Abstract

Single stranded RNA molecules are known to fold into complex protein like functional structures, consisting of stems and loops, which are further stabilized through tertiary interactions. While it is remarkable that RNA molecules are able to exhibit such structural complexity and functional specificity, with only an alphabet of four bases, one of the strategies employed for creating variety is through post-transcriptional modifications such as methylation, pseudouridylation, thiolation and isomerization. In fact, modified bases are known to play major role in providing chemical and biological diversity to RNA and contribute to overall fitness of the cell1. Base modifications are also known to help RNA molecules to exhibit alternate conformations2. The objectives of this study are: To understand (1) how these modifications affect the base pairing properties of RNA bases and (2) why nature have adopted mechanism to modified these bases. These objectives are studied through quantum chemical methods. We extracted the coordinates of 32 modified base pairs and 11 base triplets from a total of 208 RNA crystal structures from the PDB database. Of these 208 files, 128 were directly taken from HD-RNAS’s non redundant dataset3 and searched for modified bases using BPFind software4. The remaining 77 PDB files were included in the dataset based on information from HET group information from PDBSum5. We have optimized the initial geometries at B3LYP/6-31G (d,p) level and have evaluated the complete basis set (CBS) extrapolated interaction energies using RIMP2 calculation with aug-cc-pVDZ and aug-cc-pVTZ basis sets. Molecular electrostatic surface potential maps were also generated for modified base pairs. This study provides insights into the characteristics of modified base pairs and triples in complex RNA structure.

Abstract

Schistosomiasis is a disease caused by a trematode parasite, Schistosoma mansoni. The host consists of two different redox systems: Glutaredoxin (Grx) and Thioredoxin (Trx), but the parasite has only one multifunctional enzyme Thioredoxin Glutathione Reductase (TGR), which is responsible for carrying out all the redox activities, necessary for protecting the parasite against oxidative stress inside the host. TGR is a fusion of Thioredoxin Reductase (TR) with Glutaredoxin (Grx) at its N-terminus. The dependence of S. mansoni on a single protein for all its redox functions makes it a potential drug target. We have carried out structural analysis of Glutathione Reductase (GR), Thioredoxin Reductase (TR) and Thioredoxin Glutathione Reductase (TGR) using available crystal structures from PDB to understand the catalytic mechanism in these oxidoreductases. NADPH plays a major role as an electron carrier and transfers the electrons to the oxidized cofactor, FAD, which is non-covalently attached to the enzyme. This initiates further steps of the catalytic process. Here, we investigate how the interplay of conformations of these cofactors and those of the neighbouring residues facilitate the charge transfer process. TR, GR and TGR share similarity in their respective active site regions. Several conserved residues and non covalent interactions, play a major role during the electron transfer process. We hypothesise the function of NADPH during the entire charge transfer process as follows: a Tyr residue moves and facilitates the binding of NADPH to FAD in pi-stacking conformation. Two Arg residues reorient to interact with 2'-phosphate group and adenine ring of NADPH for effective binding. Lys, Glu and His residues near the active site regions form salt bridges and possibly aid the charge transfer mechanism in these redox enzymes.

Abstract

BACKGROUND: Thermostable lipases are widely used in the detergent industry and in organic synthesis. B. subtilis lipase (Lip A) is a monomeric protein, which preferentially hydrolyses C8 fatty acid esters. Though the mechanism of thermostability depends on type of lipase, some common factors include additional non-covalent interactions, increase in packing density of the hydrophobic core, stabilization of alpha-helices and shortening of loops between secondary structural elements. RESULTS: We have studied wild type Lip A (WT) and six of its thermostable mutants containing 2, 3, 4, 6, 9 and 12 point mutations respectively, derived from the wild type protein by directed evolution. Experimental observations showed that the most thermostable variant, with twelve mutations, shows remarkable enhancement in melting temperature and temperature optima of activity compared to WT, in vitro. Our MD simulations show decrease in SASA for core regions and slow unfolding rate at several key secondary structural regions due to presence of persistent salt bridges, hydrogen bonds and native contacts for the most thermostable mutant lipase. The principal component (PC) and Free energy landscape (FEL) analyses at 450K suggest that the most thermostable mutant showed least fluctuation and stayed within a single large minimum. The other less thermostable mutants and WT showed higher fluctuation and exhibited two or more minima along the first two PCs. Analysis of representative structures corresponding to each sub-states showed that the most thermostable mutant sampled conformations close to the native state most of the time during the simulation. The other less thermostable mutants and WT lipase sampled non-native conformations more frequently than native conformations. CONCLUSIONS: Our results demonstrate that, the most thermostable lipase maintains its stability and activity at high temperatures by restricting conformational fluctuation through the stabilization of key salt bridges and main-chain H-bonds, which further helped them to maintain the stability of the core regions apart from stabilizing the overall 3D fold.

Abstract

Archaeal chromatin proteins share molecular and functional similarities with both bacterial and eukaryotic chromatin proteins. These proteins play an important role in functionally organizing the genomic DNA into a compact nucleoid. Cren7 and Sul7 are two crenarchaeal nucleoidassociated proteins, which are structurally homologous, but not conserved at the sequence level. Cocrystal structures have shown that these two proteins induce a sharp bend on binding to DNA. In this study, we have investigated the architectural properties of these proteins using atomic force microscopy, molecular dynamics simulations and magnetic tweezers. We demonstrate that Cren7 and Sul7 both compact DNA molecules to a similar extent. Using a theoretical model, we quantify the number of individual proteins bound to the DNA as a function of protein concentration and show that forces up to 3.5 pN do not affect this binding. Moreover, we investigate the flexibility of the bending angle induced by Cren7 and Sul7 and show that the protein–DNA complexes differ in flexibility from analogous bacterial and eukaryotic DNA-bending proteins.

Abstract

A series of dihydrogen complexes trans-[Ru(η2-H2){SC(SR)H}(dppe)2][X][BF4] (R = CH3, X = OTf; R = C6H5CH2, X = BPh4; R = H2C=CHCH2, X = BPh4; dppe = Ph2PCH2CH2PPh2) bearing sulfur-donor ligands has been synthesized by protonation of the (alkyl dithioformate)hydrido complexes trans-[Ru(H){SC(SR)H}(dppe)2][X] by using HBF4•Et2O. Competitive substitution reactions between H2 and SC(SR)H in trans-[Ru(η2-H2){SC(SR)H}(dppe)2][X][BF4] have been studied by treatment with CH3CN, CO, and P(OCH3)3. These resulted in the expulsion of SC(SR)H from the metal center, thus indicating that the alkyl dithioformate ligand is more labile than H2. Bonding of alkyl dithioformate ligands (sulfur-donor ligands) trans to H2 have been studied by comparing the H–H distances and chemical-shift values (1H NMR spectroscopy) of the various dihydrogen complexes bearing different trans ligands. This study qualitatively suggests that the alkyl dithioformate ligands in these trans-dihydrogen complexes show a poor π effect, and it is further supported by density functional theory calculations. The first example of a dihydrogen complex bearing dithioformic acid, trans-[Ru(η2-H2){SC(SH)H}(dppe)2][BF4]2, was obtained by protonation of trans-[Ru(H){SC(S)H}(dppe)2] by using HBF4•Et2O.

Abstract

This paper presents a method to capture the orbiting objects using a robotic system mounted on a service satellite. The main objective is to manipulate the robot such that no reaction moment gets transferred to the base satellite. This will avoid use of any attitude controller resulting in fuel savings. Note that the constraints leading to zero reaction moment are nonholonomic, and this makes path planning a complex problem. In this work, first a method based on holonomic distribution of the nonholonomic constraints is discussed. As this method exploits constraints in terms of joint velocities, it does not always ensure successful capture. Next, a method based on task-level constraints, written in terms of end-effector's velocities, has been illustrated. It is shown that the path planned using this method has several singular points. In order to overcome disadvantages of the above two methods a novel approach is proposed which uses holonomic distribution to reach closer to the target and task-level constraints to finally capture the target. Efficacy of the method is shown using a 3-link robot mounted on a service satellite.

Abstract

Modern research in India on dams has entered a distinct phase subsequent to the damage to Koyna dam, located in hitherto considered stable continental part, due to an earthquake on 11th December, 1967 in Koyna district, India. Out of about 5,100 large dams in India, a significant number are in moderately high and high seismic zones. As such they may be prone to probable instability to the dam’s structure due to earthquake resultant impacts. Even though none of the dams other than Koyna got damaged in India due to high magnitude earthquake activity, since 1967, it is felt necessary to understand the behaviour of dams due to water load coupled with dynamics of faults that are present in the vicinity of the dam, as dam failures due to earthquake activity are reported from different parts of the world. In this paper, damage to Koyna dam due to a fault motion caused nearby has been studied. A concrete gravity dam is selected from the National Importance Dams of India. Structure-1(S1) as a concrete gravity dam with foundation and structure-2 (S2) as a concrete gravity dam with foundation and soil strata are numerically modeled using Applied Element Method (AEM). Displacement at the base of soil strata is given to generate reverse fault effect on the dam. Behavior of dam is studied by direct and sub-structure methods. In the direct method, the effect of fault motion on dam is studied in S2, by modeling dam at different locations on foot wall and hanging wall. In sub-structure method, free-field accelerations are recorded at different locations on foot wall and hanging wall while only the sub-structure is subjected to fault motion. The recorded accelerations on the surface are used as input to analyze super structure S1. Comparison on behavior of dam in models S1 and S2 is later drawn.

Abstract

Depth information has been shown to affect identification of visually salient regions in images. In this paper, we investigate the role of depth in saliency detection in the presence of (i) competing saliencies due to appearance,(ii) depth-induced blur and (iii) centre-bias. Having established through experiments that depth continues to be a significant contributor to saliency in the presence of these cues, we propose a 3D-saliency formulation that takes into account structural features of objects in an indoor setting to identify regions at salient depth levels. Computed 3D saliency is used in conjunction with 2D saliency models through non-linear regression using SVM to improve saliency maps. Experiments on benchmark datasets containing depth information show that the proposed fusion of 3D saliency with 2D saliency models results in an average improvement in ROC scores of about 9% over state-of-the-art 2D saliency models.

Abstract

Visual localization in crowded dynamic environments requires information about static and dynamic objects. This paper presents a robust method that learns the useful features from multiple runs in highly crowded urban environments. Useful features are identified as distinctive ones that are also reliable to extract in diverse imaging conditions. Relative importance of features is used to derive the weight for each feature. The popular Bag-of-words model is used for image retrieval and localization, where query image is the current view of the environment and database contains the visual experience from previous runs. Based on the reliability, features are augmented and eliminated over runs. This reduces the size of representation, and makes it more reliable in crowded scenes. We tested the proposed method on data sets collected from highly crowded Indian urban outdoor settings. Experiments have shown that with the help of a small subset (10%) of the detected features, we can reliably localize the camera. We achieve superior results in terms of localization accuracy even when more than 90% of the pixels are occluded or dynamic.

Abstract

Analysis and design of high-rise buildings for lateral load such as wind load and earthquake are the major issues which are playing significant role in recent decades. This paper describes a recent application of the computational fluid dynamics technique for wind analysis. Conventional wind analysis suggests wind tunnel experiment for arriving at the wind forces for a given structural form. As a case study a regular 38-story high-rise building (Jamieson place, Calgary Canada1) made of concrete with shear wall, built in downtown Calgary 2010 is selected. It is assumed that the building is located in highly seismic area. The design objective was to develop most cost-effective structural system while meeting building functionality goals and adhering to code requirement. The main structural design issues considered in this building are reviewed: Static analysis, Dynamic Analysis, Wind Analysis and Stability Analysis. Initial static and dynamic analysis is conducted in SAP and later wind analysis is conducted in Ansys as opposed to wind tunnel experiments. The building model is modeled in Ansys workbench and then the mesh file is imported to Ansys CFX for CFD simulation and analysis. After CFD analysis the wind forces on the building model are extracted in Ansys CFX-Post and imported to the structural model in SAP 2000 for the structural analysis.