Abstract

Base pairs belonging to the cis Hoogsteen: sugar-edge (H:S) family play important structural roles in folded RNA molecules. Several of these are present in internal loops, where they are involved in interactions leading to planar dinucleotide platforms which stabilize higher order structures such as base triplets and quartets. We report results of analysis of 30 representative examples spanning 16 possible base pair combinations, with several of them showing multimodality of base pairing geometry. The geometries of 23 of these base pairs were modeled directly from coordinates extracted from RNA crystal structures. The other seven were predicted structures which were modeled on the basis of observed isosteric analogues. After appropriate satisfaction of residual valencies, these structures were relaxed using the B3LYP/6-31G(d,p) method and interaction energies were derived at the RIMP2/aug-cc-pVDZ level of theory. The geometries for each of the studied base pairs have been characterized in terms of the number and nature of H-bonds, rmsd values observed on optimization, base pair geometrical parameters, and sugar pucker analysis. In addition to its evaluation, the nature of intermolecular interaction in these complexes was also analyzed using Morokuma decomposition. The gas phase interaction energies range between −5.2 and −20.6 kcal/mol and, in contrast to the H:S trans base pairs, show enhanced relative importance of the electron correlation component, indicative of the greater role of dispersion energy in stabilization of these base pairs. The rich variety of hydrogen bonding pattern, involving the flexible sugar edge, appears to hold the key to several features of structural motifs, such as planarity and propensity to participate in triplets, observed in this family of base pairs. This work explores these aspects by integrating database analysis, and detailed base pairing geometry analysis at the atomistic level, with ab initio computation of interaction energies. The study, involving alternative classification of base pairs and triplets, provides insights into intrinsic properties of these base pairs and their possible structural and functional roles.

Abstract

Cells from animals adhere to and exert mechanical forces on their surroundings. Cells must control these forces for many biological processes, and dysfunction can lead to pathologies. How the actions of molecules within a cell are coordinated to regulate the adhesive interaction with the extracellular matrix remains poorly understood. It has been observed that cytoplasmic proteins that link integrin cell-surface receptors with the actin cytoskeleton flow with varying rates from the leading edge toward the center of a cell. Here, we explore theoretically how measurable subcellular traction stresses depend on the local speed of retrograde actin flow. In the model, forces result from the stretching of molecular complexes in response to the drag from the flow; because these complexes break with extension-dependent kinetics, the flow results in a decrease in their number when sufficiently large. Competition between these

Abstract

Background Plant biologists have long speculated about the mechanisms that guide pollen tubes to ovules. Although there is now evidence that ovules emit a diffusible attractant, little is known about how this attractant mediates interactions between the pollen tube and the ovules. Results We employ a semi-in vitro assay, in which ovules dissected from Arabidopsis thaliana are arranged around a cut style on artificial medium, to elucidate how ovules release the attractant and how pollen tubes respond to it. Analysis of microscopy images of the semi-in vitro system shows that pollen tubes are more attracted to ovules that are incubated on the medium for longer times before pollen tubes emerge from the cut style. The responses of tubes are consistent with their sensing a gradient of an attractant at 100-150 μm, farther than previously reported. Our …

Abstract

The shape deformation within the optic disk (OD) is an important indicator for the detection of glaucoma. In this paper, relevant disk parameters are estimated using the OD and cup boundaries. A deformable model guided by regional statistics is used to detect the OD boundary. A cup boundary detection scheme is presented based on the appearance of pallor in Lab colour space and the expected cup symmetry. The proposed scheme is tested on 170 images comprising 40 normal and 130 glaucomatous images. The proposed method gives a mean error 0.030 for normal and 0.121 for glaucomatous images in the estimation of cup-to-disk ratio which compares well with reported figures in literature.

Abstract

Phytodiversity is affected both by natural and anthropogenic factors and in Island ecosystems these impacts can devastate or reduce diversity, if the native vegetation is lost. In addition to rich species richness and diversity, Island systems are the sites of high endemism and any threat to these ecosystems will consequently lead to loss and extinction of species. To understand the dynamics including feedbacks of these changes in phytodiversity of North Andaman Islands, a conceptual framework is proposed which focuses on understanding the land-use and land-cover changes and its impact with phytodiversity. In considering land-use and land-cover changes this work highlights the direct and indirect drivers of changes—socio-economic, biophysical and climatic factors. Migration of population, their socio economic needs and government policies were identified as major driving forces threatening the phytodiversity of these Islands. Apart from human beings, natural disasters like tsunami and introduced herbivorous animals like elephants also contributed to forest destruction in these Islands. The integrated analysis based on such framework will provide insights for holistic resource management including ecological conservation.

Abstract

We present a novel segmentation method to better capture the boundary of a non-homogeneous object such as the optic disk(OD), defined locally by two similar characteristic regions. Existing active contour models which utilise gradient information [12] or global region intensity [2] fail to localise aforementioned boundaries. We propose a region-based active contour model that uses local image information around each point of interest in multi-dimensional feature space. This model uses a local energy functional and level-set representation to achieve desired OD segmentation. The local energy functional defined on each image point provides sufficient information to determine a desired OD segmentation which is robust to the variations found in and around the OD region. This method has been evaluated against the segmentation provided by three medical experts on 138 retinal images. Both region and boundary-based assessment performed against two well established active contour models show strengths of the proposed method.

Abstract

Riboswitches are RNA-based genetic control elements that function via a conformational transition mechanism when a specific target molecule binds to its binding pocket. To facilitate an atomic detail interpretation of experimental investigations on the role of the adenine ligand on the conformational properties and kinetics of folding of the add adenine riboswitch, we performed molecular dynamics simulations in both the presence and the absence of the ligand. In the absence of ligand, structural deviations were observed in the J23 junction and the P1 stem. Destabilization of the P1 stem in the absence of ligand involves the loss of direct stabilizing interactions with the ligand, with additional contributions from the J23 junction region. The J23 junction of the riboswitch is found to be more flexible, and the tertiary contacts among the junction regions are altered in the absence of the adenine ligand; results suggest that the adenine ligand associates and dissociates from the riboswitch in the vicinity of J23. Good agreement was obtained with the experimental data with the results indicating dynamic behavior of the adenine ligand on the nanosecond time scale to be associated with the dynamic behavior of hydrogen bonding with the riboswitch. Results also predict that direct interactions of the adenine ligand with U74 of the riboswitch are not essential for stable binding although it is crucial for its recognition. The possibility of methodological artifacts and force-field inaccuracies impacting the present observations was checked by additional molecular dynamics simulations in the presence of 2,6-diaminopurine and in the crystal environment. Copyright (c) 2010 Elsevier Ltd. All rights reserved.

Abstract

Sac7d belongs to a family of chromosomal proteins, which are crucial for thermal stabilization of DNA at higher growth temperatures. It is capable of binding DNA nonspecifically, and is responsible for the increase in the melting temperature of DNA in the bound form up to 85 °C. Molecular dynamics (MD) simulations were performed at different temperatures on two protein-DNA complexes of Sac7d. Various structural and energetic parameters were calculated to examine the DNA stability and to investigate the conformational changes in DNA and the protein-DNA interactions. Room temperature simulations indicated very good agreement with the experimental structures. The protein structure is nearly unchanged at both 300 and 360 K, and only up to five base pairs of the DNA are stabilized by Sac7d at 360 K. However, the MD simulations on DNA alone systems show that they lose their helical structures at 360 K further supporting the role of Sac7d in stabilizing the oligomers. At higher temperatures (420 and 480 K), DNA undergoes denaturation in the presence and the absence of the protein. The DNA molecules were found to undergo B- to A-form transitions consistent with experimental studies, and the extent of these transitions are examined in detail. The extent of sampling B- and A-form regions was found to show temperature and sequence dependence. Multiple MD simulations yielded similar results validating the proposed model. Interaction energy calculations corresponding to protein-DNA binding indicates major contribution due to DNA backbone, explaining the nonspecific interactions of Sac7d.

Abstract

The enlarging HIV/AIDS pandemic and the virus’ ability to develop resistance to anti-retroviral therapy requires the development of new drugs based on novel targets. Viruses interact extensively with the host at the cellular and molecular levels, which is necessary for the expression of viral proteins and replication of viral genomes. At another level, these interactions also help the virus evade host immune responses. Besides the prototypic retroviral proteins (Gag, Pol and Env), HIV-1 also expresses two regulatory proteins (Tat and Rev) and four accessory proteins (Nef, Vif, Vpr and Vpu). The accessory proteins are not required for viral replication in vitro, but are critical for pathogenesis and disease development in the host. We have focused our efforts on two of these – Nef and Vpu, with an aim to understand their interactions with host proteins and the functional consequences of these interactions for HIV-1 infection and pathogenesis. The Nef protein binds to multiple host proteins to optimize the host cell environment and to enable infected cells to evade the host immune response. A major property of Nef is to downregulate surface expression of the CD4, MHC I and MHC II proteins, by increasing the endocytosis of these molecules. We also discovered that Nef binds to the cytoplasmic domains of the B7 family of costimulatory proteins – CD80 and CD86; this results in their removal from the cell surface and sequestration to the Golgi compartment (1-3). We have now developed an in vitro screen based on purified recombinant Nef proteins and a 20-mer synthetic peptide from the cytoplasmic domain of CD80 and CD86. A chemical library comprising of 1064 compounds was screened and ~7% compounds were obtained as hits, which inhibited the Nef-CD80/CD86 interaction. These compounds are now being evaluated in a cellbased assay and an independent dose dependent response assay. The top hits will be used in a combinatorial chemical approach to synthesize a large array of new molecules for further screening using the in vitro and cell-based screens. The HIV-1 Vpu protein is required for the release of new virions from the surface of infected cells; for this the transmembrane domain of Vpu is critical. Using the Topology Data Bank of Transmembrane Proteins (TOPDB) database we extracted 13 alpha-helical sequences that closely resemble the Vpu-TM domain. We have taken the top two hits and have constructed recombinant Vpu proteins in which the native TM domain was replaced by the identified sequences. These recombinant proteins were successfully expressed in HEK293 cells, and are now being tested for their effects on virion release as well as their ability to inhibit Vpu activity. We describe here two paradigms to screen for anti-HIV activity based on proteinprotein interactions. Results will be presented for both of these.

Abstract

Distance bounding protocols are used by nodes in wireless networks to calculate upper bounds on their distances to other nodes. However, dishonest nodes in the network can turn the calculations both illegitimate and inaccurate when they participate in protocol executions. It is important to analyze protocols for the possibility of such violations. Past efforts to analyze distance bounding protocols have only been manual. However, automated approaches are important since they are quite likely to find flaws that manual approaches cannot, as witnessed in literature for analysis pertaining to key establishment protocols. In this paper, we use the constraint solver tool to automatically analyze distance bounding protocols. We first formulate a new trace property called Secure Distance Bounding (SDB) that protocol executions must satisfy. We then classify the scenarios in which these protocols can operate considering the (dis) honesty of nodes and location of the attacker in the network. Finally, we extend the constraint solver so that it can be used to test protocols for violations of SDB in these scenarios and illustrate our technique on some published protocols.