Critical Roles of a RhoGEF-Anillin Module in Septin Architectural Remodeling during Cytokinesis

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Atom ordering in cuboctahedral Ni-Al nanoalloys

Energy calculations have been carried out on high-symmetry cuboctahedral Ni-Al nanoalloy clusters, of varying composition, with the interatomic interactions modelled by the Gupta many-body potential. Relaxations of cuboctahedral fragments cut from the bulk lattice of Ni₃Al, with 13-561 atoms, were undertaken, as were relaxations of high symmetry clusters with 55 and 147 atoms. The lowest energy isomers were found to be dominated by three factors: the tendency toward mixing due to the favourable energy of mixing, Δ_mixE; the size difference between nickel and aluminium; and the higher cohesive and surface energy of nickel compared to aluminium. The latter two factors favour Al-segregation to the surface. The most stable Ni:Al composition approaches 3:1 for larger clusters.     

Geometric Similarities of Protein-Protein Interfaces at Atomic Resolution Are Only Observed within Homologous Families: An Exhaustive Structural Classification Study

To elucidate the structural basis of the diversity and universality in protein-protein interactions, an exhaustive all-against-all structural comparison of all known protein interfaces in the Protein Data Bank was performed at atomic resolution. After similar interfaces were clustered, approximately 20,000 structural motifs with at least two members were identified, out of which 3678 motifs consisted of at least 10 interfaces. Except for some trivial interfaces involving single α helices, almost all motifs were found to be confined within single protein families. Furthermore, the interaction partners of each motif were found to be very limited, and, accordingly, the interaction networks of the motifs tend to be small and are much more restricted than the binding sites for small ligand molecules. These findings suggest that, at the level of atomic structures, protein-protein interactions are precisely designed; hence, protein interfaces with multiple interacting partners should involve incompletely overlapping multiple interfaces and/or accommodate structural changes upon binding to their targets.     

Deciphering Spatial Protein–Protein Interactions in Brain Using Proximity Labeling

Cellular biomolecular complexes including protein–protein, protein–RNA, and protein–DNA interactions regulate and execute most biological functions. In particular in brain, protein–protein interactions (PPIs) mediate or regulate virtually all nerve cell functions, such as neurotransmission, cell–cell communication, neurogenesis, synaptogenesis, and synaptic plasticity. Perturbations of PPIs in specific subsets of neurons and glia are thought to underly a majority of neurobiological disorders. Therefore, understanding biological functions at a cellular level requires a reasonably complete catalog of all physical interactions between proteins. An enzyme-catalyzed method to biotinylate proximal interacting proteins within 10 to 300 nm of each other is being increasingly used to characterize the spatiotemporal features of complex PPIs in brain. Thus, proximity labeling has emerged recently as a powerful tool to identify proteomes in distinct cell types in brain as well as proteomes and PPIs in structures difficult to isolate, such as the synaptic cleft, axonal projections, or astrocyte–neuron junctions. In this review, we summarize recent advances in proximity labeling methods and their application to neurobiology.     

A biomolecular recognition approach for the functionalization of cellulose with gold nanoparticles

Materials with new and improved functionalities can be obtained by modifying cellulose with gold nanoparticles (AuNPs) via the in situ reduction of a gold precursor or the deposition or covalent immobilization of pre‐synthesized AuNPs. Here, we present an alternative biomolecular recognition approach to functionalize cellulose with biotin‐AuNPs that relies on a complex of 2 recognition elements: a ZZ‐CBM3 fusion that combines a carbohydrate‐binding module (CBM) with the ZZ fragment of the staphylococcal protein A and an anti‐biotin antibody. Paper and cellulose microparticles with AuNPs immobilized via the ZZ‐CBM3:anti‐biotin IgG supramolecular complex displayed an intense red color, whereas essentially no color was detected when AuNPs were deposited over the unmodified materials. Scanning electron microscopy analysis revealed a homogeneous distribution of AuNPs when immobilized via ZZ‐CBM3:anti‐biotin IgG complexes and aggregation of AuNPs when deposited over paper, suggesting that color differences are due to interparticle plasmon coupling effects. The approach could be used to functionalize paper substrates and cellulose nanocrystals with AuNPs. More important, however, is the fact that the occurrence of a biomolecular recognition event between the CBM‐immobilized antibody and its specific, AuNP‐conjugated antigen is signaled by red color. This opens up the way for the development of simple and straightforward paper/cellulose‐based tests where detection of a target analyte can be made by direct use of color signaling.     

High-resolution crystal structures of transient intermediates in the phytochrome photocycle

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Adaptive neuro-fuzzy inference system: Estimation of soil aggregates stability

In present study, the capabilities of multiple linear regression (MLR) and adaptive neuro-fuzzy inference system (ANFIS) in developing pedotransfer functions (PTFs) for estimating geometric mean diameter (GMD) and mean weight diameter (MWD), from routine soil properties and combination of routine soil properties and fractal dimension of aggregates were evaluated. For this reason 101 samples were collected form the Northwest of Iran and some their properties such as soil texture, pH, cation exchange capacity (CEC), and organic matter (OM), fractal dimension of aggregates between number-diameter (Dn), mass-diameter (Dmt), and bulk density-diameter (Dmy) were determined and used as an input variables for determining of mean weight diameter (MWD) and geometric mean diameter (GMD) by MLR and ANFIS PTFs. Results showed that the application of fractal dimension of aggregates as a predictor in two methods improved the accuracy of PTFs. As well as, results showed that ANFIS have greater potential for determination of the relationships between soil aggregate stability indices and other soil properties in compared with MLR. Therefore using of adaptive neuro-fuzzy inference system (ANFIS) in developing pedotransfer functions is recommended.     

扎龙湿地芦苇种群不同龄级根茎构件的季节动态

克隆植物根茎具有营养繁殖和扩展种群的功能,也是芽和分株生理整合的通道。根茎构件具有出生、死亡及年龄等种群统计特征,不同龄级根茎的季节动态可以反映根茎的存活和衰老过程。采用单位土体挖掘取样,对扎龙湿地4个生境芦苇种群根茎构件进行野外调查,比较不同龄级根茎长度、生物量和干物质贮量的季节动态。结果表明:7—10月份,1a根茎长度、生物量和干物质贮量均呈指数函数增加,在生长季中后期有一个持续时间较长的生长和物质积累时期。6—10月份,2a、3a根茎长度呈线性函数增加,4—6a根茎长度呈线性函数减少;2—4a根茎生物量和2—5a根茎干物质贮量呈二次函数先减少后增加,5a、6a根茎生物量和6a根茎干物质贮量呈幂函数减少。整个生长期内,根茎长度和根茎生物量均以3a最大,根茎长度以最高的6a最小,根茎生物量以最低的1a最小;根茎干物质储量以5a最大,以最低的1a最小。4个生境芦苇种群根茎长度、生物量和干物质贮量在龄级间的差异及差异序位稳定,在新根茎的产生、老根茎的存活以及根茎寿命与养分消耗和储藏上均具有稳定的生物学特性,不同龄级根茎在种群中的地位和作用以及对种群的贡献不同。     

体外多酶分子机器的现状和最新进展

体外多酶分子机器遵循所设计的多酶催化路径,将若干种纯化或部分纯化的酶元件进行合理的优化与适配,高效地在体外将特定的底物转化为目标化合物。体外多酶分子机器反应系统呈现元件化和模块化的特点,在设计、组装和调控方面具有较高的自由度。近年来,体外多酶分子机器在实现反应过程的精准调控和提高产品得率方面的优势逐渐体现,展示了其在生物制造领域重要的应用潜力。对体外多酶分子机器的相关研究已成为合成生物学的一个重要分支领域,日益受到广泛的关注。文中系统地综述了基于酶元件/模块的体外多酶分子机器的构建策略,以及改善该分子机器中酶元件/模块之间适配性的研究进展,并分析了该生物制造平台的发展前景与挑战。