Amino Acid Sequence of Oligopeptide Causes Marked Difference in DNA Compaction and Transcription.

Compaction of T4 phage DNA (166 kbp) by short oligopeptide octamers composed of two types of amino acids, four cationic lysine (K), and four polar nonionic serine (S) having different sequence order was studied by single-molecule fluorescent microscopy. We found that efficient DNA compaction by oligopeptide octamers depends on the geometrical match between phosphate groups of DNA and cationic amines. The amino acid sequence order in octamers dramatically affects the mechanism of DNA compaction, which changes from a discrete all-or-nothing coil-globule transition induced by a less efficient (K4S4) octamer to a continuous compaction transition induced by a (KS)4 octamer with a stronger DNA-binding character. This difference in the DNA compaction mechanism dramatically changes the packaging density, and the morphology of T4 DNA condensates: DNA is folded into ordered toroidal or rod morphologies during all-or-nothing compaction, whereas disordered DNA condensates are formed as a result of the continuous DNA compaction. Furthermore, the difference in DNA compaction mechanism has a certain effect on the inhibition scenario of the DNA transcription activity, which is gradual for the continuous DNA compaction and abrupt for the all-or-nothing DNA collapse.

Molecular docking and structural analysis of cofactor-protein interaction between NAD⁺ and 11ß-hydroxysteroid dehydrogenase type 2.

Molecular docking and structural analysis of the cofactor-protein interaction between NAD(+) and human (h) or mouse (m) 11ß-hydroxysteroid dehydrogenase type 2 (11ßHSD2) were performed with the molecular operating environment (MOE). 11ßHSD1 (PDB code: 3HFG) was selected as a template for the 3D structure modeling of 11ßHSD2. The MOE docking (MOE-dock) and the alpha sphere and excluded volume-based ligand-protein docking (ASE-dock) showed that both NAD(+)-h11ßHSD2 and NAD(+)-m11ßHSD2 models have a similar binding orientation to the template cofactor-protein model. Our present study also revealed that Asp91, Phe94, Tyr232 and Thr267 could be of importance in the interaction between NAD(+) and 11ßHSD2. NADP(+) was incapable of entering into the cofactor-binding site of the 11ßHSD2 models. The present study proposes the latest models for 11ßHSD2 and its cofactor NAD(+), and to the best of our knowledge, this is the first report of a m11ßHSD2 model with NAD(+).

Mouse 11ß-hydroxysteroid dehydrogenase type 2 for human application: homology modeling, structural analysis and ligand-receptor interaction.

Mouse (m) 11ß-hydroxysteroid dehydrogenase type 2 (11ßHSD2) was homology-modeled, and its structure and ligand-receptor interaction were analyzed. The modeled m11ßHSD2 showed significant 3D similarities to the human (h) 11ßHSD1 and 2 structures. The contact energy profiles of the m11ßHSD2 model were in good agreement with those of the h11ßHSD1 and 2 structures. The secondary structure of the m11ßHSD2 model exhibited a central 6-stranded all-parallel ß-sheet sandwich-like structure, flanked on both sides by 3-helices. Ramachandran plots revealed that only 1.1% of the amino acid residues were in the disfavored region for m11ßHSD2. Further, the molecular surfaces and electrostatic analyses of the m11ßHSD2 model at the ligand-binding site exhibited that the model was almost identical to the h11ßHSD2 model. Furthermore, docking simulation and ligand-receptor interaction analyses revealed the similarity of the ligand-receptor bound conformation between the m11ßHSD2 and h11ßHSD2 models. These results indicate that the m11ßHSD2 model was successfully evaluated and analyzed. To the best of our knowledge, this is the first report of a m11ßHSD2 model with detailed analyses, and our data verify that the mouse model can be utilized for application to the human model to target 11ßHSD2 for the development of anticancer drugs.

Ligand-receptor interaction between triterpenoids and the 11beta-hydroxysteroid dehydrogenase type 2 (11betaHSD2) enzyme predicts their toxic effects against tumorigenic r/m HM-SFME-1 cells.

The present study deals with in silico prediction and in vitro evaluation of the selective cytotoxic effects of triterpenoids on tumorigenic human c-Ha-ras and mouse c-myc cotransfected highly metastatic serum-free mouse embryo-1 (r/m HM-SFME-1) cells. Ligand fitting of five different triterpenoids to 11ß-hydroxysteroid dehydrogenase type 2 (11ßHSD2) was analyzed with a molecular modeling method, and glycyrrhetinic acid (GA) was the best-fitted triterpenoid to the ligand binding site in 11ßHSD2. Analysis of antiproliferative effects revealed that GA, oleanolic acid, and ursolic acid had selective toxicity against the tumor cells and that GA was the most potent triterpenoid in its selectivity. The toxic activity of the tested triterpenoids against the tumor cells showed good correlations with the partition coefficient (logP) and polar surface area values. Time-lapse microscopy, fluorescence staining, and confocal laser scanning microscopic observation revealed that GA induced morphologic changes typical of apoptosis such as cell shrinkage and blebbing and also disrupted the cytoskeletal proteins. Furthermore, GA exhibited a strong inhibitory effect on 11ßHSD2 activity in the tumor cells. Our current results suggest that analysis of the ligand-receptor interaction between triterpenoids and 11ßHSD2 can be utilized to predict their antitumor effects and that GA can be used as a possible chemopreventive and therapeutic antitumor agent. To the best of our knowledge, this is the first report on in silico prediction of the toxic effects of triterpenoids on tumor cells by 11ßHSD2 inhibition.

Homology modeling and structural analysis of 11ß-hydroxysteroid dehydrogenase type 2.

11ß-hydroxysteroid dehydrogenase type 2 (11ßHSD2) was homology-modeled by a Boltzmann-weighted randomized modeling procedure, using the X-ray crystal structure of 11ßHSD1 (PDB code: 3HFG) as a template. The model exhibited significant 3D similarities to 11ßHSD1. The contact energy profiles of the 11ßHSD2 model were in good agreement with that of the X-ray structure of 11ßHSD1. The secondary structure of the 11ßHSD2 model exhibited a central 6-stranded all-parallel ß-sheet sandwich-like structure, flanked on both sides by 3-helices. Ramachandran plots revealed that only 1.9% of the amino acid residues were in the disfavored region for 11ßHSD2. Furthermore, the ligand-binding site (LBS) volume was calculated to be 845 Å(3), which suggests that the LBS of 11ßHSD2 is sufficiently large to contain cofactors and substrates (ligands), such as NAD(+) and cortisol. The electrostatic analysis revealed that the 11ßHSD2 model had a positive potential at the LBS, which indicates that 11ßHSD2 possibly attracts negatively charged ligands at the LBS. These results indicate that the model was successfully evaluated and analyzed. Consequently, it is proposed that the 11ßHSD2 model in the present study will be suitable for further in silico structure-based de novo antitumor drug designing. To the best of our knowledge, this is the latest report of an accurate 11ßHSD2 model to target 11ßHSD2 for the development of anticancer drugs.

Weak interaction induces an ON/OFF switch, whereas strong interaction causes gradual change: folding transition of a long duplex DNA chain by poly-L-lysine.

A large-scale conformational change in genomic DNA is an essential feature of gene activation in living cells. Considerable effort has been applied to explain the mechanism in terms of key-lock interaction between sequence-specific regulatory proteins and DNA, in addition to the modification of DNA and histones such as methylation and acetylation. However, it is still unclear whether these mechanisms can explain the ON/OFF switching of a large number of genes that accompanies differentiation, carcinogenesis, etc. In this study, using single-molecule observation of DNA molecules by fluorescence microscopy with the addition of poly-L-lysine with different numbers of monomer units (n = 3, 5, 9, and 92), we found that an ON/OFF discrete transition in the higher-order structure of long duplex DNA is induced by short poly-L-lysine, whereas a continuous gradual change is induced by long poly-L-lysine. On the other hand, polycations with a lower positive charge have less potential to induce DNA compaction. Such a drastic difference in the conformational transition of a giant DNA between short and large oligomers is discussed in relation to the mechanisms of gene regulation in a living cell.

NTP concentration switches transcriptional activity by changing the large-scale structure of DNA.

It is becoming clearer that genetic activity is closely associated with the intracellular energy state. However, the mechanisms of this association are still unclear. In this study, we focused on large-scale changes in the structure of DNA to examine the effect of the NTP concentration on the transcription reaction with T7 RNA polymerase and compared the results with long duplex DNA to those with a short persistent-length(1) fragment. The transcriptional activity dramatically changed only for long duplex DNA within a narrow range of NTP concentrations associated with changes in the large-scale structure of DNA. This result suggests that the energy state may play an essential role in regulating ON/OFF switching on transcriptional activity.