Structure‐based classification of FAD binding sites: A comparative study of structural alignment tools

A total of six different structural alignment tools (TM‐Align, TriangleMatch, CLICK, ProBis, SiteEngine and GA‐SI) were assessed for their ability to perform two particular tasks: (i) discriminating FAD (flavin adenine dinucleotide) from non‐FAD binding sites, and (ii) performing an all‐to‐all comparison on a set of 883 FAD binding sites for the purpose of classifying them. For the first task, the consistency of each alignment method was evaluated, showing that every method is able to distinguish FAD and non‐FAD binding sites with a high Matthews correlation coefficient. Additionally, GA‐SI was found to provide alignments different from those of the other approaches. The results obtained for the second task revealed more significant differences among alignment methods, as reflected in the poor correlation of their results and highlighted clearly by the independent evaluation of the structural superimpositions generated by each method. The classification itself was performed using the combined results of all methods, using the best result found for each comparison of binding sites. A number of different clustering methods (Single‐linkage, UPGMA, Complete‐linkage, SPICKER and k‐Means clustering) were also used. The groups of similar binding sites (proteins) or clusters generated by the best performing method were further analyzed in terms of local sequence identity, local structural similarity and conservation of analogous contacts with the FAD ligands. Each of the clusters was characterized by a unique set of structural features or patterns, demonstrating that the groups generated truly reflect the structural diversity of FAD binding sites. Proteins 2016; 84:1728–1747. © 2016 Wiley Periodicals, Inc.     

L.S. Vygotsky and the Theater

The article presents the analysis of L.S. Vygotsky's works dedicated to the theater arts and is organized according Vygotsky's different life and work stages. Meanwhile special attention is paid to the Gomel period during which a large number of reviews were written by Vygotsky and published in “Nash ponedel'nik” and “Polesskaia pravda” newspapers. Biographical facts are widely used in this analysis and help to clarify Vygotsky's interest in art. It is shown that even at the beginning of his oeuvre, he was interested not only in a range of problems in art, but also psychological problems related to art perception and creativeness. Vygotsky's usage of structural concept ideas about the peculiar properties of literary text composition are also explored. Vygotsky analyzes the socio-psychological mechanisms of theatrical art effect. Furthermore, those areas which are widely used by Vygotsky in determining the characteristics of cast reincarnation are examined. Special emphasis is placed on the different elements of the actor techniques (speech, movement, emotional expression, acting personality and etc.). Materials are widely used in this study and help identify the socio-cultural context that defined Vygotsky's values at different stages of his work, related to his drama criticism and his formation as a professional psychologist.     

Synthesis,Structural Characterization and Antimicrobial Evaluation of Ruthenium Complexes with Heteroaromatic Carboxylic Acids

The antibacterial and antibiofilm activities of two new ruthenium complexes against E. coli, S. aureus, P. aeruginosa PAO1 (laboratory strain) and P. aeruginosa LES B58 (clinical strain) were evaluated. Complexes, mer‐[Ru^III(2‐bimc)₃] ? H₂O ( 1 ) and cis‐[Ru^IVCl₂(2,3‐pydcH)₂] ? 4H₂O ( 2 ), were obtained using aromatic carboxylic acid ligands, namely, 1H‐benzimidazole‐2‐carboxylic acid (2‐bimcH) and pyridine‐2,3‐dicarboxylic acid (2,3‐pydcH₂). Compounds were physicochemically characterized using X‐ray diffraction, Hirshfeld surface analysis, IR and UV/VIS spectroscopies, as well as magnetic and electrochemical measurements. Structural characterization revealed that Ru(III) and Ru(IV) ions in the complexes adopt a distorted octahedral geometry. The intermolecular classical and weak hydrogen bonds, and π???π contacts significantly contribute to structure stabilization, leading to the formation of a supramolecular assembly. Biological studies have shown that the Ru complexes inhibit the growth of bacteria and biofilm formation by the tested strains and the complexes seem to be a potential as antimicrobial agents.     

Boosting the Stable Na Storage Performance in 1D Oxysulfide

Exploring new structure prototypes and phases by material design, especially anode materials, is essential to develop high‐performance Na‐ion batteries. This study proposes a new anode, Na₂Cu_2.09O_0.50S₂, with a 1D crystal structure and outstanding Na storage performance. In view of the crystal structure of Na₂Cu_2.09O_0.50S₂, [Cu₄S₄] chains act as electrically conducting units enabling conductivity as high as 0.5 S cm^?1. The residual Na₄[CuO] chains act as ionically conducting units forming rich channels for the fast conduction of Na ions as well as maintaining the structural stability even after Na ion extraction. Additional ball milling on the as‐prepared Na₂Cu_2.09O_0.50S₂ significantly decreases its grain size, achieving a capacity of 588 mA h g^?1 with a high initial Coulombic efficiency of 93% at 0.2 A g^?1. Moreover, the Na₂Cu_2.09O_0.50S₂ anode demonstrates outstanding rate capability (408 mA h g^?1 at 2 A g^?1) and extending cyclic performance (82% of capacity retention after 400 cycles). The general structural design idea based on functional units may offer a new avenue to new electrode materials.     

Death domain of p75 neurotrophin receptor: a structural perspective on an intracellular signalling hub

The death domain (DD) is a globular protein motif with a signature feature of an all‐helical Greek‐key motif. It is a primary mediator of a variety of biological activities, including apoptosis, cell survival and cytoskeletal changes, which are related to many neurodegenerative diseases, neurotrauma, and cancers. DDs exist in a wide range of signalling proteins including p75 neurotrophin receptor (p75^NTR), a member of the tumour necrosis factor receptor superfamily. The specific signalling mediated by p75^NTR in a given cell depends on the type of ligand engaging the extracellular domain and the recruitment of cytosolic interactors to the intracellular domain, especially the DD, of the receptor. In solution, the p75^NTR‐DDs mainly form a symmetric non‐covalent homodimer. In response to extracellular signals, conformational changes in the p75^NTR extracellular domain (ECD) propagate to the p75^NTR‐DD through the disulfide‐bonded transmembrane domain (TMD) and destabilize the p75^NTR‐DD homodimer, leading to protomer separation and exposure of binding sites on the DD surface. In this review, we focus on recent advances in the study of the structural mechanism of p75^NTR‐DD signalling through recruitment of diverse intracellular interactors for the regulation and control of diverse functional outputs.     

ComplexBrowser: A Tool for Identification and Quantification of Protein Complexes in Large-scale Proteomics Datasets

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Highlights

• •Automated analysis of protein complexes in proteomic experiments.
• •Quantitative measurement of the coordinated changes in protein complex components.
• •Interactive visualizations for exploratory analysis of proteomic results.

     

NaCa0.6V6O16·3H2O as an Ultra‐Stable Cathode for Zn‐Ion Batteries: The Roles of Pre‐Inserted Dual‐Cations and Structural Water in V3O8 Layer

Rechargeable aqueous batteries with Zn²⁺ as a working‐ion are promising candidates for grid‐scale energy storage because of their intrinsic safety, low‐cost, and high energy‐intensity. However, suitable cathode materials with excellent Zn²⁺‐storage cyclability must be found in order for Zinc‐ion batteries (ZIBs) to find practical applications. Herein, NaCa_0.6V₆O₁₆·3H₂O (NaCaVO) barnesite nanobelts are reported as an ultra‐stable ZIB cathode material. The original capacity reaches 347 mAh g^?1 at 0.1 A g^?1, and the capacity retention rate is 94% after 2000 cycles at 2 A g^?1 and 83% after 10 000 cycles at 5 A g^?1, respectively. Through a combined theoretical and experimental approach, it is discovered that the unique V₃O₈ layered structure in NaCaVO is energetically favorable for Zn²⁺ diffusion and the structural water situated between V₃O₈ layers promotes a fast charge‐transfer and bulk migration of Zn²⁺ by enlarging gallery spacing and providing more Zn‐ion storage sites. It is also found that Na⁺ and Ca²⁺ alternately suited in V₃O₈ layers are the essential stabilizers for the layered structure, which play a crucial role in retaining long‐term cycling stability.