Representing and comparing protein folds and fold families using three‐dimensional shape‐density representations

The question of how best to compare and classify the (three‐dimensional) structures of proteins is one of the most important unsolved problems in computational biology. To help tackle this problem, we have developed a novel shape‐density superposition algorithm called 3D‐Blast which represents and superposes the shapes of protein backbone folds using the spherical polar Fourier correlation technique originally developed by us for protein docking. The utility of this approach is compared with several well‐known protein structure alignment algorithms using receiver‐operator‐characteristic plots of queries against the “gold standard” CATH database. Despite being completely independent of protein sequences and using no information about the internal geometry of proteins, our results from searching the CATH database show that 3D‐Blast is highly competitive compared to current state‐of‐the‐art protein structure alignment algorithms. A novel and potentially very useful feature of our approach is that it allows an average or “consensus” fold to be calculated easily for a given group of protein structures. We find that using consensus shapes to represent entire fold families also gives very good database query performance. We propose that using the notion of consensus fold shapes could provide a powerful new way to index existing protein structure databases, and that it offers an objective way to cluster and classify all of the currently known folds in the protein universe. Proteins 2012. © 2011 Wiley Periodicals, Inc.     

Camps 2.0: exploring the sequence and structure space of prokaryotic, eukaryotic, and viral membrane proteins

Structural bioinformatics of membrane proteins is still in its infancy, and the picture of their fold space is only beginning to emerge. Because only a handful of three-dimensional structures are available, sequence comparison and structure prediction remain the main tools for investigating sequence-structure relationships in membrane protein families. Here we present a comprehensive analysis of the structural families corresponding to α-helical membrane proteins with at least three transmembrane helices. The new version of our CAMPS database (CAMPS 2.0) covers nearly 1300 eukaryotic, prokaryotic, and viral genomes. Using an advanced classification procedure, which is based on high-order hidden Markov models and considers both sequence similarity as well as the number of transmembrane helices and loop lengths, we identified 1353 structurally homogeneous clusters roughly corresponding to membrane protein folds. Only 53 clusters are associated with experimentally determined three-dimensional structures, and for these clusters CAMPS is in reasonable agreement with structure-based classification approaches such as SCOP and CATH. We therefore estimate that ～1300 structures would need to be determined to provide a sufficient structural coverage of polytopic membrane proteins. CAMPS 2.0 is available at http://webclu.bio.wzw.tum.de/CAMPS2.0/.     

蛋白质-蛋白质分子对接方法中分子柔性处理与近天然结构筛选的研究

蛋白质-蛋白质分子对接方法是研究蛋白质分子间相互作用与识别的重要理论方法。该方法主要涉及复合物结合模式的构象搜索和近天然结构的筛选两个问题。在构象搜索中,分子柔性的处理是重点也是难点,围绕这一问题,近年来提出了许多新的方法。针对近天然结构的筛选问题,目前主要采用三种解决策略:结合位点信息的利用、相似结构的聚类和打分函数对结构的评价。本文围绕以上问题,就国内外研究进展和本研究小组的工作作详细的综述,并对进一步的研究方向进行了展望。     

半干旱黄土区植被恢复对土壤团聚体稳定性及抗侵蚀能力的影响

土壤水稳性团聚体强烈影响土壤过程和功能,是反映土壤质量和土壤抗侵蚀能力的重要指标。为探究半干旱黄土区植被恢复对土壤抗侵蚀能力的影响,以甘肃省定西市龙滩流域为研究区,选取3种恢复方式（天然荒草、自然恢复、人工恢复）7种植被类型（大针茅草地、长芒草草地、赖草草地、苜蓿草地、柠条灌丛、山杏林以及油松林）为研究对象,通过测定0-20 cm、20-40 cm和40-60 cm土壤水稳性团聚体,分析土壤团聚体组成、稳定性及抗侵蚀能力特征。结果表明：1）不同恢复方式不同植被类型间土壤水稳性团聚体稳定性差异显著（P<0.05）,自然恢复方式的土壤水稳性团聚体平均重量直径显著高于天然荒草和人工恢复方式,且7种植被类型土壤大团聚体质量百分比均在67.97%-90.12%之间;人工恢复方式土壤水稳性团聚体稳定性较差,其中油松林稳定性最差。2）土壤团聚体破坏率和土壤抗侵蚀能力均表现出自然恢复方式更有利于土壤结构稳定性的提高。3）土壤水稳性大团聚体含量越高,土壤团聚体越稳定,土壤结构稳定性就越好;平均重量直径与土壤可蚀性因子K值呈极显著性负相关（P<0.01）。本研究结果表明自然恢复方式能够显著提高土壤团聚体的稳定性,从而提升土壤的抗侵蚀能力,建议当地在未来植被恢复规划中采取自然恢复方式更有利于生态恢复的有效进行。     

武汉市湿地公园昆虫群落多样性及季节动态研究

本文系统调查了武汉市解放公园和月湖公园人工湿地区不同季节、不同植物类群昆虫群落多样性,共采集昆虫标本7313头,隶属于13目、81科、198种。群落特征研究结果显示9月为昆虫多样性最高的月份,Shan-non-Wiener指数分别为解放公园4.7949,月湖公园4.4611;昆虫群落的季节变化情况是温度升高,多样性指数升高,但温度过高会抑制昆虫多样性;不同植物种类间昆虫多样性差别很大,种类极不相似,昆虫群落多样性最高的植物群落是千屈菜。     

Poly(ethylene glycol) cross-linked hemoglobin with antioxidant enzymes protects pancreatic islets from hypoxic and free radical stress and extends islet functionality

The objective of this study was to investigate the efficiency of multifunctional poly(ethylene glycol)-based hemoglobin conjugates crosslinked with antioxidant enzymes for their ability to protect an oxygen carrier (hemoglobin) and insulin secreting islets from the combination of hypoxic and free radical stress under simulated transplantation conditions. In this study, RINm5F cells and isolated pancreatic islets were challenged with oxidants (H(2)O(2) or xanthine and xanthine oxidase) and incubated with conjugates (hemoglobin-hemoglobin or superoxide dismutase-catalase-hemoglobin) in normoxia (21% oxygen) or hypoxia (6% or 1% oxygen). Hemoglobin protection, intracellular free radical activity and cell viability in RINm5F cells measured by methemoglobin, dichlorofluorescein-diacetate, and (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide) assay, respectively, showed that cells were better protected by conjugates containing antioxidant enzymes. Insulin secretion from islets and qualitative confocal evaluation of viability showed beta cells were protected by conjugates containing antioxidant enzymes when exposed to induced stress. Our study suggested that antioxidant enzymes play a significant role in hemoglobin protection and thus extended cell protection.     

The Effect of Spatial Structure of Pasture Tree Cover on Avian Frugivores in Eastern Amazonia

The movement of frugivores between remnant forests and successional areas is vital for tropical forest tree species to colonize successional habitats. The response of these species to the spatial structure of pasture tree cover is largely unknown. We studied avian frugivores that were found in primary forest edges and large pastures in eastern Amazonia, Brazil. We determined how the small‐scale spatial structure of pasture trees at forest edges affects five response variables: bird presence, visitation rate, duration of visit, species richness, and an index accounting for species’ level of frugivory and abundance in forests. We used hierarchical linear models to estimate the effect of four predictor variables on response variables: (1) clustering of pasture trees; (2) percent canopy cover of pasture trees; (3) distance of pasture tree to forest edge; and (4) tree crown area. The study species, many of which are widely distributed in the Neotropics, were generally insensitive to percent cover and clustering of trees. Frugivore visitation to individual trees remained constant as cover increased. Visitation was positively correlated with focal tree distance to forest edge and crown area. The positive relationship between distance and visitation rates may be due to the increased abundance of some resource further from forests. If pastures were abandoned the distance from forest edges would not likely limit frugivore visitation and seed deposition under large pasture trees in our study (i.e., up to 200 m distant).     

真藓属（Bryum Hedw.）蒴齿形态特征及其分类学意义

通过光学显微镜和扫描电子显微镜观察了中国产真藓属（Bryum Hedw.）12种植物蒴齿的形态特征。结果显示,根据真藓属齿片的曲向可以分为近直立、齿片伸入齿条间和齿片向外反曲等3种类型。根据齿毛的有无,也可分为3个类群。同时利用STATISTICA 6.0统计软件对12种真藓属植物进行聚类分析及主成分分析。研究结果显示,齿片的曲向类型、齿毛是否发育等形态特征可作为真藓属植物种间的分类依据,为藓类植物蒴齿形态特征与分类和系统进化关系的研究提供了新的资料。