RNABPDB: Molecular Modeling of RNA Structure-From Base Pair Analysis in Crystals to Structure Prediction.

The stable three-dimensional structure of RNA is known to play several important biochemical roles, from post-transcriptional gene regulation to enzymatic action. These structures contain double-helical regions, which often have different types of non-canonical base pairs in addition to Watson-Crick base pairs. Hence, it is important to study their structures from experimentally obtained or even predicted ones, to understand their role, or to develop a drug against the potential targets. Molecular Modeling of RNA double helices containing non-canonical base pairs is a difficult process, particularly due to the unavailability of structural features of non-Watson-Crick base pairs. Here we show a composite web-server with an associated database that allows one to generate the structure of RNA double helix containing non-canonical base pairs using consensus parameters obtained from the database. The database classification is followed by an evaluation of the central tendency of the structural parameters as well as a quantitative estimation of interaction strengths. These parameters are used to construct three-dimensional structures of double helices composed of Watson-Crick and/or non-canonical base pairs. Our benchmark study to regenerate double-helical fragments of many experimentally derived RNA structures indicate very high accuracy. This composite server is expected to be highly useful in understanding functions of various pre-miRNA by modeling structures of the molecules and estimating binding efficiency. The database can be accessed from http://hdrnas.saha.ac.in/rnabpdb .

Stacking geometry between two sheared Watson-Crick basepairs: Computational chemistry and bioinformatics based prediction.

BACKGROUND: Molecular modeling of RNA double helices is possible using most probable values of basepair parameters obtained from crystal structure database. The A:A w:wC non-canonical basepair, involving Watson-Crick edges of two Adenines in cis orientation, appears quite frequently in database. Bimodal distribution of its Shear, due to two different H-bonding schemes, introduces the confusion in assigning most the probable value. Its effect is pronounced when the A:A w:wC basepair stacks on Sheared wobble G:U W:WC basepairs. METHODS: We employed molecular dynamics simulations of three possible double helices with GAG, UAG and GAU sequence motifs at their centers and quantum chemical calculation for non-canonical A:A w:wC basepair stacked on G:U W:WC basepair. RESULTS: We noticed stable structures of GAG motif with specifically negative Shear of the A:A basepair but stabilities of the other motifs were not found with A:A w:wC basepairing. Hybrid DFT-D and MP2 stacking energy analyses on dinucleotide step sequences, A:A w:wC::G:U W:WC and A:A w:wC::U:G W:WC reveal that viable orientation of A:A::G:U prefers one of the H-bonding modes with negative Shear, supported by crystal structure database. The A:A::U:G dinucleotide, however, prefers structure with only positive Shear. CONCLUSIONS: The quantum chemical calculations explain why MD simulations of GAG sequence motif only appear stable. In the cases of the GAU and UAG motifs "tug of war" situation between positive and negative Shears of A:A w:wC basepair induces conformational plasticity. GENERAL SIGNIFICANCE: We have projected comprehensive reason behind the promiscuous nature of A:A w:wC basepair which brings occasional structural plasticity.

Stacking interactions involving non-Watson-Crick basepairs: dispersion corrected density functional theory studies.

The G:A basepair, stabilized by hydrogen bonding through the sugar edge of guanine and Hoogsteen edge of adenine in trans orientation (G:A S:HT), appears very frequently in the solved RNA structures and is very stable. We have carried out stacking energy analyses of two sequences, namely C:G W:WC::G:A S:HT and G:C W:WC::G:A S:HT (':' represents basepairing and '::' represents stacking interactions), formed by this non-Watson-Crick basepair, by DFT-D. We have scanned nearly the complete phase space by modeling structures of these sequences using different values of the basepair orientation parameters to determine the most stable conformations. It is found that the most stable conformations are rather far from the most frequently found orientations. We have considered the effect of sugar-phosphate backbone connectivity as an energy penalty arising from deformation of pseudo bond lengths between C1' atoms of successive bases along the strands. Augmentation of stacking energy from DFT-D by this coarse grain energy gives predicted structures extremely similar to the experimentally determined ones. It has been observed that the best stacking with small twist values is associated with positive roll and negative slide values, which are similar to their values in A-RNA structures for most sequences. Among the two base pair steps, C:G W:WC::G:A S:HT appears to be more stable in terms of stacking energy as compared to G:C W:WC::G:A S:HT possibly due to larger stacking overlap in the former one.

Dynamic and Static Water Molecules Complement the TN16 Conformational Heterogeneity inside the Tubulin Cavity.

TN16 is one of the most promising inhibitors of α, ß dimer of tubulin that occupies the cavity in the ß-subunit located at the dimeric interface, known as the colchicine binding site. The experimentally determined structure of the complex (Protein Data Bank entry 3HKD) presents the conformation and position of the ligand based on the "best fit", keeping the controversy of other significant binding modes open for further investigation. Computation has already revealed that TN16 experiences fluctuations within the binding pocket, but the insight from that previous report was limited by the shorter windows of sampling and by the approximations on the surrounding environment by implicit solvation. This article reports that in most of the cases straightforward MMGBSA calculations of binding energy revealed a gradual loss of stabilization that was inconsistent with the structural observations, and thus, it indicated the lack of consideration of stabilizing factors with appropriate weightage. Consideration of the structurally packed water molecules in the space between the ligand and receptor successfully eliminated such discrepancies between the structure and stability, serving as the "litmus test" of the importance of explicit consideration of such structurally packed water in the calculations. Such consideration has further evidenced a quasi-degenerate character of the different binding modes of TN16 that has rationalized the observed intrinsic fluctuations of TN16 within the pocket, which is likely to be the most critical insight into its entropy-dominated binding. Quantum mechanical calculations have revealed a relay of electron density from TN16 to the protein via a water molecule in a concerted manner.

Plant regeneration from callus cultures of Vitex trifolia (Lamiales: Lamiaceae): a potential medicinal plant.

Vitex trifolia is a shrub species with popular use as a medicinal plant, for which leaves, roots and flowers have been reported to heal different distresses. The increasing exploitation of these plants has endangered its conservation, and has importantly justified the use of biotechnological tools for their propagation. Our aim was to present an efficient protocol for plant regeneration through organogenesis; and simultaneously, to analyze the genetic homogeneity of the established clonal lines by Randomly Amplified Polymorphic DNA (RAPD) and Inter Simple Sequence Repeat (ISSR) markers. Plantlet regeneration was achieved in callus cultures derived from stem, leaf and petiole explants of V. trifolia on a differently supplemented Murashige & Skoog medium, and incubated at 25 +/-2 degrees C under a light intensity of 61 micromol/m2s from cool white fluorescent lamps and a 16 h photoperiod. The rate of shoot bud regeneration was positively correlated with the concentration of hormones in the nutrient media. Shoot buds regenerated more rapidly from stem and petiole explants as compared to leaf explants on medium containing 11.10 microM BAP in combination with 0.54 microMNAA. Addition of 135.74-271.50 microM adenine sulphate (Ads) and 0.72-1.44 microM gibberellic acid (GA3) to the culture medium increased the growth of shoot buds. The highest rate of shoot bud regeneration responses was obtained in stem explants using 11.10 microM BAP in combination with 0.54 microM NAA, 271.50 microM Ads and 1.44 microM GA3. In vitro rooting of the differentiated shoots was achieved in media containing 1.23 microM indole butyric acid (IBA) with 2% (w/v) sucrose. Regenerated plantlets were successfully established in soil with 86% survival under field condition. Randomly Amplified Polymorphic DNA and Inter Simple Sequence Repeat markers analyses have confirmed the genetic uniformity of the regenerated plantlets derived from the second up to fifth subcultures. This protocol may help in mass propagation and conservation of this important medicinal plant of great therapeutic potential.

Plant regeneration from callus cultures of Vitex trifolia (Lamiales: Lamiaceae): a potential medicinal plant / Regeneración de plantas a partir de cultivos de callos de Vitex trifolia (Lamiales: Lamiaceae): una planta medicinal potencial

Vitex trifolia is a shrub species with popular use as a medicinal plant, for which leaves, roots and flowers have been reported to heal different distresses. The increasing exploitation of these plants has endangered its conservation, and has importantly justified the use of biotechnological tools for their propagation. Our aim was to present an efficient protocol for plant regeneration through organogenesis; and simultaneously, to analyze the genetic homogeneity of the established clonal lines by Randomly Amplified Polymorphic DNA (RAPD) and Inter Simple Sequence Repeat (ISSR) markers. Plantlet regeneration was achieved in callus cultures derived from stem, leaf and petiole explants of V. trifolia on a differently supple mented Murashige & Skoog medium, and incubated at 25±2ºC under a light intensity of 61µmol/m2s from cool white fluorescent lamps and a 16h photoperiod. The rate of shoot bud regeneration was positively correlated with the concentration of hormones in the nutrient media. Shoot buds regenerated more rapidly from stem and petiole explants as compared to leaf explants on medium containing 11.10µM BAP in combination with 0.54µMNAA. Addition of 135.74-271.50µM adenine sulphate (Ads) and 0.72-1.44µM gibberellic acid (GA3) to the culture medium increased the growth of shoot buds. The highest rate of shoot bud regeneration responses was obtained in stem explants using 11.10µM BAP in combination with 0.54µM NAA, 271.50µM Ads and 1.44µM GA3. In vitro rooting of the differentiated shoots was achieved in media containing 1.23µM indole butyric acid (IBA) with 2% (w/v) sucrose. Regenerated plantlets were successfully established in soil with 86% survival under field condition. Randomly Amplified Polymorphic DNA and Inter Simple Sequence Repeat markers analyses have confirmed the genetic uniformity of the regenerated plantlets derived from the second up to fifth subcultures. This protocol may help in mass propagation and conservation of this important medicinal plant of great therapeutic potential.

Vitex trifolia es una especie arbustiva de uso popular como planta medicinal, sus hojas, raíces y flores se han reportado para la cura de diferentes aflicciones. El aumento de la explotación de estas plantas ha puesto en peligro su conservación y ha justificado el uso de herramientas biotecnológicas para su propagación. El objetivo de esta investigación fue presentar un protocolo eficiente para la regeneración de estas plantas a través de la organogénesis, y analizar la homogeneidad genética de las líneas clonales establecidas por ADN polimórfico amplificado aleatoriamente (RAPD) mediante la repetición de marcadores de inter secuencia simple (ISSR). La regeneración de plántulas se logró en cultivos de callos derivados de explantes de tallo, hoja y pecíolo de V. trifolia en un medio diferenciado Murashige & Skoog, que se incubaron a 25±2ºC bajo una intensidad de luz de 61μmol/m2s con lámparas fluorescentes blancas y un fotoperíodo de 16h. La tasa de regeneración de brotes se correlacionó positivamente con la concentración de las hormonas en el medio nutritivo. Los brotes se regeneraron más rápidamente a partir de explantes de tallo y pecíolos en comparación con explantes de hoja. La mayor tasa de regeneración de brotes se obtuvo en los explantes de tallo utilizando 11.10μM BAP en combinación con 0.54μM NAA, 271.50μM Ads y 1.44μM GA3. Este protocolo puede ayudar a la propagación masiva y conservación de esta importante planta medicinal de gran potencial terapéutico.

Factors influencing rapid clonal propagation of Chlorophytum arundinaceum (Liliales: Liliaceae), an endangered medicinal plant.

Chlorophytum arundinaceum is an important medicinal plant and its tuberous roots are used for various health ailment treatments. It has become an endangered species in the Eastern Ghats, and a rare medicinal herb in India, due to its excessive collection from its natural habitat and its destructive harvesting techniques, coupled with poor seed germination and low vegetative multiplication ratio. In order to contribute to its production systems, an efficient protocol was developed for in vitro clonal propagation through shoot bud culture. For this, multiple shoots were induced from shoot bud explants on Murashige and Skoog's medium supplemented with 2.5-3.0 mg/L BAP, 0.01-0.1 mg/LNAA and 3% (w/v) sucrose. Inclusion of Adenine Sulphate (25mg/L) in the culture medium improved the frequency of multiple shoot production and recovered the chlorotic symptoms of the leaves. Media having pH 5.9 and 4% sucrose showed significant improvement on shoot bud multiplication and growth. In vitro flowering was observed when the subcultures were carried out for over four months in the same multiplication media. Rooting was readily achieved upon transferring the shoots on to half- strength MS medium supplemented with 0.1 mg/L IBA and 2% (w/v) sucrose. Micropropagated plantlets were hardened in the green house, successfully established, and flowered in the field. This method could effectively be applied for the conservation and clonal propagation to meet the demand of planting materials.

Factors influencing rapid clonal propagation of Chlorophytum arundinaceum (Liliales: Liliaceae), an endangered medicinal plant

Chlorophytum arundinaceum is an important medicinal plant and its tuberous roots are used for various health ailment treatments. It has become an endangered species in the Eastern Ghats, and a rare medicinal herb in India, due to its excessive collection from its natural habitat and its destructive harvesting techniques, coupled with poor seed germination and low vegetative multiplication ratio. In order to contribute to its production systems, an efficient protocol was developed for in vitro clonal propagation through shoot bud culture. For this, multiple shoots were induced from shoot bud explants on Murashige and Skoog’s medium supplemented with 2.5-3.0mg/L BAP, 0.01-0.1mg/L NAA and 3% (w/v) sucrose. Inclusion of Adenine Sulphate (25mg/L) in the culture medium improved the frequency of multiple shoot production and recovered the chlorotic symptoms of the leaves. Media having pH 5.9 and 4% sucrose showed significant improvement on shoot bud multiplication and growth. In vitro flowering was observed when the subcultures were carried out for over four months in the same multiplication media. Rooting was readily achieved upon transferring the shoots on to half- strength MS medium supplemented with 0.1mg/L IBA and 2% (w/v) sucrose. Micropropagated plantlets were hardened in the green house, successfully established, and flowered in the field. This method could effectively be applied for the conservation and clonal propagation to meet the demand of planting materials. Rev. Biol. Trop. 59 (1): 435-445. Epub 2011 March 01.

Chlorophytum arundinaceum es una planta medicinal importante y sus raíces se utilizan en diversos tratamientos contra enfermedades. Se ha convertido en una especie en peligro de extinción en el Ghats Oriental y una hierba medicinal rara en la India, debido a la recolecta excesiva en su hábitat natural y la manera destructiva de cosecharla, asociado con una mala germinación y pobre multiplicación vegetativa. Para contribuir con sus sistemas de producción, se desarrolló un protocolo eficiente para la propagación clonal in vitro a través del cultivo de brotes. Para ello, los retoños múltiples fueron inducidos a partir de sus brotes en un medio Murashige y Skoog enriquecido con 2.5-3.0mg/L de BAP, 0.01-0.1mg/L de NAA y el 3% (w/v) sucrosa. La inclusión de sulfato de adenina (25mg/L) en el medio de cultivo mejoró la frecuencia de producción de brotes múltiples y se recuperaron los síntomas de clorosis de las hojas. Los medios con un pH de 5.9 y 4% de sucrosa mostraron una mejoría significativa en la multiplicación y crecimiento de las yemas. En la floración in vitro se observó cuando los subcultivos se llevaron a cabo durante más de cuatro meses para los mismos medios de multiplicación. El enraizamiento se logró fácilmente al transferir los brotes a un medio MS de intensidad media enriquecido con 0.1 mg/l de IBA y 2% (w/v) de sucrosa. Las plántulas micropropagadas maduraron en el invernadero, se establecieron exitosamente y florearon en el campo. Este método se podría aplicar para la conservación y propagación clonal con el fin de satisfacer la demanda de material de siembra.