Abstract

Protonation and deprotonation of RNA bases, although energetically unfavorable, are known to play a key role in stabilization of the global structure of the RNA molecules and in regulating their functionalities. In this study an attempt has been made to look at the gas phase energies of the individual protonated and deprotonated bases, and the accompanying changes in their respective geometries and charge distribution. . Geometry optimization and energy calculations were carried out using QM methods at different levels of theory and approximations (B3LYP/6-31G++(2d,2p) and MP2/aug-ccpvdz). As expected, free energy calculations show that protonation/deprotonation at any possible site of a RNA base as a disfavored process characterized by a positive free energy change. It is however important to note that protonation at any exocyclic site or at ring imino nitrogen sites, and deprotonation from any site lead to planar and stable geometry of the corresponding conjugate acids and bases respectively. Protonation of secondary amino nitrogen atoms in the ring, such as N1of G or N3 of U, on the other hand, give significantly deformed structures where covalent bonds are also broken. Comparison of the geometrical parameters and Mulliken charge distribution in the neutral bases, with those of the corresponding charged species, showed interesting variations depending on the identity of the bases as well as on their respective protonation/deprotonation sites. It has been found that protonation at imino nitrogen atoms are not only energetically less costly, geometrical changes and charge redistribution that take place in the protonated species also help the protonated base to take part in non-covalent interactions like hydrogen bonding. Protonation at N7 position of Guanine is found to be most favorable among all possible protonation sites in any RNA base. Similar free energy calculation for nucleosides also showed the same trend and N7 protonation of Guanosine comes out to be the energetically least costly process. When we examined experimentally detected protonated base pairs involving N7 of guanine, and carried out geometry optimization for the two protonation possibilities, it was remarkable to note that it was the partner base-protonated configuration which turned out to be more stable. In fact, geometry optimization of the configuration, containing N7-protonated Guanine, resulted in the transfer of proton from N7 of Guanine to the nearest electronegative atom of the partner base. This may be because of enhanced hydrogen bonding in the alternate configuration. The next best possible protonation site among the nucleic acid bases is N3 of Cytosine, which also has many other biochemical roles. N7 protonation of Guanine, however, leads to variation of several theoretically calculated IR frequencies, some of which may destabilize the glycosidic bond. As the protonated bases are quite stable, they may play greater role in base pairing interactions in RNA.

Abstract

Riboswitches are RNA elements, in the leader region of mRNAs, which control gene expression through metabolite binding. They consist of an aptamer domain which can communicate specific ligand binding event with the expression platform. With growing number of riboswitches being discovered, the molecular basis of discriminative ligand binding, and consequent conformational changes which facilitate the communication with the expression platform, is an important area of research. We have shown earlier, that quantum chemical studies of noncovalent interactions in riboswitches, with and without the bound ligand, can help us to supplement biophysical experiments in this regard. In this study, we have chosen, PreQ1 riboswitch, which exhibits the smallest known ligand – binding domain. It has efficient structural organization and high affinity interactions with guanine derived metabolites such as 7-cyano-7-deazaguanine (PreQ0) and 7-aminomethyl-7-deazaguanine (PreQ1). To understand systematically the physicochemical basis of ligand - aptamer interaction, gas phase quantum chemical studies on the models consisting ligand (PreQ1 and PreQ0) and conserved nucleotides of mRNA aptamer that stabilizes the ligand through hydrogen bonding and stacking interactions. The optimal geometries and interaction energies of models, evaluated at B3LYP/6-31G(d,p)//RIMP2/aug-cc-pVDZ level respectively. The models that include stacking interactions are studied using DFT-D with PBE functional. Contribution of pairwise interactions of individual nucleotides with ligand, towards the total binding energy of the ligand – aptamer complex is studied. Cooperative effect arising out of interactions of ligand and surrounding bases are also calculated. The results from above calculations highlight the crucial importance of in depth quantitative understanding of different types of noncovalent interactions in the context of molecular recognition and switching processes.

Abstract

vin the wider biochemical context of their occurrence in functional RNA structures, using a combination of gas phase quantum chemical computations and structural (database) analysis methods. [1-10] Reported studies show that the geometries and intrinsic stabilities of noncanonical base pairs are largely determined by a rich variety of hydrogen bonding patterns, including bifurcated H-bonds, C-H mediated weak H-bonds, amino-acceptor interactions, and those involving interactions of the flexible sugar edge. There are however some special challenges in analyzing base pairs involving protonated nucleobases, which play important roles in mediating global macromolecular conformational changes and in facilitation of catalysis in a variety of functional RNA molecules. Firstly there is the challenge of detection and characterization of protonated base pairs in X-ray crystal structures, where proton coordinates are not available. This constitutes the prerequisite for investigating the context: the roles of protonated base pairs in RNA functions. To address this, we have used a modified version of BPFind to identify and characterize 18 distinct protonated base pair combinations from representative dataset of RNA crystal structure. The experimental base pair geometries were optimized at the B3LYP/cc-pVTZ level, and the interaction energies were calculated at the RIMP2/aug-cc-pVDZ level of theory. Based on our studies, we suggest resolution of structural ambiguities and correlate their geometric and energetic features with their structural and functional roles. In addition we also examine the suitability of specific base pairs as key elements in molecular switches and as nucleators for higher order structures such as base triplets and quartets.[11] However, we have only been able to partially address the other challenge i. e. to understand: “How nucleobases, which have pKa values for imino nitrogens around 4 or less, get protonated at physiological pH?” We will also discuss some of our ongoing efforts in this direction.

Abstract

The detailed molecular level understanding of physiochemical interactions responsible for the overall architecture and dynamics of functional RNA molecules embodies a major challenge to the scientific community. RNA 3D structure is currently analyzed in terms of strongly hydrogenbonded secondary structural elements interacting through primarily noncanonical tertiary base pairing interactions. Identification of recurring combinations of such elements as motifs, important in terms of architecture or as anchors for association, enhances our understanding of the RNA tertiary structures. Current approaches in motif mining are constrained by their dependence on identification of strongly hydrogen bonded base pairs. In our work, we have attempted a bottom-up approach towards identifying and characterizing structural features responsible for the complex architecture and dynamics of functional RNA molecules. At the lower end we have studied, noncovalent interactions such as inter-nucleotide hydrogen bonding interactions, water and ion mediated interactions; and at the higher end we have tried to capture the recurrent structural motifs made of several base-pairs and higher order. To study all the important weak and 'other than base base' interactions, within a non-redundant dataset of functional RNA molecules, we have developed a python based automated tool Inter-Nucleotide Contact Annotator in RNA (INCAR). INCAR efficiently manages space and time complexity to capture, categorize and suitably annotate all significant non-covalent interactions, such as hydrogen bonded and ion mediated interactions. Results are with high specificity, without compromising on sensitivity, with respect to currently available benchmarks like BPFIND and FR3D. Key features of our analysis include a) classification of bifurcated geometries, b) Identification of various structural elements such as platforms, bulges, loops, stems etc. c) significance of weak hydrogen bonds d) classification of higher order interactions such as triplets and quartets and e) use of a new automated centroid based approach which doesn't require a prior knowledge on standard base-pair geometries and atoms involving in hydrogen bonding is designed and implemented for detection of glycosidic bond orientation of various standard and non-standard base-pairing geometries (bifurcated, single hydrogen bonded, deformed). We have identified a new structurally important A-A Di-loop and an interesting tertiary interaction in a ribozyme. In addition, INCAR has been applied in several areas such as comparative analysis to investigate the structural conservancy of a class of sequence variants, investigation of motifs in terms of 'other than base-base' contacts and analysis of molecular dynamics simulation trajectories of RNA molecules.

Abstract

Protein domains are minimal structural units that can independently fold and carry out discrete biological functions. Evolutionary divergence amongst proteins not only cause considerable sequence changes of protein domains of similar folds and functions, but can also give rise to remarkable length variations. Rapid and heuristic sequence search algorithms are generally sensitive and effective in recognizing protein domains that are distantly related within large sequence databases, but are not well-suited to identify remote homologues of varying lengths. It is also challenging to distinguish reliable hits from a vast number of putative false positives that could have suboptimal sequence similarities. Here, we present a data-mining approach that provides stage-specific filters in sequence searches to reliably accumulate remote homologues which encourages sampling of length variations albeit no compensation on the validity of hitherto identified distant relationships. Realization of remote homologues with vivid length variations could contribute to better understanding of functional variety within protein domain superfamilies.

Abstract

Dipterocarpaceae is one of the important timber families of Andaman Islands whose members were largely exploited for their timber in the past. The current study discusses in detail about the family Dipterocarpaceae of North Andaman forest with reference to its species composition, population structure and other ecological entities. Data was analyzed using various ecological and statistical methods. Dipterocarps were encountered in 97 plots, occupying 80% of the sampled area with 68 stems ha-1 and basal area of 8.2 m2 ha-1. Dipterocarpaceae ranked 3rd with reference to stem density (11%) and 1st with respect to basal area (18%). The family showed five species viz., Dipterocarpus alatus, D. costatus, D. gracilis, D. grandiflorus and Hopea odorata compounded from two genera–

Abstract

Advances in sensing and data gathering technologies have resulted in an explosion in the volume of data that is being generated, processed, and archived. In particular, this information overload calls for new methods for querying large spatial datasets, since users are often not interested in merely retrieving a list of all data items satisfying a query, but would, instead, like a more informative \summary" of the retrieved items. An example is the so-called top-k problem, where the goal is to retrieve from a set of n weighted points in IRd the k most signicant points, ranked by their weights, that lie in an orthogonal query box in IRd (rather than get a list of all points lying in the query box). In this paper, ecient and output-sensitive solutions are presented for this problem in two settings. In the rst setting, the k points are reported in arbitrary order and the underlying set can be updated dynamically through insertions and deletions of points. In the second setting, the k points are reported in sorted order of their weights.

Abstract

In this paper we consider range-aggregate query problems wherein we wish to preprocess a set S of geometric objects such that given a query orthogonal range q, a certain aggregation function on the objects S0 = S \ q can be answered eciently. Range-aggregate version of point enclosure queries, 1-d segment intersection, 2-d orthogonal seg- ment intersection (with/without distance constraint) are revisited and we improve the existing results for these problems. We also provide semi- dynamic (insertions) solutions to some of these problems. This paper is the rst attempt to provide dynamic solutions to problems involving geometric aggregation operations.

Abstract

Hierarchical Ring Networks are widely used in communication systems, logistics and shared multiprocessors. It is hence imperative that efficient design of these structures has to be carried out, to reduce costs of their installation and help increase the ease of management. In this paper, we look at the problem of designing efficient 2- level Hierarchical Ring Networks, in the context of link costs optimization. 2-level HRNs only have two kinds of rings - local rings to connect disjoint sets of nodes and a global ring to interconnect all the local rings. We present an algorithm that is based on Simulated Annealing. We present results for scenarios containing upto 300 nodes. The results obtained from the algorithm are most encouraging.

Abstract

t Tropical islands are special and sensitive ecosystems which are subjected to various disturbances imposed by human activities and natural disasters. A detailed study about the changing landscape scenarios of these fragile island systems induced by various driving factors could be used for setting up measurements in support of conservation and sustainable development projects. The current research is a meta-analysis of the studies carried out in Andaman and Nicobar islands which analyzed the impact of tsunami of 2004 using geospatial tools. Based on the analysis, it was observed that the Nicobar islands were more affected compared to the Andaman islands. The majority of the researchers used preand post-tsunami satellite imagery and adopted visual interpretation method to delineate the changed classes. The study infers uplift of land in Andaman (exposing) and subsidence in Nicobar islands (inundation) with severe damage to the coastal elements like mangroves, coral reefs, plantations and in few cases interior forest. The analysis showed there were no records of the damage for some small islands. Finally, it is concluded that utility of microwave satellite data for change analysis will prove better in regions like Andaman and Nicobar where it is difficult to get cloud free optical data because of the high monsoon periods in these islands. It is also suggested that future work utilizing suitable temporal satellite imagery should focus on the extent of recovery of vegetation and other coastal elements which suffer the impact of disaster.