Sujata Roy

20ns Molecular Dynamics Simulation of the Antennapedia Homeodomain-DNA Complex: Water Interaction and DNA Structure Analysis

Abstract Homeodomains are one of the important families of eukaryotic DNA-binding motifs and provide an important model system for studying protein-DNA interactions. The crystal structure and NMR structure of the antennapedia homeodomain-DNA complex and comparison between them is available. Although earlier works have shown that the direct contacts and water mediated contacts are important for the binding and specificity. The detail dynamical structural characteristics of the complex, water mediating interactions in the complex and also the detail study of the free DNA and protein has not done. In the present paper we have reported the results of 20ns MD simulation of this complex with the presence of explicit water and also the 20ns MD simulation of the protein and the DNA separately in explicit water. The results show that the complex remains stable during the last 8ns of the simulation. The part of the protein which is interacting with the DNA has fewer fluctuations than other part of the protein. The pattern of water distribution around the interacting center has a typical pattern for this complex and it is quite different from the free protein and the free DNA. Water molecules penetrate into the interacting center during the simulation. Several water bridges have been identified which is responsible for recognition but not observed in the crystal structure. The recognized DNA sequence (14 mer) has been characterized by helical and step parameters. The correlated motions of the DNA and the protein in the complexed form and the free form has been analyzed

A simple approach for indexing the oral druglikeness of a compound: discriminating druglike compounds from nondruglike ones.

A knowledge-based simple score has been developed for indexing the oral druglikeness of compounds based on the concept that oral druglikeness should be independent of the drug targets and, thus, are closely related to the global absorption, distribution, metabolism, and excretion related properties. We have considered several simple molecular descriptors as the key determinants of druglikeness. The patterns of the distributions of these molecular descriptors for a set of drug molecules have been extracted using a nonlinear neural network method. We assumed direct correlations of these patterns to the expectation values that a given compound may behave like a drug. On the basis of this assumption, we have defined a simple druglike index or score (DLS) combining the contributions coming from the descriptors considered. This index scales the druglikeness of a compound in the range 0.0-1.0, 1.0 being the highest druglikeness. The index applied for a drug data set, a mixed data set, and three different bioactive databases produced expected features and indicated that even the marketed drugs have druglike scores varying over a considerable range. A total of 73.3% of the drugs considered showed DLS > 0.5, while it is only 44.7% for the HIC-Up compounds (unbiased ligand database). For the ChemBank, Asinex-Gold collection, and NCI databases 61.2%, 76.0%, and 79.1% of the compounds have DLS > 0.5.

Two models of Smad4 and Hoxa9 complex are proposed: structural and interactional perspective.

Abstract Transforming growth factor-beta superfamily growth factors (TGF-β) regulate a diverse range of cellular functions, including proliferation, differentiation, extracellular matrix secretion and cell adhesion. TGF-β is also one of the most abundant of the known growth factors. Osteopontin (OPN), the major non-collagenous bone matrix protein is a secreted, arginine-glycine-aspertate containing phosphorylated glycoprotein. Analysis of the OPN promoter sequence reveals both Hoxc8 and Hoxa9 (mouse homeotic gene) recognize and utilize the same consensus TAAT motif in the binding sequence to mediate the repression. Hoxa9 functions as a strong transcriptional repressor, similar to Hoxc-8 (X. Shi, X. Yang, D. Chen, Z. Chang, and X. Cao, J Biol Chem 274, 13711-13717, 1999). The DNA-binding protein Hoxa9 interacts with Smad4 (X. Shi, S. Bai, L. Li and X, and Cao X, J Biol Chem 276, 850-855, 2001), but not with Smad3 (which binds to OPN promoter), and the interaction between Smad4 and Hoxa9 results in the transcriptional activation of OPN in response to TGF- stimulation. In this paper we have proposed two possible model structures of Hoxa9 and Smad4 complex. These have been modeled based on homology modeling and a new method has been used to model the flexible loop part. Manual docking has been used to achieve the final model involving the Hoxa9 -Smad4 complex which tallies with the experimental results. We have mutated some selective important residues and looked at their effect in terms of interaction energy in complex formation in both the models.

Homology Modeling Based Solution Structure of Hoxc8-DNA Complex: Role of Context Bases Outside TAAT Stretch

Abstract The 3D structure of neither Hoxc8 nor Hoxc8-DNA complex is known. The repressor protein Hoxc8 binds to the TAAT stretch of the promoter of the osteopontin gene and modulates its expression. Over expression of the osteopontin gene is related to diseases like osteoporosis, multiple sclerosis, cancer et cetera. In this paper we have proposed a 3D structure of Hoxc8-DNA complex obtained by Homology modeling and molecular dynamics (MD) simulation in explicit water. The crystal structure (9ant.pdb) of Antennapedia homeodomain in complex with its DNA sequence was chosen as the template based on (i) high sequence identity (85% for the protein and 60% for the DNA) and (ii) the presence of the TAAT stretch in interaction with the protein. The resulting model was refined by MD simulation for 2.0ns in explicit water. This refined model was then characterized in terms of the structural and the interactional features to improve our understanding of the mechanism of Hoxc8-DNA recognition. The interaction pattern shows that the residues Ile195, Gln198, and Asn199, and the bases S2-4TAATG8 are most important for recognition suggesting the stretch TAATG as the ‘true recognition element’ in the present case. A strong and long-lived water bridge connecting Gln198 and the base of S1-C7 complementary to S2-G8 was observed. Our predicted model of Hoxc8-DNA complex provides us with features that are consistent with the available experimental data on Hoxc8 and the general features of other homeodomain-DNA complexes. The predictions based on the model are also amenable to experimental verification.

Draft Genome Sequence of a Phosphate-Accumulating Bacillus sp., WBUNB004

ABSTRACT The draft genome sequence of a nitrate- and phosphate-removing, Gram-positive Bacillus sp. with optimum growth at 37°C and pH 7 in nitrate broth (HiMedia M439) isolated from rhizosphere of a water lily, with a genome size of 5,465,157 bp and a G+C content of 35.0%, is reported here.

Molecular Modeling and Molecular Dynamics Simulation Studies of Delta-Notch Complex

Abstract Notch is a single-pass transmembrane receptor protein which is composed of a short extracellular region, a single-pass transmembrane domain and a small intracellular region. Notch ligand like Delta, member of the DSL protein family, is also single-pass transmembrane protein. It has been demonstrated that of the 36 EGF repeats of Notch, 11th and 12th are sufficient to mediate interactions with Delta. Crystal structure of mammalian Notch extracellular ligand binding domain contains 11 and 12 EGF-like repeats. Here a portion of the Delta protein of Drosophila, known to interact with Notch extracellular domain (ECD) has been modeled using homology modeling. The structure of the Delta-Notch complex was subsequently modeled by protein docking method using GRAMM. MD simulations of the modeled structures were performed. The structure for Delta-Notch complex has been proposed based on interaction energy parameter and planarity studies.

Inhibition of PKCβ Mediates Cardioprotective Activity of Ambrex against Isoproterenol-Induced Myocardial Necrosis: in vivo and in silico Studies

Aims and objectives: The current study characterized the morphology of Ambrex formulation by Scanning Electron Microscopy and assessed its cardioprotective activity against Isoproterenol (ISPH)-induced myocardial necrosis in rats by biochemical and histopathological evaluations, and also attempted to predict the prospective protein-targets of Ambrex and the signaling pathway that mediates this activity through molecular docking approach. Materials and methods: Sprague–Dawley male rats (4 groups, 6 rats per group) chosen for the current study were acclimatized to the laboratory conditions for 7 days prior to actual treatment; they were pretreated with Ambrex (40 mg/kg b.wt/day, p.o) everday for 21 days and then intoxicated with ISPH (85 mg/kg b.wt, s.c) on day-20 and 21 to experimentally induce myocardial necrosis. The extent of ISPH-induced myocardial necrosis was quantified in terms of the serum levels of two cardiac biomarkers: creatine kinase-MB and lactate dehydrogenase. The extent of ISPH-induced oxidative stress was quantified in terms of the tissue levels of five oxidative stress biomarkers: superoxide dismutase, catalase, reduced glutathione, glutathione peroxidase and lipid peroxidation. Results and discussion: The Scanning Electron Microscopy image of Ambrex formulation showed the formation of nanoparticles with thickness of 65 nm, making Ambrex a unique metal-deficient Siddha-medicine based polyherbal nano-formulation characterized and evaluated in India. Pretreatment with Ambrex attenuated the extent of ISPH-induced oxidative stress, lipid peroxidation and generation of reactive oxygen species as reflected by biochemical evaluations, and also ameliorated the degree of ISPH-induced myocardial necrosis and membrane damage as reflected by histopathological evaluations. The results of molecular docking revealed that Withaferin-A and Methyl Commate-A (the key metabolites of Withania somnifera and Ambrex respectively) inhibit Protein KinaseC Beta, and renders Ambrex its cardioprotective activity by maintaining the intracellular antioxidant homeostasis and myocardial membrane architecture.

Draft Genome Sequence of a Nitrate- and Phosphate-Removing Bacillus sp., WBUNB009

ABSTRACT The draft genome sequence (5,868,741 bp) of a nitrate- and phosphate-removing Bacillus sp., WBUNB009, isolated from a raw sewage canal in nitrate broth (Himedia M439) with a G+C content of 34.9% is reported. It removes 60.23% nitrate and 96% phosphate within 16 h at 37°C.

Analysis of Delta–Notch interaction by molecular modeling and molecular dynamic simulation studies

Notch is a single-pass transmembrane receptor protein. Delta (member of the DSL protein family), a Notch ligand, is also single-pass transmembrane protein that can interact with Notch to form the Delta–Notch complex. It has been demonstrated that of the 36 Epidermal Growth Factor (EGF) repeats of Notch, 11th and 12th are sufficient to mediate interactions with Delta. Crystal structure of mammalian Notch1 extracellular ligand binding domain shows the presence of 11th and 12th EGF-like repeats. Here a portion of the Drosophila Delta protein, known to interact with Notch extracellular domain, has been modeled using homology modeling. The structure of the Delta–Notch complex was subsequently modeled by protein-docking method using GRAMM. Molecular dynamic simulations of the modeled structures were performed. The probable structures for Delta–Notch complex have been proposed based on interaction energy parameter and planarity studies.