Structural studies on chimeric Sesbania mosaic virus coat protein: Revisiting SeMV assembly

The capsid protein (CP) of Sesbania mosaic virus (SeMV, a T=3 plant virus) consists of a disordered N-terminal R-domain and an ordered S-domain. Removal of the R-domain results in the formation of T=1 particles. In the current study, the R-domain was replaced with unrelated polypeptides of similar lengths: the B-domain of Staphylococcus aureus SpA, and SeMV encoded polypeptides P8 and P10. The chimeric proteins contained T=3 or larger virus-like particles (VLPs) and could not be crystallized. The presence of metal ions during purification resulted in a large number of heterogeneous nucleoprotein complexes. N Delta 65-B (R domain replaced with B domain) could also be purified in a dimeric form. Its crystal structure revealed T=1 particles devoid of metal ions and the B-domain was disordered. However, the B-domain was functional in N Delta 65-B VLPs, suggesting possible biotechnological applications. These studies illustrate the importance of N-terminal residues, metal ions and robustness of the assembly process. (C) 2015 Elsevier Inc. All rights reserved.

Four- and five-component molecular solids: crystal engineering strategies based on structural inequivalence

A synthetic strategy is described for the co-crystallization of four-and five-component molecular crystals, based on the fact that if any particular chemical constituent of a lower cocrystal is found in two different structural environments, these differences may be exploited to increase the number of components in the solid. 2-Methylresorcinol and tetramethylpyrazine are basic template molecules that allow for further supramolecular homologation. Ten stoichiometric quaternary cocrystals and one quintinary cocrystal with some solid solution character are reported. Cocrystals that do not lend themselves to such homologation are termed synthetic dead ends.

Structural, Optical, and Piezoelectric Response of Lead-Free Ba0.95Mg0.05Zr0.1Ti0.9O3 Nanocrystalline Powder

Nanocrystalline powders of Ba1-xMgxZr0.1Ti0.9O3 (x = 0.025-0.1) were synthesized via citrate assisted sol-gel method. Interestingly, the one with x = 0.05 in the system Ba1-xMgxZr0.1Ti0.9O3 exhibited fairly good piezoelectric response aside from the other physical properties. The phase and structural confirmation of synthesized powder was established by X-ray powder diffraction (XRD) and Raman Spectroscopic techniques. Two distinct Raman bands i.e., 303 and 723 cm(-1) characteristic of tetragonal phase were observed. Thermogravimetric analysis (TGA) was performed to evaluate the phase decomposition of the as-synthesized Ba0.95Mg0.05Zr0.1Ti0.9O3 sample as a function of temperature. The average crystallite size associated with Ba0.95Mg0.05Zr0.1Ti0.9O3 was calculated using Scherrer formula based on the XRD data and was found to be 25 nm. However, Scanning and Transmission Electron Microscopy studies revealed the average crystallite size to be in the range of 30-40 nm, respectively. Kubelka-Munk function was employed to determine the optical band gap of these nanocrystallites. A piezoelectric response of 26 pm/V was observed for Ba0.95Mg0.05Zr0.1Ti0.9O3 nanocrystal by Piezoresponse Force Microscopy (PFM) technique. Photoluminescence (PL) study carried out on these nanocrystals exhibited a blue emission (470 nm) at room temperature.

Ionothermal Synthesis of High-Voltage Alluaudite Na2+2xFe2-x(SO4)(3) Sodium Insertion Compound: Structural, Electronic, and Magnetic Insights

Exploring future cathode materials for sodium-ion batteries, alluaudite class of Na2Fe2II(SO4)(3) has been recently unveiled as a 3.8 V positive insertion candidate (Barpanda et al. Nat. Commun. 2014, 5, 4358). It forms an Fe-based polyanionic compound delivering the highest Fe-redox potential along with excellent rate kinetics and reversibility. However, like all known SO4-based insertion materials, its synthesis is cumbersome that warrants careful processing avoiding any aqueous exposure. Here, an alternate low temperature ionothermal synthesis has been described to produce the alluaudite Na2+2xFe2-xII(SO4)(3). It marks the first demonstration of solvothermal synthesis of alluaudite Na2+2xM2-xII(SO4)(3) (M = 3d metals) family of cathodes. Unlike classical solid-state route, this solvothermal route favors sustainable synthesis of homogeneous nanostructured alluaudite products at only 300 degrees C, the lowest temperature value until date. The current work reports the synthetic aspects of pristine and modified ionothermal synthesis of Na2+2xFe2-xII(SO4)(3) having tunable size (300 nm similar to 5 mu m) and morphology. It shows antiferromagnetic ordering below 12 K. A reversible capacity in excess of 80 mAh/g was obtained with good rate kinetics and cycling stability over 50 cycles. Using a synergistic approach combining experimental and ab initio DFT analysis, the structural, magnetic, electronic, and electrochemical properties and the structural limitation to extract full capacity have been described.

Structural analysis of dihydrofolate reductases enables rationalization of antifolate binding affinities and suggests repurposing possibilities

Antifolates are competitive inhibitors of dihydrofolate reductase ( DHFR), a conserved enzyme that is central to metabolism and widely targeted in pathogenic diseases, cancer and autoimmune disorders. Although most clinically used antifolates are known to be target specific, some display a fair degree of cross-reactivity with DHFRs from other species. A method that enables identification of determinants of affinity and specificity in target DHFRs from different species and provides guidelines for the design of antifolates is currently lacking. To address this, we first captured the potential druggable space of a DHFR in a substructure called the `supersite' and classified supersites of DHFRs from 56 species into 16 `site-types' based on pairwise structural similarity. Analysis of supersites across these site-types revealed that DHFRs exhibit varying extents of dissimilarity at structurally equivalent positions in and around the binding site. We were able to explain the pattern of affinities towards chemically diverse antifolates exhibited by DHFRs of different site-types based on these structural differences. We then generated an antifolate-DHFR network by mapping known high-affinity antifolates to their respective supersites and used this to identify antifolates that can be repurposed based on similarity between supersites or antifolates. Thus, we identified 177 human-specific and 458 pathogen-specific antifolates, a large number of which are supported by available experimental data. Thus, in the light of the clinical importance of DHFR, we present a novel approach to identifying differences in the druggable space of DHFRs that can be utilized for rational design of antifolates.

Insights into the Structural Dynamics of Nucleocytoplasmic Transport of tRNA by Exportin-t

Exportin-t (Xpot) transports mature 5'- and 3'-end processed tRNA from the nucleus to the cytoplasm by associating with a small G-protein Ran (RAs-related nuclear protein), in the nucleus. The release of tRNA in cytoplasm involves RanGTP hydrolysis. Despite the availability of crystal structures of nuclear and cytosolic forms of Xpot, the molecular details regarding the sequential events leading to tRNA release and subsequent conformational changes occurring in Xpot remain unknown. We have performed a combination of classical all-atom and accelerated molecular dynamics simulations on a set of complexes involving Xpot to study a range of features including conformational flexibility of free and cargo-bound Xpot and functionally critical contacts between Xpot and its cargo. The systems investigated include free Xpot and its different complexes, bound either to Ran (GTP/GDP) or tRNA or both. This approach provided a statistically reliable estimate of structural dynamics of Xpot after cargo release. The mechanistic basis for Xpot opening after cargo release has been explained in terms of dynamic structural hinges, about which neighboring region could be displaced to facilitate the nuclear to cytosolic state transition. Post-RanGTP hydrolysis, a cascade of events including local conformational change in RanGTP and loss of critical contacts at Xpot/tRNA interface suggest factors responsible for eventual release of tRNA. The level of flexibility in different Xpot complexes varied depending on the arrangement of individual HEAT repeats. Current study provides one of the most comprehensive and robust analysis carried out on this protein using molecular dynamics schemes.

Long-period modulated structure and electric-field-induced structural transformation in Na0.5Bi0.5TiO3-based lead-free piezoelectrics

Na0.5Bi0.5TiO3- based lead-free piezoelectrics exhibiting giant piezostrain are technologically interesting materials for actuator applications. The lack of clarity with regard to the structure of the nonpolar phase of this system has hindered the understanding of the structural mechanism associated with the giant piezostrain and other related phenomena. In this paper, we have investigated the structure and field-induced phase transformation behavior of a model system (0.94 - x) Na0.5Bi0.5TiO3-0.06BaTiO(3)-xK(0.5)Na(0.5)NbO(3) (0.0 <= x <= 0.025). A detailed structural analysis using neutron powder diffraction revealed that the nonpolar phase is neither cubic nor a mixture of rhombohedral (R3c) and tetragonal (P4bm) phases as commonly reported in literature but exhibits a long-period modulated structure, which is most probably of the type root 2 x root 2 x n with n = 16. Our results suggest that the giant piezoelectric strain is associated with a field-induced phase transformation of the long-period modulated structure to rhombohedral R3c structure above a critical field. We also demonstrate that the giant piezostrain is lost if the system retains a fraction of the field-induced R3c phase. A possible correlation among depolarization temperature, giant piezostrain, and its electrical fatigue behavior has also been indicated.

A systematic asymptotic approach to determine the dispersion characteristics of structural-acoustic waveguides with arbitrary fluid loading

Structural-acoustic waveguides of two different geometries are considered: a 2-D rectangular and a circular cylindrical geometry. The objective is to obtain asymptotic expansions of the fluid-structure coupled wavenumbers. The required asymptotic parameters are derived in a systematic way, in contrast to the usual intuitive methods used in such problems. The systematic way involves analyzing the phase change of a wave incident on a single boundary of the waveguide. Then, the coupled wavenumber expansions are derived using these asymptotic parameters. The phase change is also used to qualitatively demarcate the dispersion diagram as dominantly structure-originated, fluid originated or fully coupled. In contrast to intuitively obtained asymptotic parameters, this approach does not involve any restriction on the material and geometry of the structure. The derived closed-form solutions are compared with the numerical solutions and a good match is obtained. (C) 2016 Elsevier Ltd. All rights reserved.