Abstract

Characterization of native, intermediate, and denatured states is crucial for understanding the factors influencing the stability of proteins. We have carried out molecular dynamics simulations to study the unfolding of three peripheral subunit binding domains (PSBDs): E. coli BBL, Bacillus stearothermophilus E3BD, and human hbSBD, at three different temperatures: 300, 330, and 400 K, and in the presence of two solvents: water and 5 M guanidinium hydrochloride (GndCl) solution. These proteins share similar folds, with two parallel helices, maintained via a hydrophobic core comprising residues from their interconnecting loop. BBL is more sensitive to thermal and chemical denaturation in comparison to hbSBD, and E3BD is the most stable of all of the three proteins. The effect of temperature on the stability of these proteins is more pronounced in “water-only” simulations compared to that in the presence of guanidium hydrochloride in high concentrations. Our results show cooperative unfolding transitions of these proteins, which are triggered by an initial melting of the C-terminal helix H2. The consequent loss of interhelical interactions or native contacts, as observed, leads to the subsequent melting of the N-terminal helix H1.

Abstract

Charged nucleobases have been found to occur in several known RNA molecules and are considered essential for their structure and function. The mechanism of their involvement is however not yet fully understood. Revelation of the role of N7-protonated guanine, in modulating the geometry and stability of noncanonical base pairs formed through its unprotonated edges [Watson−Crick (WC) and sugar], has triggered the need to evaluate the feasibility of similar roles of other protonated nucleobases [Halder et al., Phys Chem Chem Phys, 2015, 17, 26249]. In this context, N3 protonation of guanine makes an interesting case as its influence on the charge distribution of the WC edge is similar to that of N7 protonation, though its thermodynamic cost of protonation is significantly higher. In this work, we have carried out structural bioinformatics analyses and quantum mechanics-based calculations to show that N3 protonation of guanine may take place in a cellular environment, at least in the G:C W:W Trans and G:G W:H Cis base pairs. Our results provide a reasonable starting point for future investigations in order to address the larger mechanistic question.

Abstract

Noncoding RNA molecules are composed of a large variety of noncanonical base pairs that shape up their functionally competent folded structures. Each base pair is composed of at least two interbase hydrogen bonds (H-bonds). It is expected that the characteristic geometry and stability of different noncanonical base pairs are determined collectively by the properties of these interbase H-bonds. We have studied the ground-state electronic properties [using density functional theory (DFT) and DFT-D3-based methods] of all the 118 normal base pairs and 36 modified base pairs, belonging to 12 different geometric families (cis and trans of WW, WH, HH, WS, HS, and SS) that occur in a nonredundant set of high-resolution RNA crystal structures. Having addressed some of the limitations of the earlier approaches, we provide here a comprehensive compilation of the average energies of different types of interbase H-bonds (EHB). We have also characterized each interbase H-bond using 13 different parameters that describe its geometry, charge distribution at its bond critical point (BCP), and n → σ*-type charge transfer from filled π orbitals of the H-bond acceptor to the empty antibonding orbital of the H-bond donor. On the basis of the extent of their linear correlation with the H-bonding energy, we have shortlisted five parameters to model linear equations for predicting EHB values. They are (i) electron density at the BCP: ρ, (ii) its Laplacian: ∇2 ρ, (iii) stabilization energy due to n → σ*-type charge transfer: E(2), (iv) donor−hydrogen distance, and (v) hydrogen−acceptor distance. We have performed single variable and multivariable linear regression analysis over the normal base pairs and have modeled sets of linear relationships between these five parameters and EHB. Performance testing of our model over the set of modified base pairs shows promising results, at least for the moderately strong H-bonds.

Abstract

Identification and characterization of base-multiplets, which are essentially mediated by base-pairing interactions, can provide insights into the diversity in the structure and dynamics of complex functional RNAs, and thus facilitate hypothesis driven biological research. The necessary nomenclature scheme, an extension of the geometric classification scheme for base-pairs by Leontis and Westhof, is however available only for base-triplets. In the absence of information on topology, this scheme is not applicable to quartets and higher order multiplets. Here we propose a topology-based classification scheme which, in conjunction with a graph-based algorithm, can be used for the automated identification and characterization of higher order base-multiplets in RNA structures. Here, the RNA structure is represented as a graph, where nodes represent nucleotides and edges represent base-pairing connectivity. Sets of connected components (of n nodes) within these graphs constitute subgraphs representing multiplets of “n” nucleotides. The different topological variants of the RNA multiplets thus correspond to different nonisomorphic forms of these subgraphs. To annotate RNA base-multiplets unambiguously, we propose a set of topology-based nomenclature rules for quartets, which are extendable to higher multiplets. We also demonstrate the utility of our approach toward the identification and annotation of higher order RNA multiplets, by investigating the occurrence contexts of selected examples in order to gain insights regarding their probable functional roles.

Abstract

Studies on how pancreatic islets respond under physiological and pathological conditions are obtained mostly based on the analysis of whole-islet transcriptome. However, the measurement from the whole islets quantifies the average behaviour of dominant cell types, thereby making it difficult to understand the cell-type-specific changes. Recently, the advent of single-cell RNA sequencing (scRNA-seq) technique has generated valuable resource on islet biology and type 2 diabetes (T2D). This provides an opportunity to understand the different cell types/states at both the network and individual gene expression levels. Here, we inferred the gene regulatory networks (GRNs) of pancreatic cells from publicly available scRNA-seq data in healthy and T2D using single-cell regulatory network inference and clustering workflow. Clustering of cells based on GRNs identifies endocrine and exocrine cells and …

Abstract

Understanding the structure-function relationships of RNA has become increasingly important given the realization of its functional role in various cellular processes. Chemical denaturation of RNA by urea has been shown to be beneficial in investigating RNA stability and folding. Elucidation of the mechanism of unfolding of RNA by urea is important for understanding the folding pathways. In addition to studying denaturation of RNA in aqueous urea, it is important to understand the nature and strength of interactions of the building blocks of RNA. In this study, a systematic examination of the structural features and energetic factors involving interactions between nucleobases and urea is presented. Results from molecular dynamics (MD) simulations on each of the five DNA/RNA bases in water and eight different concentrations of aqueous urea, and free energy calculations using the thermodynamic integration method are presented. The interaction energies between all the nucleobases with the solvent environment and the transfer free energies become more favorable with respect to increase in the concentration of urea. Preferential interactions of urea versus water molecules with all model systems determined using Kirkwood-Buff integrals and two-domain models indicate preference of urea by nucleobases in comparison to water. The modes of interaction between urea and the nucleobases were analyzed in detail. In addition to the previously identified hydrogen bonding and stacking interactions between urea and nucleobases that stabilize the unfolded states of RNA in aqueous solution, NH-π interactions are proposed to be important. Dynamic properties of each of these three modes of interactions have been presented. The study provides fundamental insights into the nature of interaction of urea molecules with nucleobases and how it disrupts nucleic acids.

Abstract

Understanding synergistic effect by calculating electronic structure is essential to fine-tune the catalytic properties of bimetallic nanoalloy clusters which might be used for design of novel efficient catalysts. Density functional theory PBE0 calculations were performed to investigate the structure and energetics of various intermediates involved in the CO oxidation reaction catalyzed by Au3-xYx (x= 0–3 and Y denotes Ag or, Pt or, Pd) trimeric clusters through two possible pathways: Eley-Rideal (ER) and Langmuir-Hinshelwood (LH). The results of this investigation show that the catalytic behavior of the nanocluster highly depends on its composition and the reaction site taken into consideration. The most active reaction centres of goldsilver, gold-palladium, gold-platinum clusters are gold, palladium and platinum atoms respectively. The gold-silver clusters and AuPt2 prefer ER mechanism whereas, gold-palladium and Au2Pt selectively favour LH mechanism in comparison to the other. Bimetallic clusters, in general, are more efficient in comparison to their pristine mono-metallic counterparts, in activating the OO bond for the reaction and have relatively easy CO2 dissociation. Overall results indicate that the alloyed clusters could potentially have a better catalytic activity as compared to pure gold clusters for CO oxidation at low temperatures.

Abstract

We are interested in the problem of enabling transformation of existing, already published web pages. We call this Renarration of web content. In our earlier work, we had already established the role and importance of renarration for improving Web Accessibility. There are nearly a billion websites on the web, making transformation of pages a domain on its own. In this paper, we present the development of a Domain-Specific Language (DSL) for the purpose of web page transformation. We show how the design and implementation of our DSL is driven by our problem domain, its terminology and its unique requirements. We take up an existing online video-course delivery system, which has accessibility challenges, as a specific case to demonstrate our DSL. We end with insights and reflections for future work in both DSL and web page transformations.

Abstract

With the rise of Virtual Reality (VR) footprint in many organizations, it was unclear if traditional software engineering practices are still exercised during VR product development. As part of our research, we conducted a year-long multi-level exploratory study to understand the various software development practices within VR product development teams. An empirical study on VR practitioners from 6 different countries was done to examine their development strategies, methods, and models adopted along with the various challenges faced during the course of VR product release. We found that VR practitioners adopted hybrid Software engineering approaches in VR product development. In this paper, we present our insights from the empirical study and stress on the need for a diverse software development model for VR products.

Abstract

VR development practices have a diverse set of practices compared to traditional software development. Tasks like scene design, acoustic design, vergence manipulation, image depth, etc. are specific to VR apps and hence require evaluation processes that may be different from the traditional means. Usability Evaluation is one such process which is being executed in an unconventional way by Industrial Practitioners today. In this paper, the researchers detail a Systematic Literature Review of the Usability Evaluation Methods practised by Industrial researchers while building VR Products. The researchers found that VR Product teams follow unique methods to improve usability in their products. Further, the researchers consolidate these methods and provide insights into choosing the best to build a real-world VR Product based on the defined product constraints.