ion of CAV and its immediate environment is similar to that of the other CA isozymes. Differences in the mechanism of CAV are probably due to differences 6 to 8 A distant from the zinc ion. (2) The bulky side chain of Phe 65 compromises the proton transfer abilities of the residue at position 64. (3) Tyr 64 is not the native proton shuttle, however, a His residue at position 64 is a proton transfer group. Proton transfer at this position is greatly increased by replacing Phe 65 with Ala. (4) Inhibitor tails have preferred binding interactions. Nonaromatic pendant groups bind to the Leu 198/Pro 202 hydrophobic wall; aromatic pendant groups interact with Phe 131. (5) The thienothiazine ring system of the inhibitors has a preferred mode of interaction. Deviations from this binding mode increase the dissociation constant of the inhibitor. In addition, this ring system confers much of the binding affinity of these inhibitors

Structural studies of carbonic anhydrase isozymes

The studies contained in this thesis provide insights into structure/function relationships of the carbonic anhydrase isozymes. The X-ray crystallographic structure of wild-type CAV has complemented the kinetic studies investigating the unique proton transfer pathway in this mitochondrial isozyme. The crystal structures of CA-inhibitor complexes have allowed visualization of the binding modes of these inhibitors in the CAII and CAV active sites and have provided a foundation for understanding their high affinity binding. Additionally, these studies provide a starting point for the design of isozyme-specific inhibitors. The major conclusions drawn from this thesis are as follows: (1) The tetrahedrally-coordinated zinc ion of CAV and its immediate environment is similar to that of the other CA isozymes. Differences in the mechanism of CAV are probably due to differences 6 to 8 A distant from the zinc ion. (2) The bulky side chain of Phe 65 compromises the proton transfer abilities of the residue at position 64. (3) Tyr 64 is not the native proton shuttle, however, a His residue at position 64 is a proton transfer group. Proton transfer at this position is greatly increased by replacing Phe 65 with Ala. (4) Inhibitor tails have preferred binding interactions. Nonaromatic pendant groups bind to the Leu 198/Pro 202 hydrophobic wall; aromatic pendant groups interact with Phe 131. (5) The thienothiazine ring system of the inhibitors has a preferred mode of interaction. Deviations from this binding mode increase the dissociation constant of the inhibitor. In addition, this ring system confers much of the binding affinity of these inhibitors

CARM1 Preferentially Methylates H3R17 over H3R26 through a Random Kinetic Mechanism

CARM1 is a type I arginine methyltransferase involved in the regulation of transcription, pre-mRNA splicing, cell cycle progression, and the DNA damage response. CARM1 overexpression has been implicated in breast, prostate, and liver cancers and therefore is an attractive target for cancer therapy. To date, little about the kinetic properties of CARM1 is known. In this study, substrate specificity and the kinetic mechanism of the human enzyme were determined. Substrate specificity was examined by testing CARM1 activity with several histone H3-based peptides in a radiometric assay. Comparison of <i>k</i>_cat/<i>K</i>_M values reveals that methylation of H3R17 is preferred over that of H3R26. These effects are <i>K</i>_M-driven as <i>k</i>_cat values remain relatively constant for the peptides tested. Shortening the peptide at the C-terminus by five amino acid residues greatly reduced binding affinity, indicating distal residues may contribute to substrate binding. CARM1 appears to bind monomethylated peptides with an affinity similar to that of unmethylated peptides. Monitoring of the CARM1-dependent production of monomethylated and dimethylated peptides over time by self-assembled monolayer and matrix-assisted laser desorption ionization mass spectrometry revealed that methylation by CARM1 is distributive. Additionally, dead-end and product inhibition studies suggest CARM1 conforms to a random sequential kinetic mechanism. By defining the kinetic properties and mechanism of CARM1, these studies may aid in the development of small molecule CARM1 inhibitors

Characterization of the Enzymatic Activity of SETDB1 and Its 1:1 Complex with ATF7IP

The protein methyltransferase (PMT) SETDB1 is a strong candidate oncogene in melanoma and lung carcinomas. SETDB1 methylates lysine 9 of histone 3 (H3K9), utilizing <i>S</i>-adenosylmethionine (SAM) as the methyl donor and its catalytic activity, has been reported to be regulated by a partner protein ATF7IP. Here, we examine the contribution of ATF7IP to the <i>in vitro</i> activity and substrate specificity of SETDB1. SETDB1 and ATF7IP were co-expressed and 1:1 stoichiometric complexes were purified for comparison against SETDB1 enzyme alone. We employed both radiometric flashplate-based and SAMDI mass spectrometry assays to follow methylation on histone H3 15-mer peptides, where lysine 9 was either unmodified, monomethylated, or dimethylated. Results show that SETDB1 and the SETDB1:ATF7IP complex efficiently catalyze both monomethylation and dimethylation of H3K9 peptide substrates. The activity of the binary complex was 4-fold lower than SETDB1 alone. This difference was due to a decrease in the value of <i>k</i>_cat as the substrate <i>K</i>_M values were comparable between SETDB1 and the SETDB1:ATF7IP complex. H3K9 methylation by SETDB1 occurred in a distributive manner, and this too was unaffected by the presence of ATF7IP. This finding is important as H3K9 can be methylated by HMTs other than SETDB1 and a distributive mechanism would allow for interplay between multiple HMTs on H3K9. Our results indicate that ATF7IP does not directly modulate SETDB1 catalytic activity, suggesting alternate roles, such as affecting cellular localization or mediating interaction with additional binding partners

Identification of a peptide inhibitor for the histone methyltransferase WHSC1

<div><p>WHSC1 is a histone methyltransferase that is responsible for mono- and dimethylation of lysine 36 on histone H3 and has been implicated as a driver in a variety of hematological and solid tumors. Currently, there is a complete lack of validated chemical matter for this important drug discovery target. Herein we report on the first fully validated WHSC1 inhibitor, PTD2, a norleucine-containing peptide derived from the histone H4 sequence. This peptide exhibits micromolar affinity towards WHSC1 in biochemical and biophysical assays. Furthermore, a crystal structure was solved with the peptide in complex with SAM and the SET domain of WHSC1L1. This inhibitor is an important first step in creating potent, selective WHSC1 tool compounds for the purposes of understanding the complex biology in relation to human disease.</p></div