Insights into the dynamics of cyclic diguanosine monophosphate I riboswitch using molecular dynamics simulation

208-218Riboswitches are key cis-regulatory elements, present at 5' UTRs of several prokaryotic mRNAs, involved in gene expression regulation by binding selectively to specific ligands followed by conformational changes. However, understanding of ligand-free riboswitch, conformational changes between the ligand-free and ligand-bound riboswitch and binding mechanism of ligand to the aptamer of riboswitch is limited. In the present paper we describe the structural and dynamical properties of ligand-free c-di-GMP I riboswitch aptamer and its possible binding mechanism with c-di-GMP by means of all-atom molecular dynamics (MD) simulations. Various analyses such as principal component analysis, cross correlation dynamics analysis, network analysis and trajectory analyses were carried out. The ligand-free structure shows stable conformation with folded P2, P3 and an unwind P1 helix with open binding pocket at helix-join-helix junction while the ligand-bound structure showed closed binding pocket structure compared to the ligand-free structure. The junction residues significantly showed anti-correlations with P1 helix and weak correlated motions with each other in the open conformation of the ligand-free aptamer of riboswitch. The networks analysis of binding pocket residues suggested interaction among the identified key residues of the binding pocket (G20, A47, C92) and P1 helix illustrating the role of P1 helix in binding of ligand. The structural insights, on c-di-GMP I riboswitch, presented in this paper can be useful for the development of therapeutics against V. cholerae. The understanding of the c-di-GMP I riboswitch at dynamic molecular level provides a potential solution for riboswitch drug design

Insights into the dynamics of cyclic diguanosine monophosphate I riboswitch using molecular dynamics simulation

Riboswitches are key cis-regulatory elements, present at 5' UTRs of several prokaryotic mRNAs, involved in gene expression regulation by binding selectively to specific ligands followed by conformational changes. However, understanding of ligand-free riboswitch, conformational changes between the ligand-free and ligand-bound riboswitch and binding mechanism of ligand to the aptamer of riboswitch is limited. In the present paper we describe the structural and dynamical properties of ligand-free c-di-GMP I riboswitch aptamer and its possible binding mechanism with c-di-GMP by means of all-atom molecular dynamics (MD) simulations. Various analyses such as principal component analysis, cross correlation dynamics analysis, network analysis and trajectory analyses were carried out. The ligand-free structure shows stable conformation with folded P2, P3 and an unwind P1 helix with open binding pocket at helix-join-helix junction while the ligand-bound structure showed closed binding pocket structure compared to the ligand-free structure. The junction residues significantly showed anti-correlations with P1 helix and weak correlated motions with each other in the open conformation of the ligand-free aptamer of riboswitch. The networks analysis of binding pocket residues suggested interaction among the identified key residues of the binding pocket (G20, A47, C92) and P1 helix illustrating the role of P1 helix in binding of ligand. The structural insights, on c-di-GMP I riboswitch, presented in this paper can be useful for the development of therapeutics against V. cholerae. The understanding of the c-di-GMP I riboswitch at dynamic molecular level provides a potential solution for riboswitch drug design

The PluriNetWork: An Electronic Representation of the Network Underlying Pluripotency in Mouse, and Its Applications

BACKGROUND: Analysis of the mechanisms underlying pluripotency and reprogramming would benefit substantially from easy access to an electronic network of genes, proteins and mechanisms. Moreover, interpreting gene expression data needs to move beyond just the identification of the up-/downregulation of key genes and of overrepresented processes and pathways, towards clarifying the essential effects of the experiment in molecular terms. METHODOLOGY/PRINCIPAL FINDINGS: We have assembled a network of 574 molecular interactions, stimulations and inhibitions, based on a collection of research data from 177 publications until June 2010, involving 274 mouse genes/proteins, all in a standard electronic format, enabling analyses by readily available software such as Cytoscape and its plugins. The network includes the core circuit of Oct4 (Pou5f1), Sox2 and Nanog, its periphery (such as Stat3, Klf4, Esrrb, and c-Myc), connections to upstream signaling pathways (such as Activin, WNT, FGF, BMP, Insulin, Notch and LIF), and epigenetic regulators as well as some other relevant genes/proteins, such as proteins involved in nuclear import/export. We describe the general properties of the network, as well as a Gene Ontology analysis of the genes included. We use several expression data sets to condense the network to a set of network links that are affected in the course of an experiment, yielding hypotheses about the underlying mechanisms. CONCLUSIONS/SIGNIFICANCE: We have initiated an electronic data repository that will be useful to understand pluripotency and to facilitate the interpretation of high-throughput data. To keep up with the growth of knowledge on the fundamental processes of pluripotency and reprogramming, we suggest to combine Wiki and social networking software towards a community curation system that is easy to use and flexible, and tailored to provide a benefit for the scientist, and to improve communication and exchange of research results. A PluriNetWork tutorial is available at http://www.ibima.med.uni-rostock.de/IBIMA/PluriNetWork/

ExprEssence - Revealing the essence of differential experimental data in the context of an interaction/regulation net-work

<p>Abstract</p> <p>Background</p> <p>Experimentalists are overwhelmed by high-throughput data and there is an urgent need to condense information into simple hypotheses. For example, large amounts of microarray and deep sequencing data are becoming available, describing a variety of experimental conditions such as gene knockout and knockdown, the effect of interventions, and the differences between tissues and cell lines.</p> <p>Results</p> <p>To address this challenge, we developed a method, implemented as a Cytoscape plugin called <it>ExprEssence</it>. As input we take a network of interaction, stimulation and/or inhibition links between genes/proteins, and differential data, such as gene expression data, tracking an intervention or development in time. We condense the network, highlighting those links across which the largest changes can be observed. Highlighting is based on a simple formula inspired by the law of mass action. We can interactively modify the threshold for highlighting and instantaneously visualize results. We applied <it>ExprEssence </it>to three scenarios describing kidney podocyte biology, pluripotency and ageing: 1) We identify putative processes involved in podocyte (de-)differentiation and validate one prediction experimentally. 2) We predict and validate the expression level of a transcription factor involved in pluripotency. 3) Finally, we generate plausible hypotheses on the role of apoptosis, cell cycle deregulation and DNA repair in ageing data obtained from the hippocampus.</p> <p>Conclusion</p> <p>Reducing the size of gene/protein networks to the few links affected by large changes allows to screen for putative mechanistic relationships among the genes/proteins that are involved in adaptation to different experimental conditions, yielding important hypotheses, insights and suggestions for new experiments. We note that we do not focus on the identification of 'active subnetworks'. Instead we focus on the identification of single links (which may or may not form subnetworks), and these single links are much easier to validate experimentally than submodules. <it>ExprEssence </it>is available at <url>http://sourceforge.net/projects/expressence/</url>.</p

Reconstruction, visualization and explorative analysis of human pluripotency network

Identification of genes/proteins involved in pluripotency and their inter-relationships is important for understanding the induction/loss and maintenance of pluripotency. With the availability of large volume of data on interaction/regulation of pluripotency scattered across a large number of biological databases and hundreds of scientific journals, it is required a systematic integration of data which will create a complete view of pluripotency network. Describing and interpreting such a network of interaction and regulation (i.e., stimulation and inhibition) links are essential tasks of computational biology, an important first step in systems-level understanding of the underlying mechanisms of pluripotency. To address this, we have assembled a network of 166 molecular interactions, stimulations and inhibitions, based on a collection of research data from 147 publications, involving 122 human genes/proteins, all in a standard electronic format, enabling analyses by readily available software such as Cytoscape and its Apps (formerly called "Plugins"). The network includes the core circuit of OCT4 (POU5F1), SOX2 and NANOG, its periphery (such as STAT3, KLF4, UTF1, ZIC3, and c-MYC), connections to upstream signaling pathways (such as ACTIVIN, WNT, FGF, and BMP), and epigenetic regulators (such as L1TD1, LSD1 and PRC2). We describe the general properties of the network and compare it with other literature-based networks. Gene Ontology (GO) analysis is being performed to find out the over-represented GO terms in the network. We use several expression datasets to condense the network to a set of network links that identify the key players (genes/proteins) and the pathways involved in transition from one state of pluripotency to other state (i.e., native to primed state, primed to non-pluripotent state and pluripotent to non-pluripotent state)

(2-Cyclohexyl-1-methylpropyl) cyclohexane isolated from garlic extract exhibits antidepressant-like activity: extraction, docking, drug-like properties, molecular dynamics simulations and MM/GBSA studies

Depressive disorders are among most common psychiatric diseases and second most common form of psychiatric illness globally. Commonly available chemical drugs used for treatment of nervous system disorders exert undesirable effects. Therefore, there is a growing need towards exploring novel antidepressants of herbal origin. Earlier, the antidepressant effect of methanolic extract of garlic has been shown. In this study, the ethanolic extract of garlic was prepared and chemically analysed using Gas Chromatography – Mass Spectrometry (GC-MS) screening. A total of 35 compounds were found to be present, which might act as antidepressant. Using computational analyses, these compounds were screened as potential inhibitors (selective serotonin reuptake inhibitor (SSRI)) against serotonin transporter (SERT)/leucine receptor (LEUT). In silico docking studies and other physicochemical, bioactivity and ADMET studies resulted in the selection of compound 1 ((2-Cyclohexyl-1-methylpropyl) cyclohexane) as potential SSRI (binding energy −8.1 kcal/mol) compared to known reference SSRI fluoxetine (binding energy −8.0 kcal/mol). Analysis of conformational stability, residue flexibility, compactness, binding interactions, solvent accessible surface area (SASA), dynamic correlation, and binding free energy predicted from molecular mechanics (MD) with generalised Born and surface area solvation (MM/GBSA) studies revealed formation of a more stable SSRI like complex with compound 1 having strong inhibitory interaction compared to known SSRI fluoxetine/reference complex. Thus, compound 1 may act as an active SSRI leading to discovery of potential antidepressant drug. Communicated by Ramaswamy H. Sarma</p