Thermodynamic and computational studies on the binding of p53-derived peptides and peptidomimetic inhibitors to HDM2.

Helix power: The binding interactions of linear and constrained beta-hairpin-shaped peptides with HDM2 were compared by using experimental and theoretical methods. The entropic advantages enjoyed by the constrained peptides were found to be largely offset by reduced enthalpic contributions to binding of the cyclic mimetics. Formation of hydrogen bonds upon helix folding could contribute significantly to the enhanced enthalpy observed in binding of the linear peptides.The human double minute 2 protein (HDM2) binds a short peptide derived from the N terminus of the tumor-suppressor protein, p53. This peptide (p53 residues 15-29) is flexible in free solution, but upon binding to HDM2 it folds into an amphipathic alpha-helical conformation. Three residues along one face of the p53 helix (Phe19, Trp23, and Leu26) dock into hydrophobic pockets on the surface of HDM2. A conformationally constrained cyclic beta-hairpin peptidomimetic of p53, with residues Phe1, 6-chloro-Trp3, and Leu4 in one strand of the beta-hairpin, was shown earlier to dock into the same pockets on HDM2. Here, we show by isothermal titration calorimetry that the entropy loss upon binding of the constrained peptide to HDM2 is, as would be expected, much lower (TDeltaS approximately 10 kcal mol(-1) at 300 K) than that for the linear peptide. However, the entropic advantage enjoyed by the constrained peptide is largely offset by a reduced enthalpic contribution, relative to the linear peptide, to binding of the cyclic mimetic. To explore the electronic nature of the interactions between the energetically important residues in each ligand and HDM2, hybrid quantum mechanical and electrostatic Poisson-Boltzmann computational studies were performed. The calculations reveal that significant stabilizing van der Waals interactions and polarization effects occur between the Trp side chain in each ligand and aromatic and aliphatic residues in HDM2. These stabilizing interactions are enhanced when a 6-chloro substituent is incorporated into the Trp, in agreement with the experimental studies. In addition, the calculations suggest that at least one stabilizing hydrogen bond is formed, between the Trp indole-NH in both ligands and HDM2. Other hydrogen-bonding interactions also arise, however, along the alpha-helical backbone of the linear peptide upon binding to HDM2, but are not mimicked in the constrained inhibitor-HDM2 complex. The formation of these hydrogen bonds upon helix folding could contribute significantly to the enhanced enthalpy observed in binding of the linear peptide to HDM2.

An improved version of the DNA Methylation database (MethDB).

Cytosine methylation is a characteristic property of prokaryotic and eukaryotic genomes. In the latter, it is indispensable for a healthy development of the organism and uncontrolled changes in the distribution of 5-methylcytosine (5mC) have been linked to severe disorders, in particular cancer. The growing scientific interest in DNA methylation has led to a considerable amount of data about this epigenetic phenomenon. In order to make these data readily available, we have established a dedicated database. The DNA Methylation database (MethDB) is currently the only public database for DNA methylation (http://www.methdb.net). This constantly growing database has become a key resource in the field of DNA methylation research. The database contains currently methylation patterns, profiles and total methylation content data for 46 species, 160 tissues and 72 phenotypes coming from a total of 6667 experiments (as of September 4, 2002). About 14% of the data have not been published elsewhere. These data can be conveniently searched and represented in different ways. Recently, we have included an on-line submission tool that permits the scientific public to directly enter new data into MethDB.