El área urbana funcional de Madrid (1991-2011). Metodología y resultados de una propuesta de delimitación y caracterización multicriterio

Esta investigación centra su atención en el análisis de los procesos constitutivos de lo urbano, más allá de las delimitaciones territoriales administrativas. Es fundamental arrojar luz sobre dichos procesos para estudiar las dinámicas y disyuntivas que enfrentan nuestros desiguales territorios urbanos. Con esta visión se propone una metodología para delimitar el área urbana funcional de Madrid y establecer sobre ella una diferenciación zonal que conjugue la existencia de un gradiente de intensidad de sus procesos constitutivos con la fracturación social de su espacio. Por último, un análisis multicriterio, a través de la generación de índices sintéticos, comparativos entre las diferentes zonas demarcadas, aportará una base descriptiva sobre la que evaluar tanto el acierto metodológico de la delimitación y caracterización del área funcional como su modelo evolutivo de desarrollo durante las últimas dos décadas. Los datos obtenidos arrojan luz sobre la validez de la tradicional dicotomía madrileña noroeste-sureste, así como, sobre la insostenibilidad del modelo en generación

A Distance Ruler for RNA Using EPR and Site-Directed Spin Labeling

AbstractAs a basic model study for measuring distances in RNA molecules using continuous wave (CW) EPR spectroscopy, site-directed spin-labeled 10-mer RNA duplexes and HIV-1 TAR RNA motifs with various interspin distances were examined. The spin labels were attached to the 2′-NH2 positions of appropriately placed uridines in the duplexes, and interspin distances were measured from both molecular dynamics simulations (MD) and Fourier deconvolution methods (FD) [13]. The 10-mer duplexes have interspin distances ranging from 10 Å to 30 Å based on MD; however, dipolar line broadening of the CW EPR spectrum is only observed for the RNAs for predicted interspin distances of 10–21 Å and not for distances over 25 Å. The conformational changes in TAR (transactivating responsive region) RNA in the presence and in the absence of different divalent metal ions were monitored by measuring distances between two nucleotides in the bulge region. The predicted interspin distances obtained from the FD method and those from MD calculations match well for both the model RNA duplexes and the structural changes predicted for TAR RNA. These results demonstrate that distance measurement using EPR spectroscopy is a potentially powerful method to help predict the structures of RNA molecules

Additional file 2: of A computational assessment of pH-dependent differential interaction of T7 lysozyme with T7 RNA polymerase

HADDOCK docking results of T7RNAP and Lysozyme (at pH 5). A surface representation of the docked complex is shown. (DOCX 276 kb

pH modulates the role of SP6 RNA polymerase in transcription process: an <i>in silico</i> study

SP6 RNA polymerase (SP6 RNAP) is an essential enzyme for the transcription process in SP6 bacteriophage. SP6 RNAP plays a vital role in mRNA vaccine designing technology and other translational biotechnology research due to the high specificity towards its promoter. The self-replicating performance also put this polymerase to study extensively. Despite of the reports emphasizing the function of this enzyme, a detailed structural and functional understanding of RNA polymerase is not reported so far. Here, we report the first-ever information about SP6RNAP structure and its effect on promoter binding at different pH environments using molecular docking and molecular dynamics simulation (MDS) study. We also report the changes in polymerase conformations in different pH conditions using in-silico approach. The docking study was also performed for SP6 RNAP with SP6 promoter at different pH environments using the in-silico docking tools and conducted the MDS study for complexes. MM/PBSA and per residue energy contribution has been performed at three different pH environments. The structural aspects confirmed that the pH 7.9 state favors the polymerase functional activity in the transcription process which was in the range reported using transcription assay. This polymerase’s unique features may play its emerging role as an efficient transcription factor in translational biological research. Communicated by Ramaswamy H. Sarma The PRL and PBL of polymerase maintain a minimum distance from the promoter site at pH 7.9, leading to a possible transcription model for SP6 bacteriophage.HIGHLIGHTSThe structure of SP6 RNA polymerase (SP6RNAP) was modelled using in silico tools. This model is essential as no structure was solved for this enzyme using any of the standard structural biology techniques.The modelled structure was used to understand the interactions between SP6 RNAP and its promoter.The structure of the SP6 RNAP-SP6 promoter was subjected to various pH states to analyze the stability of the complex using in silico tools.The model was successfully able to explain the pH-dependent activity of the polymerase reported in the literature.A possible mechanism for the change in the activity of the polymerase was proposed. The structure of SP6 RNA polymerase (SP6RNAP) was modelled using in silico tools. This model is essential as no structure was solved for this enzyme using any of the standard structural biology techniques. The modelled structure was used to understand the interactions between SP6 RNAP and its promoter. The structure of the SP6 RNAP-SP6 promoter was subjected to various pH states to analyze the stability of the complex using in silico tools. The model was successfully able to explain the pH-dependent activity of the polymerase reported in the literature. A possible mechanism for the change in the activity of the polymerase was proposed.</p

Interaction Analysis of T7 RNA Polymerase with Heparin and Its Low Molecular Weight Derivatives – An in Silico Approach

The single subunit T7 RNA polymerase (T7RNAP) is a model enzyme for studying the transcription process and for various biochemical and biophysical studies. Heparin is a commonly used inhibitor against T7RNAP and other RNA polymerases. However, exact interaction between heparin and T7RNAP is still not completely understood. In this work, we analyzed the binding pattern of heparin by docking heparin and few of its low molecular weight derivatives to T7RNAP, which helps in better understanding of T7RNAP inhibition mechanism. The efficiency of the compounds was calculated by docking the selected compounds and post-docking molecular mechanics/generalized Born surface area analysis. Evaluation of the simulation trajectories and binding free energies of the complexes after simulation showed enoxaparin to be the best among low molecular weight heparins. Binding free energy analysis revealed that van der Waals interactions and polar solvation energy provided the substantial driving force for the binding process. Furthermore, per-residue free energy decomposition analysis revealed that the residues Asp 471, Asp 506, Asp 537, Tyr 571, Met 635, Asp 653, Pro 780, and Asp 812 are important for heparin interaction. Apart from these residues, most favorable contribution in all the three complexes came from Asp 506, Tyr 571, Met 635, Glu 652, and Asp 653, which can be essential for binding of heparin-like structures with T7RNAP. The results obtained from this study will be valuable for the future rational design of novel and potent inhibitors against T7RNAP and related proteins