Energetic approach to the folding of alpha/beta barrels

The folding of a polypeptide into a parallel (alpha/beta)8 barrel (which is also called a circularly permuted beta 8 alpha 8 barrel) has been investigated in terms of energy minimization. According to the arrangement of hydrogen bonds between two neighboring beta-strands of the central barrel therein, such an alpha/beta barrel structure can be folded into six different types: (1) left-tilted, left-handed crossover; (2) left-tilted, right-handed crossover; (3) nontilted, left-handed crossover; (4) nontilted, right-handed crossover; (5) right-tilted, left-handed crossover; and (6) right-tilted, right-handed crossover. Here "tilt" refers to the orientational relation of the beta-strands to the axis of the central beta-barrel, and "crossover" to the beta alpha beta folding connection feature of the parallel beta-barrel. It has been found that the right-tilted, right-handed crossover alpha/beta barrel possesses much lower energy than the other five types of alpha/beta barrels, elucidating why the observed alpha/beta barrels in proteins always assume the form of right tilt and right-handed crossover connection. As observed, the beta-strands in the energy-minimized right-tilted, right-handed crossover (alpha/beta)8-barrel are of strong right-handed twist. The value of root-mean-square fits also indicates that the central barrel contained in the lowest energy (alpha/beta)8 structure thus found coincides very well with the observed 8-stranded parallel beta-barrel in triose phosphate isomerase (TIM). Furthermore, an energetic analysis has been made demonstrating why the right-tilt, right-handed crossover barrel is the most stable structure. Our calculations and analysis support the principle that it is possible to account for the main features of frequently occurring folding patterns in proteins by means of conformational energy calculations even for very complicated structures such as (alpha/beta)8 barrels.     

3D structure of bovine pancreatic ribonuclease A in aqueous solution: An approach to tertiary structure determination from a small basis of1H NMR NOE correlations

Summary A method is proposed to generate initial structures in cases where the distance geometry method may fail, such as when the set of¹H NMR NOE-based distance constraints is small in relation to the size of the protein. The method introduces an initial correlation between the and backbone angles (based on empirical observations) which is relaxed in later stages of the calculation. The obtained initial structures are refined by well-established methods of energy minimization and restrained molecular dynamics. The method is applied to determine the solution structure of Ribonuclease A (124 residues) from a NOE basis consisting of 467 NOE cross-correlations (97 intra-residue, 206 sequential, 23 medium-range and 141 long-range) obtained at 360 MHz. The global shape and backbone overall fold of the eight final refined structures are close to those shown by the crystal structure. A meaningful difference in the positioning of the catalytically important His¹¹⁹ side chain in the solution and crystal structures has been detected.     

The subacrosomal granule and its evolution during spermiogenesis in a lizard

Summary Some aspects of spermiogenesis have been studied in the testis of the teiid lizard Cnemidophorus lemniscatus lemniscatus by electron microscopy. Shortly after the acrosomal vesicle is lodged in a nuclear concavity of the spermatid, a dense granule differentiates in the center of the subacrosomal space. It is cone-shaped and shows a longitudinal striation. Its base applies to the acrosomal membrane and, through this, to the acrosomal granule. Its rounded vertex causes a depression of the nuclear membranes which, initially juxtaposed, separates at this point to form a vesicle. The granule develops and becomes a rod when spermiogenesis is advanced and the subacrosomal space has taken the form of a secondary cap. The rod is cylindrical, retains its original striation and has a convex acrosomal end. It encloses the vesicle formed by the nuclear envelope in its base and follows the apex of the nucleus. Meanwhile, the acrosomal granule loses its identity and the acrosomal cap is filled with a dense substance, in which a fringe of translucent material differentiates. This fringe lies in the dorsal and apical margins of the acrosome and is incompletely divided by longitudinal crests of the dense acrosomal substance. A projection of the Sertoli cell forms an accessory cap which envelops the acrosome and is in turn covered by the cytoplasm of the spermatid, constituting an intricate association. Two reflex membranes underlie the plasmalemma in the outer surface of the projection of the Sertoli cell. They are continuous with one another at their ends and with the cell membrane in the edge of pores. In the peripheral cytoplasm of the spermatid facing the accessory cap, numerous microtubules run longitudinally. By means of thin membranes some are interconnected or connected with the plasmalemma, from which they seem to originate.This research forms part of project N. 31.26.S1-0244 supported by the Consejo Nacional de Investigaciones Científicas y Tecnológicas     

Endopolyploidy inHelianthus annuus (Asteraceae), A scanning cytophotometric study

Endopolyploidy has been detected in some varieties ofHelianthus annuus L. (Asteraceae/Compositae) by means of scanning photometry of Feulgen-stained nuclei and analysis of nuclear structure. In the hypocotyl cells of seedlings, ploidy levels reach respectively 8 C and 16 C in different varieties, in the root cells 8 C and 16 C; in the cotyledons of ripening seeds 4 C to 8 C values have been found, while all nuclei of the inflorescence axis of one variety exhibit a DNA content of 4 C.—This is the first report of endopolyploidy in a non-succulentAsteraceae species. The characteristic distribution of the endopolyploidy levels in different varieties suggests a strong genetic and/or hormonal control of the final nuclear DNA content in differentiated cells.     

Substrate Binding Mechanism of a Type I Extradiol Dioxygenase

A meta-cleavage pathway for the aerobic degradation of aromatic hydrocarbons is catalyzed by extradiol dioxygenases via a two-step mechanism: catechol substrate binding and dioxygen incorporation. The binding of substrate triggers the release of water, thereby opening a coordination site for molecular oxygen. The crystal structures of AkbC, a type I extradiol dioxygenase, and the enzyme substrate (3-methylcatechol) complex revealed the substrate binding process of extradiol dioxygenase. AkbC is composed of an N-domain and an active C-domain, which contains iron coordinated by a 2-His-1-carboxylate facial triad motif. The C-domain includes a β-hairpin structure and a C-terminal tail. In substrate-bound AkbC, 3-methylcatechol interacts with the iron via a single hydroxyl group, which represents an intermediate stage in the substrate binding process. Structure-based mutagenesis revealed that the C-terminal tail and β-hairpin form part of the substrate binding pocket that is responsible for substrate specificity by blocking substrate entry. Once a substrate enters the active site, these structural elements also play a role in the correct positioning of the substrate. Based on the results presented here, a putative substrate binding mechanism is proposed.     

A new precursor for organo-osmium complexes

The use of potassium osmate, K₂[OsO₂(OH)₄], as a precursor for some cyclopentadienyl-osmium complexes is described. The X-ray structures of OsBr(PPh₃)₂Cp, OsCl(dppe)Cp and OsX(dppe)Cp^∗ (X = Cl, Br) are reported.     

虎杖象甲培植真菌营养特性及对菌丝附属物形成的影响

虎杖象甲培植共生真菌形成的共生体系是植菌昆虫菌业中的典型代表。共生真菌Penicillium herquei如何向虎杖象甲Euops chinensis提供营养尚未明确。本研究发现共生真菌P. herquei的菌丝表面存在大量瘤状凸起物及由凸起物衍生的附属丝等特化结构,该结构可能为虎杖象甲提供营养;对共生真菌的营养研究表明,共生真菌能高效利用山梨醇、蔗糖、海藻糖、葡萄糖等单糖或双糖,以及酪氨酸、甘氨酸、谷氨酰胺等昆虫非必须氨基酸,同时在高碳和最适碳源条件下有利于菌丝特化附属物的产生。研究结果不仅提供了植菌卷叶象甲菌业中共生真菌在营养方面的适应性进化证据,而且为进一步揭示共生真菌适应卷叶象甲的营养机制奠定了基础。     

Understanding Molecular Structures of Buried Interfaces in Halide Perovskite Photovoltaic Devices Nondestructively with Sub‐Monolayer Sensitivity Using Sum Frequency Generation Vibrational Spectroscopy

As performance of halide perovskite devices progresses, the device structure becomes more complex with more layers. Molecular interfacial structures between different layers play an increasingly important role in determining the overall performance in a halide perovskite device. However, current understanding of such interfacial structures at a molecular level nondestructively is limited, partially due to a lack of appropriate analytical tools to probe buried interfacial molecular structures in situ. Here, sum frequency generation (SFG) vibrational spectroscopy, a state‐of‐the‐art nonlinear interface sensitive spectroscopy, is introduced to the halide perovskite research community and is presented as a powerful tool to understand molecule behavior at buried halide perovskite interfaces in situ. It is found that interfacial molecular orientations revealed by SFG can be directly correlated to halide perovskite device performance. Here how SFG can examine molecular structures (e.g., orientations) at the perovskite/hole transporting layer and perovskite/electron transporting layer interfaces is discussed. This will promote the use of SFG to investigate molecular structures of buried interfaces in various halide perovskite materials and devices in situ nondestructively with a sub‐monolayer interface sensitivity. Such research will help to elucidate structure–function relationships of buried interfaces, aiding in the rational design/development of halide perovskite materials/devices with improved performance.     

2D Metal Zn Nanostructure Electrodes for High‐Performance Zn Ion Supercapacitors

Recent supercapacitors show a high power density with long‐term cycle life time in energy‐powering applications. A supercapacitor based on a single metal electrode accompanying multivalent cations, multiple charging/discharging kinetics, and high electrical conductivity is a promising energy‐storing system that replaces conventionally used oxide and sulfide materials. Here, a hierarchically nanostructured 2D‐Zn metal electrode‐ion supercapacitor (ZIC) is reported which significantly enhances the ion diffusion ability and overall energy storage performance. Those nanostructures can also be successfully plated on various flat‐type and fiber‐type current collectors by a controlled electroplating method. The ZIC exhibits excellent pseudocapacitive performance with a high energy density of 208 W h kg^?1 and a power density from 500 W kg^?1, which are significantly higher than those of previously reported supercapacitors with oxide and sulfide materials. Furthermore, the fiber‐type ZIC also shows high energy‐storing performance, outstanding mechanical flexibility, and waterproof characteristics, without any significant capacitance degradation during bending tests. These results highlight the promising possibility of nanostructured 2D Zn metal electrodes with the controlled electroplating method for future energy storage applications.