EasyModeller: A graphical interface to MODELLER

<p>Abstract</p> <p>Background</p> <p>MODELLER is a program for automated protein Homology Modeling. It is one of the most widely used tool for homology or comparative modeling of protein three-dimensional structures, but most users find it a bit difficult to start with MODELLER as it is command line based and requires knowledge of basic Python scripting to use it efficiently.</p> <p>Findings</p> <p>The study was designed with an aim to develop of "EasyModeller" tool as a frontend graphical interface to MODELLER using Perl/Tk, which can be used as a standalone tool in windows platform with MODELLER and Python preinstalled. It helps inexperienced users to perform modeling, assessment, visualization, and optimization of protein models in a simple and straightforward way.</p> <p>Conclusion</p> <p>EasyModeller provides a graphical straight forward interface and functions as a stand-alone tool which can be used in a standard personal computer with Microsoft Windows as the operating system.</p

Replication data for:The augmenting effects of Desolvation and Conformational energy terms on the predictions of docking programs against mPGES-1

These files contain all teh input and poutput files used in teh study titled:The augmenting effects of Desolvation and Conformational energy terms on the predictions of docking programs against mPGES-1. One can view or download these files from here for replicating the present work

Deciphering the mechanism behind the varied binding activities of COXIBs through Molecular Dynamic Simulations, MM-PBSA binding energy calculations and per-residue energy decomposition studies

<p>COX-2 is a well-known drug target in inflammatory disorders. COX-1/COX-2 selectivity of NSAIDs is crucial in assessing the gastrointestinal side effects associated with COX-1 inhibition. Celecoxib, rofecoxib, and valdecoxib are well-known specific COX-2 inhibiting drugs. Recently, polmacoxib, a COX-2/CA-II dual inhibitor has been approved by the Korean FDA. These COXIBs have similar structure with diverse activity range. Present study focuses on unraveling the mechanism behind the 10-fold difference in the activities of these sulfonamide-containing COXIBs. In order to obtain insights into their binding with COX-2 at molecular level, molecular dynamics simulations studies, and MM-PBSA approaches were employed. Further, per-residue decomposition of these energies led to the identification of crucial amino acids and interactions contributing to the differential binding of COXIBs. The results clearly indicated that Leu338, Ser339, Arg499, Ile503, Phe504, Val509, and Ser516 (Leu352, Ser353, Arg513, Ile517, Phe518, Val523, and Ser530 in PGHS-1 numbering) were imperative in determining the activity of these COXIBs. The binding energies and energy contribution of various residues were similar in all the three simulations. The results suggest that hydrogen bond interaction between the hydroxyl group of Ser516 and five-membered ring of diarylheterocycles augments the affinity in COXIBs. The SAR of the inhibitors studied and the per-residue energy decomposition values suggested the importance of Ser516. Additionally, the positive binding energy obtained with Arg106 explains the binding of COXIBs in hydrophobic channel deep in the COX-2 active site. The findings of the present work would aid in the development of potent COX-2 inhibitors.</p

Bony Fish Arachidonic Acid 15-Lipoxygenases Exhibit Different Catalytic Properties than Their Mammalian Orthologs, Suggesting Functional Enzyme Evolution during Vertebrate Development

The human genome involves six functional arachidonic acid lipoxygenase (ALOX) genes and the corresponding enzymes (ALOX15, ALOX15B, ALOX12, ALOX12B, ALOXE3, ALOX5) have been implicated in cell differentiation and in the pathogenesis of inflammatory, hyperproliferative, metabolic, and neurological disorders. In other vertebrates, ALOX-isoforms have also been identified, but they occur less frequently. Since bony fish represent the most abundant subclass of vertebrates, we recently expressed and characterized putative ALOX15 orthologs of three different bony fish species (Nothobranchius furzeri, Pundamilia nyererei, Scleropages formosus). To explore whether these enzymes represent functional equivalents of mammalian ALOX15 orthologs, we here compared a number of structural and functional characteristics of these ALOX-isoforms with those of mammalian enzymes. We found that in contrast to mammalian ALOX15 orthologs, which exhibit a broad substrate specificity, a membrane oxygenase activity, and a special type of dual reaction specificity, the putative bony fish ALOX15 orthologs strongly prefer C20 fatty acids, lack any membrane oxygenase activity and exhibit a different type of dual reaction specificity with arachidonic acid. Moreover, mutagenesis studies indicated that the Triad Concept, which explains the reaction specificity of all mammalian ALOX15 orthologs, is not applicable for the putative bony fish enzymes. The observed functional differences between putative bony fish ALOX15 orthologs and corresponding mammalian enzymes suggest a targeted optimization of the catalytic properties of ALOX15 orthologs during vertebrate development

3D structures.

<p>(A) (a) AjAPN1 (model) and (b) tricorn interacting factor F3 (PDB code: 1Z1W) and (c) human endoplasmic reticulum aminopeptidase-1 (Erap1) (PDB code: 3QNF) (templates). (B) (a) <i>B. mori</i> midgut APN (model) and (b) soluble domain of human Erap1 (PDB code: 2YD0) (template). (C) Structure of APN activity and Zn⁺⁺ binding motifs of AjAPN1. The important residues are shown in ball and stick. The APN catalytic amino acid residues are shown in white backbone while Zn⁺⁺ binding amino acid residues are highlighted in pink.</p

RNAi-mediated knockdown of <i>AjAPN1</i> transcript and its encoded protein.

<p>Third instar larvae were intrahemocoelically injected with target and control gene siRNA duplexes at dose of 5 µg/100 mg body weight followed by analyses of target gene/protein expression level at different time points. Observations obtained at 66 h post-injection are represented. Values represented are mean±standard deviation of three independent experiments (n = 3). Significance between groups was tested by One-Way ANOVA followed by Student-Newman-Keuls’ (SNK) test using SigmaPlot 11.0 software. *indicate statistical significance (P<0.05). Control (Cont): double-stranded <i>GFP</i> siRNA injected and Experimental (Expt): double-stranded <i>AjAPN1</i> siRNA injected insects. (A) Real-time quantitative PCR analysis. 18S rRNA was used as an internal endogenous control. Note that the fold decrease in <i>AjAPN1</i> transcript level in fat body and Malpighian tubule was 1.9 and 2.8 respectively. Semi-quantitative analysis is represented by the gel images. Here, <i>β</i>-actin gene was used as an internal endogenous control (lower panel). (B) Western blot analysis. Note the substantial reduction in the 113 kDa AjAPN1 protein band of fat body and Malpighian tubule of the target gene siRNA injected insects. β-actin expression was used as an internal endogenous control (lower panel). (C) APN activity analysis. Note the significant decrease in the APN activity level of fat body and Malpighian tubule of the target gene siRNA injected insects. Fb: fat body, Mt: Malpighian tubule and Sg: salivary gland.</p

Functional Interpretation of a Non-Gut Hemocoelic Tissue Aminopeptidase N (APN) in a Lepidopteran Insect Pest <i>Achaea janata</i>

<div><p>Insect midgut membrane-anchored aminopeptidases N <b>(</b>APNs) are Zn⁺⁺ dependent metalloproteases. Their primary role in dietary protein digestion and also as receptors in Cry toxin-induced pathogenesis is well documented. APN expression in few non-gut hemocoelic tissues of lepidopteran insects has also been reported but their functions are widely unknown. In the present study, we observed specific <i>in vitro</i> interaction of Cry1Aa toxin with a 113 kDa AjAPN1 membrane protein of larval fat body, Malpighian tubule and salivary gland of <i>Achaea janata</i>. Analyses of 3D molecular structure of AjAPN1, the predominantly expressed APN isoform in these non-gut hemocoelic tissues of <i>A. janata</i> showed high structural similarity to the Cry1Aa toxin binding midgut APN of <i>Bombyx mori</i>, especially in the toxin binding region. Structural similarity was further substantiated by <i>in vitro</i> binding of Cry1Aa toxin. RNA interference (RNAi) resulted in significant down-regulation of <i>AjAPN1</i> transcript and protein expression in fat body and Malpighian tubule but not in salivary gland. Consequently, reduced AjAPN1 expression resulted in larval mortality, larval growth arrest, development of lethal larval-pupal intermediates, development of smaller pupae and emergence of viable defective adults. <i>In vitro</i> Cry1Aa toxin binding analysis of non-gut hemocoelic tissues of AjAPN1 knockdown larvae showed reduced interaction of Cry1Aa toxin with the 113 kDa AjAPN1 protein, correlating well with the significant silencing of AjAPN1 expression. Thus, our observations suggest AjAPN1 expression in non-gut hemocoelic tissues to play important physiological role(s) during post-embryonic development of <i>A. janata</i>. Though specific interaction of Cry1Aa toxin with AjAPN1 of non-gut hemocoelic tissues of <i>A. janata</i> was demonstrated, evidences to prove its functional role as a Cry1Aa toxin receptor will require more in-depth investigation.</p></div