Abstract

Trans Hoogsteen/sugar edge (H/SE) RNA base pairs form one of the six families of RNA base pairs that utilize the 2-hydroxyl group of ribose for base pairing and play key roles in stabilizing folded RNA molecules. Here, we provide a detailed quantum chemical characterization of intrinsic structures and interaction energies of this base pair family, along with the evaluation of solvent screening effects by a continuum solvent approach. We report DFT-optimized geometries and MP2 interaction energies for all 10 crystallographically identified members of the family, for a representative set of them, using complete basis set extrapolation. For 6 of the 10 base pairs, we had to apply geometric constraints to keep the geometries relevant to RNA. We confirm that the remaining, hitherto undetected, possible members of this family do not have appropriate steric features required to establish stable base pairing in the trans H/SE fashion. The interaction patterns in the trans H/SE family are highly diverse, with gas-phase interaction energies in the range from 1 to 17 kcal/mol. Except for the C/rC and G/rG trans H/SE base pairs, the interaction energy is roughly evenly distributed between the HF and correlation components. Thus, in the trans H/SE base pairs, the relative importance of electron correlation is noticeably smaller than in the cis WC/SE or cis and trans SE/SE base pairs, but still larger than in canonical base pairs. The trans H/SE A/rG base pair is the intrinsically most stable member of this family. This base pair is also known as the sheared AG base pair and belongs to the most prominent set of RNA base pairs utilized in molecular building blocks of functional RNAs. For all trans H/SE base pairs that we identified, in addition to conventional base pairing, viable alternative structures were stabilized by amino-acceptor interactions. In the QM calculations, these amino-acceptor complexes appear to be equally as stable as those with common H-bonds, and more importantly, the switch to amino-acceptor interaction does not require any significant geometrical rearrangement of the base pairs. Such interactions are worthy of further investigations, as X-ray crystallography cannot unambiguously distinguish between conventional and amino-acceptor interactions involving the 2-hydroxyl group, formation of such interactions is usually not considered, and molecular modeling force fields do not include such interactions properly as a result of neglect of amino-group pyramidalization.

Abstract

Riboswitches are structural cis-acting genetic regulatory elements in 5' UTRs of mRNAs, consisting of an aptamer domain which regulates the behavior of an expression platform in response to its recognition of, and binding to, specific ligands. While our understanding of the ligand-bound structure of the aptamer domain of adenine riboswitches is, based on crystal structure X-Ray data and is well characterized, understanding of the structure and dynamics of the ligand free aptamer is limited to indirect inferences from physico-chemical probing experiments. Here we report results of 15ns long explicit-solvent molecular dynamics simulations of the add A-riboswitch crystal structure (1Y26), both in the adenine bound (CLOSED) state and in the adenine free (OPEN) state. Root mean square deviation (RMSD), root mean square fluctuation (RMSF), dynamic cross correlation (DCC) and backbone torsion angle analyses carried out on the two trajectories; and solvent accessible surface area (SASA) analysis of the two average structures, are benchmarked against available experimental data and are shown to constitute the basis for obtaining reliable insights into the molecular level details of the binding and switching mechanism. Our analysis reveals the interaction network responsible for, and conformational changes associated with, the communication between the binding pocket and the expression platform. It further highlights the significance of a, hither to unreported, non canonical W:H trans base pairing between A73 and A24, in the OPEN state, and also helps us to propose a possibly crucial role of U51 in the context of ligand binding and ligand discrimination.

Abstract

Schistosoma mansoni, a trematode parasite, which causes schistosomiasis and affects more than 200 million people worldwide, lives in an aerobic environment and therefore needs an effective redox mechanism for surviving reactive oxygen species from its host. Although, the host has two different redox systems: glutaredoxin and thioredoxin , the parasite has only one unique multifunctional enzyme, thioredoxin glutathione reductase (TGR) involving a fusion of two proteins, glutaredoxin (Grx) and thioredoxin reductase (TR), for performing all the redox activities. This dependence of S. mansoni on a single protein, TGR, for its protection from oxidative stress, makes it a promising drug target. Here, we describe a suitably validated, homology model for S. mansoni TGR (SmTGR), developed using both TR and Grx templates, functionally complete in the dimeric form with cofactors NADP(H) and FAD. Comparative analysis of substrate and inhibitor binding pockets of our model with crystal structures of parent TR as well as with that of glutathione reductase (GR), which is an essential component of the Grx system, appears to provide greater insight into the functioning of TGR. This also augments recent observations reported on the basis of X-ray structure data on SmTGR monomer lacking the C-terminal selenocysteine tail

Abstract

Graph theoretic concepts have been applied to the dynamic cross-correlation data obtained from MD simulation of adenine riboswitch, in absence and presence of adenine. Our hybrid approach combines community detection algorithms that support edge weights and cliques. The effect of variations in the values of nearest neighbors (NN) and correlation coefficient threshold (T) in the community detection algorithm have been applied to identify and filter out coincidental correlations between rogue nodes. Our results have identified the correlations within the structural regions of the molecule, which provide strong clues regarding the functionality and stability of the molecule in absence and presence of adenine. Our results show that a prior application of our algorithm applied to the simulation data of biomolecules in automated fashion can provide strong leads for hypothesis formulation and subsequent hypothesis-driven manual investigation.

Abstract

There is a widely held perception that science today, under the impact of computer science, is on the verge of a revolutionary shift in paradigm. This perception has been elaborated in detail in a recent document: Towards 2020 Science published by Microsoft Research Cambridge, which has been prepared by 34 scientists of international repute. The report examines the value added aspects, involving new conceptual and technological tools, of computer science with respect to mathematical computations and computing power of computers. It goes on to suggest that these aspects make computer science ideally suited for getting embedded into the very methodology of science that is emerging today, particularly in the context of understanding complex multi component information-processing systems, as e. g. seen in the field of biological sciences. The proposition is Computer science is poised to become as fundamental to science, and in particular the natural sciences, as mathematics has become to science, and in particular the physical sciences. Borrowing liberally from the above document, this article reviews some of the advances that are taking place in natural sciences research, as a result of its nexus with computer science.

Abstract

We present gas phase quantum chemical studies on the metabolite binding interactions in two important purine riboswitches, the adenine and guanine riboswitches, at the B3LYP/6-31G(d,p) level of theory. In order to gain insights into the strucutral basis of their discriminative abilities of regulating gene expression, the structural properties and binding energies for the gas phase optimized geometries of the metabolite bound binding pocket are analyzed and compared with their respective crystal geometries. Kitaura-Morokuma analysis has been carried out to calculate and decompose the interaction energy into various components. NBO and AIM analysis has been carried out to understand the strength and nature of binding of the individual aptamer bases with their respective purine metabolites. The Y74 base, U in case of adenine riboswitch and C in case of guanine riboswitch constitutes the only differentiating element between the two binding pockets. As expected, with W:W cis G:C74 interaction contributing more than 50% of the total binding energy, the interaction energy for metabolite binding as calculated for guanine (-46.43 Kcal/mol) is nearly double compared to the corresponding value for that of adenine (-24.73 Kcal/mol) in the crystal context. Variations in the optimized geometries for different models and comparison of relative contribution to metabolite binding involving four conserved bases reveal the possible role of U47:U51 W:H trans pair in the conformational transition of the riboswitch from the metabolite free to metabolite bound state. Our results are also indicative of significant contributions from stacking and magnesium ion interactions toward cooperativity effects in metabolite recognition

Abstract

Schistosoma mansoni, a trematode parasite, which causes schistosomiasis and affects more than 200 million people worldwide, lives in an aerobic environment and therefore needs an effective redox mechanism for surviving reactive oxygen species from its host. Although, the host has two different redox systems: glutaredoxin and thioredoxin , the parasite has only one unique multifunctional enzyme, thioredoxin glutathione reductase (TGR) involving a fusion of two proteins, glutaredoxin (Grx) and thioredoxin reductase (TR), for performing all the redox activities. This dependence of S. mansoni on a single protein, TGR, for its protection from oxidative stress, makes it a promising drug target. Here, we describe a suitably validated, homology model for S. mansoni TGR (SmTGR), developed using both TR and Grx templates, functionally complete in the dimeric form with cofactors NADP(H) and FAD. Comparative analysis of substrate and inhibitor binding pockets of our model with crystal structures of parent TR as well as with that of glutathione reductase (GR), which is an essential component of the Grx system, appears to provide greater insight in to the functioning of TGR. This also augments recent observations reported on the basis of X-ray structure data on SmTGR monomer lacking the C-terminal selenocysteine tail. Keywords: Schistosoma mansoni; Thioredoxin glutathione reductase; Glutathione disulfide; Homology modeling; Docking

Abstract

Design Rule Checking (DRC) in VLSI design involves checking if a given VLSI layout satisfies a given set of rules, and reporting the violations if any. We propose data structures for reporting violations of the minimum extension rule in a query window of interest.

Abstract

Semantic annotation or tagging of images can greatly improve the accuracy and efficiency of image search engines. However, humans rarely annotate images as they find the task of image annotation boring and laborious despites its benefits in terms of search and retrieval. In this paper, we introduce a novel approach of luring users into image annotation: by embedding image annotation into a CAPTCHA design. A CAPTCHA is a standard security mechanism used by popular commercial websites to prevent automated programs from abusing the online services. Millions of users solve CAPTCHAs daily in order to access web content and services. We aim to utilize human effort spent in solving the CAPTCHA into a productive work of image annotation. We introduce iCAPTCHA, a user friendly and productive CAPTCHA design. Our premise is based on the human ability to recognize images and label them in proper categories. Each time a user solves an iCAPTCHA, he/she is helping to label images in proper categories which will in turn improve image search and retrieval.

Abstract

In the PSMT problem, a sender S and a receiver R are part of a distributed network and connected through n node disjoint paths, also called as wires among which at most t are controlled by an all powerful Byzantine adversary At. S has a message m, which S intends to send to R. The challenge is to design a protocol, such that at the end, R should correctly output m without any error (perfect reliability) and At should not get any information about m, what so ever, in information theoretic sense (perfect security). The problem of USMT is same as PSMT, except that R should output m with a small probability of error.Sayeed et al. [15] have given a PSMT protocol in an asynchronous network tolerating At, where S and R are connected by n = 2t + 1 wires. However, we show that their protocol does not provide perfect security. We then prove that in an asynchronous network, if all the n wires are directed from S to R, then any PSMT protocol tolerating At is possible iff n > 3t. Surprisingly, we further prove that even if all the n wires are bi-directional, then any PSMT protocol in asynchronous network tolerating At is possible iff n > 3t. This is quite interesting because for synchronous networks, by the results of Dolev et al. [6], if all the wires are unidirectional (directed from S to R), then PSMT tolerating At is possible iff n > 3t, where as if all the wires are bi-directional then PSMT tolerating At is possible iff n > 2t. This shows that synchrony of the network affects the connectivity requirement for PSMT protocols. However, we show that n > 2t wires are necessary and sufficient for the existence of any USMT protocol in asynchronous network tolerating At, irrespective of whether the n wires are unidirectional from S to R or the n wires are bi-directional.