成年牦牛心室壁微血管的形态特征

用ABS血管铸型、扫描电镜观察法和血管炭素墨水灌注、组织切片法研究了成年牦牛心脏微血管的构筑特征,首次对各级微血管的管径和毛细血管的密度进行了测量,并对成年牦牛心室壁的微血管进行了分类.结果显示:成年牦牛心脏微动脉、毛细血管前微动脉和毛细血管的管径平均值分别为为 78.50±10.23 μm ,16.24±2.27 μm ,6.57±2.28 μm.其管径范围分别为12.5～100 μm,12.50～19.99 μm,6.25～12.50 μm.成年牦牛心脏微动脉一般经3-4级分支才发出毛细血管,其第一、第二、第三和第四级分支的管径平均值分别为87.64±4.87 μm, 69.46±6.67 μm, 48.52±5.77 μm,30.45±5.44 μm.其范围分别为79.55～95 μm, 59.31～79.55 μm,37.50～59.31 μm,19.99～37.50 μm.成年牦牛心肌层毛细血管的密度为2 528±263根/mm2,靠近心外膜处毛细血管的密度为1 864±179根/mm2,心内膜毛细血管的密度为1 636±235根/ mm2.成年牦牛心脏微动脉铸型表面呈典型的"树皮样"结构,偶尔可见卵圆形的内皮细胞核压痕.成年牦牛心脏毛细血管前微动脉铸型形态呈锥状,铸型表面有环行缩窄.成年牦牛心脏的毛细血管铸型表面光滑,有环形缩窄,无内皮细胞核压痕.成年牦牛心肌层中毛细血管与心肌纤维平行,并形成"H"形或"Y"形的广泛吻合,而在靠近心内膜处毛细血管形态较为扭曲,毛细血管多形成平面或立体的吻合.成年牦牛心脏微静脉管径多在300 μm以下,管腔扁且不规则,微静脉铸型呈"树根"样结构.     

亚热带常绿阔叶林冠层附生植物叶片形态结构及生理功能特征的适应性研究

以南亚热带常绿阔叶林林冠层不同部位的4种附生植物:瓜子金(Dischidia chinensis Champ.ex Benth.)、蔓九节(Psychotria serpens L.)、白背瓜馥木(Fissistigma glaucescens (Hance) Merr.)和山萎(Piper hancei Maxim.)为研究对象,比较其叶片解剖结构和光合、蒸腾等生理特性,探讨附生植物叶片形态结构、生理生态功能对冠层不同部位水、热和光资源的适应以及叶片形态结构与生理生态功能的联系.结果表明:着生在冠层上部的两种附生植物瓜子金和蔓九节叶片小而厚(厚度分别为3558±63 μm和217.1±33.1 μm),气孔面积小(分别为185.7±3.7 μm2和225 4±5.2 μm2)且覆盖角质膜,有利于降低蒸腾速率(两者分别为0.17±0.02 mmol H2O和0.34±0.05 mmol H2O),提高水分利用效率WUE(分别为11.35±0.87 μmol CO2/mmolH2O和7.88±1.31 μmol COJmmol H2O),更适应冠层顶部高温、低湿、强光照的生境.这些结构特征却不利于气体交换,会致使瓜子金和蔓九节的光合作用降低(二者最大净光合速率Pmax分别为2.2±0.1 μmol CO2 ·m-2·s-1和3.2±0 4 μmol CO2·m-2·s-1).冠层中下部的白背瓜馥木和山蒌叶片相对较薄(厚度分别为90.8±9.9 μm和114 9±18.2 μm),气孔面积较大(分别为260.6±6.3 μm2和362.5±8.7 μm2),叶肉细胞分化明显,海绵组织排列松散,有利于提高对弱光的利用,增强光合能力(二者Pmax分别为9.5±1.3 μmol CO2·m-2·s-1和7.1±0.8 μmol CO2·m-2·s-1,是瓜子金和蔓九节Pmax的3～4倍),更适应冠层中下部低温、高湿、弱光照环境.这些结构同时会导致白背瓜馥木和山蒌蒸腾速率提高(两者分别为0.67±0.10 mmol H2O和0.74 +0.13 mmol H2O),WUE下降(分别为4.4±1.01μmol CO2/mmol H2O和3.4±0.9 μmol CO2/mmol H2O,仅为瓜子金和蔓九节WUE的30％ -48％).这表明着生在林冠层不同部位的附生植物叶片形态结构特征随着光合有效辐射、温度、湿度等微环境因子的变化表现出显著的差异,并致使各自的生理生态功能发生了相应的适应,是植物适应环境条件的重要表现.     

海城碘泡虫(黏体动物门，黏孢子纲)补充描述及基于18S rDNA系统发育分析

海城碘泡虫原始描述中形态数据较为简单,且存在多个宿主及寄生部位,其有效性有待确定。利用现行主流的黏孢子虫形态特征和基因标记系统分析相结合的分类学方法,对采自太湖棒花鱼鳃丝的海城碘泡虫进行了补充描述。该碘泡虫孢囊呈白色,圆形,大小为(0.6—1.1) mm。成熟孢子正面观近似椭圆形,上端稍尖,侧面观呈纺锤型,孢子长(10.8±0.7) μm (10.1—11.5 μm),孢子宽:(8.1±0.5) μm (7.5—9.0 μm),孢子厚:(5.7±0.4) μm (5.2—9.0 μm);两极囊呈梨形,大小存在细微差别,极囊顶端存在突起,大极囊长:(4.7±0.5) μm (4.8—6.7 μm),宽:(2.5±0.2) μm (3.2—4.3 μm),小极囊长:(4.4±0.2) μm (4.1—4.8 μm),宽:(2.2±0.1) μm (2.0—2.5 μm);极丝盘绕4—5圈。基于18S rDNA序列(GenBank登录号:KY965936)比对分析,该碘泡虫与放射孢子虫Hexactinomyxon type 2相似率最高,为97%。系统发育分析表明,该碘泡虫与Hexactinomyxon type 2、Hexactinomyxon type 1、Hexactinomyxon type SH-2006、Myxobolus pfeifferi、Myxobolus caudatus和Myxobolus squamae聚为独立分支,和其他已报道的黏孢子虫亲缘关系较远。研究在补充了海城碘泡虫形态学、基因标记序列信息基础上,推断了该虫生活史。     

5种温带森林生态系统细根的时间动态及其影响因子

细根(直径≤2 mm)的生长和死亡动态及其影响因子是森林生态系统能量流动和物质循环的重要研究内容,但因受到研究方法的限制而了解甚少.于2010年5-10月采用微根管技术对东北东部山区5种温带森林生态系统的细根生长量(FRP)和死亡量(FRM)进行了动态跟踪测定,并同步测定了土壤温度(Ts)、土壤湿度(Ms)、叶面积指数(LAI)等相关因子.结果表明:不同林型和取样时间的FRP和FRM均差异显著(P＜0.001).杨桦林、硬阔叶林、兴安落叶松林、红松林、蒙古栎林的FRP和FRM分别为:(13.34 ±0.90) μm·cm-2·d-1(平均值±标准误)和(5.02±0.36) μm· cm-2·d-1、(13.04±0.82)μm·cm-2·d-1和(6.85±0.32) μm· cm-2·d-1、(8.74±1.44) μm·cm-2·d-1和(5.05±0.61) μm·cm-2·d-1、(8.02±2.27) μm·cm-2·d-1和(3.88±0.35)μm·em-2·d-1、(7.59±0.82) μm·cm-2·d-1和(3.88±0.61) μm· cm-2·d-1.所有林型生长季期间FRP的时间变化均呈现明显的单峰型,但峰值出现的时间却因林型而异.FRM随生长季的进程而逐渐增加,杨桦林和硬阔叶林FRM在8月初出现峰值,而红松林、兴安落叶松林和蒙古栎林的FRM峰值均出现在生长季末期.Ts、Ms和LAI对FRP和FRM均存在显著的正效应(P＜0.05),3个因子的综合作用对各个林型FRP和FRM变异性的解释率分别达68％和53％以上,表明这些温带森林生态系统细根生长和死亡的时间动态主要受土壤温湿度和叶面积变化的联合影响.     

Hematology of Wild Caught Hoplobatrachus rugulosus in Northern Thailand

The rice field frog Hoplobatrachus rugulosus is an important anuran species found in wetlands throughout Thailand. At present, the hematological parameters of wild populations are unknown. Therefore, hematological and morphological characteristics of peripheral blood cells of wild-caught H. rugulosus were examined. Thirty-three adult frogs(17 male and 16 female frogs) were collected from a natural population in Nan Province, northern Thailand during the wet season of 2014. Blood samples were analyzed by packed cell volume(PCV) and blood cell counts from hemocytometer and Giemsa-stained blood smears. The mean PCV of male frogs(30.70% ± 6.07%) was significantly higher than that of the female frogs(25.09% ± 4.85%). The mean number of lymphocytes and neutrophils also showed significant sex-related differences. Moreover, the morphometric analysis of blood cells revealed dimensions as follows: erythrocytes(17.96 ± 1.44 μm length × 11.50 ± 1.09 μm width), immature erythrocytes(14.91 ± 2.20 μm diameter), thrombocytes(13.93 ± 3.14 μm length × 7.05 ± 1.31 μm width), lymphocytes(11.01 ± 2.69 μm diameter), monocytes(12.04 ± 2.40 μm diameter), neutrophils(12.58 ± 2.08 μm diameter), basophils(13.60 ± 2.17 μm diameter) and eosinophils(12.33 ± 2.95 μm diameter). Overall, the hematological parameters obtained in this study could be regarded as the first report and a crucial baseline data of wild H.rugulosus in Thailand that can be used for monitoring the health status of this anuran.     

务川臭蛙皮肤及指趾组织学特征

务川臭蛙仅分布于贵州省务川县溶洞内,属极危物种.以牛蛙为对照,通过形态解剖学和组织学方法对务川臭蛙的皮肤和吸盘结构进行研究,结果显示,务川臭蛙头部背侧、后肢背侧以及躯干腹侧皮肤总厚度分别为372.50 μm±29.7 μm、453.25 μm ± 13.9 μm及237.92 μm±31.8 μm,各部分皮肤真皮层所占比例分别为(88.86±1.41)％、(90.65 ±0.81)％和(86.59±1.77)％,其中分布着大量的颗粒腺和粘液腺;前后肢每个指(趾)末端的吸盘,腹面有明显的柱状凸起表皮结构,其间有小孔和粘液腺,是务川臭蛙在溶洞壁上攀爬捕食的结构基础.务川臭蛙具有的特殊生理结构,是珍贵的遗传资源,应当加强科学保护.     

狐蝠科3种蝙蝠舌长度及结构比较

为探讨旧大陆食果和食蜜蝙蝠的食性类型不同是否造成其取食器官舌长度及结构的差异,本研究以2种食果蝙蝠犬蝠(Cynopterus sphinx)和棕果蝠(Rousettus leschenaultii)以及1种食蜜蝙蝠长舌果蝠(Eonycteris spelaea)为研究对象,比较了这3个物种间舌的差异.犬蝠、棕果蝠和长舌果蝠伸入直径为2 cm试管的最大舌长度L1(包括伸入试管的吻部和吻部以外的舌长)分别为(29.19±0.52)mm、(35.05±0.82) mm、(49.34±1.64) mm;伸出吻端外部的舌长L3分别为(16.25±0.53)mm、(19.25±0.79) mm、(31.88 ± 1.56) mm;与体重转换后的最大舌长度,即转换L1分别为(8.57±0.17) mm/g1/3、(7.90 ±0.27) mm/g1/3、(12.41 ±0.40) mm/g1/3;与体重转换后的伸出吻端外部的舌长,即转换L3分别为(4.77±0.16) mm/g1/3、(4.34±0.22) mm/g1/3、(8.01 ±0.38) mm/g1/3;与体重转换后的解剖舌长分别为(5.56 ±0.16) mm/g1/3、(5.35 ±0.14) mm/g1/3、(6.65±0.38)mm/g1/3.此5个参数种间比较均差异显著,食蜜类的长舌果蝠的5个参数均显著长于食果类犬蝠和棕果蝠的相应参数.通过比较3种蝙蝠的舌结构发现,长舌果蝠的舌尖尖细且具有毛刷状丝状乳头结构,舌面及两侧凹槽较多;犬蝠和棕果蝠的舌尖钝圆,舌面乳头和凹槽较少而平缓.本文结果表明,旧大陆食蜜蝙蝠与食果蝙蝠在舌长度和舌结构上存在明显差异,可能与捕食行为的差异有关.     

3种淡水肉食性鱼类胰脏及胰液导管系统的组织学比较

应用解剖学和组织学技术对翘嘴鲌Culter alburnus、大鳍鳠Mystus macropterus和斑鳜Siniperca scherzeri的胰脏进行观察.结果表明,翘嘴鲌和大鳍鳠胰脏为弥漫混合型(suffusion-mix type),斑鳜为散布致密型(disperse-dense type).翘嘴鲌和大鳍鳠胰脏被膜较薄,厚度分别为4.33 μm±1.12 μm和7.24 μm±3.69 μm,而斑鳜胰脏被膜较厚,为50.96 μm±11.02 μm.翘嘴鲌胰小叶不明显,大鳍鳠非常明显,斑鳜比较明显.3种鱼胰腺细胞体积较大,核仁大而明显,细胞质内均有大量深色网络状或羽毛状结构和颗粒物质分布;胰脏内胰液运输管道均由闰管、小叶内导管、小叶间导管和集合导管组成,其中集合导管结构比较典型,管壁分为3层,即内层由单层柱状上皮和固有膜组成,中层由平滑肌细胞组成,外层由结缔组织组成.翘嘴鲌胰岛相对较小和分散,单位面积数量较少;大鳍鳠胰岛相对较大和分散,单位面积数量也较少;斑鳜胰岛最大,相对集中,单位面积数量较多.3种鱼胰岛外均被结缔组织被膜,结缔组织伸入胰岛内将胰岛细胞分隔为细胞小团或细胞索;G-醛复红染色仅观察到A细胞和B细胞,胞质颗粒分别被染成紫红色和黄色;B细胞占优势.     

尖形碘泡虫(黏体门: 碘泡虫科)的重描述及其分子系统学研究

研究基于形态和分子信息重描述了寄生于嘉陵江重庆段鲫(Carassius auratus Linnaeus)鳃部和胆囊的尖形碘泡虫(Myxobolus acutus Wu and Chen, 1987), 并获得了该虫体的18S rDNA和ITS1 rDNA序列。尖形碘泡虫成熟孢子壳面观呈梨形, 前端稍尖, 后端钝圆, 缝面观呈宽纺锤形。孢子长(13.6±0.9) μm [(11.4—15.3) μm], 宽(10.2±0.9) μm [(7.5—12.8) μm], 厚(7.6±0.6) μm [(6.9—8.3) μm]。两梨形极囊开口处紧靠并位于孢子前端, 极囊大小不等, 大极囊长(6.2±0.4) μm [(5.1—7.5) μm], 宽(3.8±0.4) μm [(2.8—4.7) μm], 极丝盘绕5—8圈, 小极囊长(2.7±0.4) μm [(1.7—3.7) μm], 宽(1.4±0.2) μm [(0.9—1.9) μm], 极丝盘绕2—3圈。基于18S rDNA为分子标记的系统发育分析显示: 尖形碘泡虫与中华单极虫(Thelohanellus sinensis)有最近的亲缘关系, 两物种形成的进化支与贝壳碘泡虫(M. musseliusae)、苍梧碘泡虫(M. tsangwuensis)和鳃基碘泡虫(M. basilamellaris)形成的进化支呈姐妹群关系。通过系统发育与寄生部位关系的分析结果推测, 尖形碘泡虫的初始寄生部位可能为鳃, 而胆囊则是该物种后来适应的新的寄生部位。     

鲤肠道寄生岳阳碘泡虫新种的形态特征及系统发育分析

在洞庭湖岳阳地区开展鱼类寄生虫调查中,发现一种寄生于鲤Cyprinus carpio L.肠道的黏孢子虫。该黏孢子虫的孢囊呈白色,椭圆形,大小为(1.0±0.2) mm (0.8—1.2 mm)。成熟孢子具有壳瓣,壳面观近似圆形,后端有4—6个“V”形褶皱;缝面观呈纺锤形,缝脊直而粗;孢质均匀,含有一个嗜碘泡;孢子长(9.8±0.6) μm (9.6—10.0 μm),孢子宽(8.2±0.3) μm (8.0—8.5μm),孢子厚(7.3±0.1) μm (7.0—7.5 μm);2个极囊梨形,位于孢子顶端,大小相等,呈“八”字形;极囊长(4.4±0.4) μm (3.8—5.1 μm),宽(2.7±0.2) μm (2.2—3.2 μm),极丝4—5圈。该黏孢子虫与肠膜碘泡虫、丑陋圆形碘泡形态特征非常相似,但其极囊/孢子小于1/2;与文献已报道的鲤肠道寄生北京碘泡虫和鲤肠碘泡虫相比较,其在孢子形态、孢子和极囊大小方面分别存在明显差异。基于该黏孢子虫18S rDNA基因序列(GenBank登录号KY203795)比对分析,该黏孢子虫与山东碘泡虫相似率最高,仅为96%。系统发育分析发现,该黏孢子虫与山东碘泡虫、倪李碘泡虫、住心碘泡虫、Myxobolus encephalicus、Sphaerospora molnari、多涅茨尾孢虫和Henneguya zikaweiensis聚为独立分支,和其他已报道的黏孢子虫亲缘关系较远。综合形态学和18S rDNA基因序列数据,文章报道的鲤肠道寄生黏孢子虫为碘泡虫属一新物种,将其命名为岳阳碘泡虫。     

Contact patterns between helices and strands of sheet define protein folding patterns

Comparing and classifying protein folding patterns allows organizing the known structures and enumerating possible protein structural patterns including those not yet observed. We capture the essence of protein folding patterns in a concise tableau representation based on the order and contact patterns of secondary structures: helices and strands of sheet. The tableaux are intelligible to both humans and computers. They provide a database, derived from the Protein Data Bank, mineable in studies of protein architecture. Using this database, we have: (i) determined statistical properties of secondary structure contacts in an unbiased set of protein domains from ASTRAL, (ii) observed that in 98% of cases, the tableau is a faithful representation of the folding pattern as classified in SCOP, (iii) demonstrated that to a large extent the local structure of proteins indicates their complete folding topology, and (iv) studied the use of the representation for fold identification.     

Conformations of cysteine disulfides of peptide toxins: Advantage of differentiating forward and reverse asymmetric disulfide conformers

Conformations of cysteine disulfides were analyzed in X-ray, nuclear magnetic resonance (NMR), and co-crystal structures of peptide toxins retrieved from Protein Data Bank. The parameters side chain torsional angles, disulfide strain energy, interatomic Cα/Cβ distances, and Ramachandran angles were used as probes to derive conformational features of cysteine disulfides. Schmidt, Ho, and Hogg (2006 Schmidt, B., Ho, L., &; Hogg, P. J. (2006). Allosteric disulfide bonds. Biochemistry, 45, 7429–7433.[Crossref], [PubMed], [Web of Science ®] , [Google Scholar]) Allosteric disulfide bonds. Biochemistry, 45, 7429–7433 scheme was adapted to classify the disulfide conformations of peptide toxins. Anomalies were observed while treating “forward” and “reverse” asymmetric disulfide conformers as same disulfide conformation in peptide toxins. Thus, new scheme was proposed to classify “forward” and “reverse” asymmetric disulfide conformers separately. Total available conformers space for classification of toxins disulfides is 32. Interestingly, all 32 disulfide conformations are observed in peptide toxins. –LHSpiral is predominant disulfide conformation of peptide toxins. Significant variations were observed in population of occurrence of disulfide conformers, disulfide strain energy, and distribution of D_Cα-Cα and D_Cβ-Cβ values between X-ray, NMR, and co-crystal structures of peptide toxins. The observed differences in conformations of disulfides of same peptide toxins between different states were used as platform to demonstrate advantage of differentiating forward and reverse asymmetric disulfide conformers. Newly proposed scheme allows accurate representation of true conformational diversity of disulfides between X-ray and NMR structures of same peptide toxins. Newly proposed scheme also permits to derive additional structural information from nomenclature which was illustrated by comparing conformations of disulfides between unbound and bound form of toxin with channel/receptor. The results will be of interest for growing field of structural venomics and conformational analysis of peptide/protein disulfides.

Communicated by Ramaswamy H. Sarma     

Definition of a New Information-Based Per-Residue Quality Parameter

For biomolecular NMR structures typically only a poor correspondence is observed between statistics derived from the experimental input data and structural quality indicators obtained from the structure ensembles. Here, we investigate the relationship between the amount of available NMR data and structure quality. By generating datasets with a predetermined information content and evaluating the quality of the resulting structure ensembles we show that there is, in contrast to previous findings, a linear relation between the information contained in experimental data and structural quality. From this relation, a new quality parameter is derived that provides direct insight, on a per-residue basis, into the extent to which structural quality is governed by the experimental input data.     

The cluster structure of barley amylopectins of different genetic backgrounds

The unit chains of amylopectin are organized into clusters. In this study, the cluster structure was analysed in detail in four different genotypes of barley, of which two possessed the amo1 genetic background. Amylose content of the barley starches differed from 0 to 32.6%. Isolated amylopectin was hydrolysed with α-amylase from Bacillus subtilis into domains, defined as groups of clusters, which were size-fractionated by methanol. The domain fractions were further treated with α-amylase to release single clusters. Amylopectin, domains and clusters were subsequently treated with phosphorylase and β-amylase to produce φ,β-limit dextrins and the detailed internal structures of these different structure levels were investigated. Analysis was performed with gel-permeation and anion-exchange chromatography. Equal amount of A-chains were detected in all barleys, but the distribution of B-chains differed. At least two types of domain structures were identified in all four barley varieties. Large domains were built up by large clusters and small domains by small clusters. In all four barley samples the number of long chains was small suggesting that shorter chains with a degree of polymerization of 25-35 also are involved in the interconnection of clusters. The cluster structure of the amylopectin correlated with the genetic background. The two barley samples with amo1 genetic background possessed a more dense structure. Internal chain lengths in these two barleys were shorter resulting in larger domains built up by larger clusters.     

Quantitative Analysis of the Conservation of the Tertiary Structure of Protein Segments

The publication of the crystallographic structure of calmodulin protein has offered an example leading us to believe that it is possible for many protein sequence segments to exhibit multiple 3D structures referred to as multi-structural segments. To this end, this paper presents statistical analysis of uniqueness of the 3D-structure of all possible protein sequence segments stored in the Protein Data Bank (PDB, Jan. of 2003, release 103) that occur at least twice and whose lengths are greater than 10 amino acids (AAs). We refined the set of segments by choosing only those that are not parts of longer segments, which resulted in 9297 segments called a sponge set. By adding 8197 signature segments, which occur uniquely in the PDB, into the sponge set we have generated a benchmark set. Statistical analysis of the sponge set demonstrates that rotating, missing and disarranging operations described in the text, result in the segments becoming multi-structural. It turns out that missing segments do not exhibit a change of shape in the 3D-structure of a multi-structural segment. We use the root mean square distance for unit vector sequence (URMSD) as an improved measure to describe the characteristics of hinge rotations, missing, and disarranging segments. We estimated the rate of occurrence for rotating and disarranging segments in the sponge set and divided it by the number of sequences in the benchmark set which is found to be less than 0.85%. Since two of the structure changing operations concern negligible number of segment and the third one is found not to have impact on the structure, we conclude that the 3D-structure of proteins is conserved statistically for more than 98% of the segments. At the same time, the remaining 2% of the sequences may pose problems for the sequence alignment based structure prediction methods.*Jishou Ruan research was supported by Liuhui Center for Applied Mathematics, China-Canada exchange program administered by MITACS and NSFC (10271061). ^#Ke Chen and Lukasz A. Kurgan research was partially supported by NSERC Canada. ^†Jack A. Tuszynkski research has been supported by MITACS, NSERC Canada and the Allard Foundation.     

GeneticStudio: a suite of programs for spatial analysis of genetic-marker data

The analysis of genetic marker data is increasingly being conducted in the context of the spatial arrangement of strata (e.g. populations) necessitating a more flexible set of analysis tools. GeneticStudio consists of four interacting programs: (i) Geno a spreadsheet-like interface for the analysis of spatially explicit marker-based genetic variation; (ii) Graph software for the analysis of Population Graph and network topologies, (iii) Manteller, a general purpose for matrix analysis program; and (iv) SNPFinder, a program for identifying single nucleotide polymorphisms. The GeneticStudio suite is available as source code as well as binaries for OSX and Windows and is distributed under the GNU General Public License.     

TASSER-based refinement of NMR structures

The TASSER structure prediction algorithm is employed to investigate whether NMR structures can be moved closer to their corresponding X-ray counterparts by automatic refinement procedures. The benchmark protein dataset includes 61 nonhomologous proteins whose structures have been determined by both NMR and X-ray experiments. Interestingly, by starting from NMR structures, the majority (79%) of TASSER refined models show a structural shift toward their X-ray structures. On average, the TASSER refined models have a root-mean-square-deviation (RMSD) from the X-ray structure of 1.785 A (1.556 A) over the entire chain (aligned region), while the average RMSD between NMR and X-ray structures (RMSD(NMR_X-ray)) is 2.080 A (1.731 A). For all proteins having a RMSD(NMR_X-ray) >2 A, the TASSER refined structures show consistent improvement. However, for the 34 proteins with a RMSD(NMR_X-ray) <2 A, there are only 21 cases (60%) where the TASSER model is closer to the X-ray structure than NMR, which may be due to the inherent resolution of TASSER. We also compare the TASSER models with 12 NMR models in the RECOORD database that have been recalculated recently by Nederveen et al. from original NMR restraints using the newest molecular dynamics tools. In 8 of 12 cases, TASSER models show a smaller RMSD to X-ray structures; in 3 of 12 cases, where RMSD(NMR_X-ray) <1 A, RECOORD does better than TASSER. These results suggest that TASSER can be a useful tool to improve the quality of NMR structures.     

Using multiple templates to improve quality of homology models in automated homology modeling

When researchers build high-quality models of protein structure from sequence homology, it is today common to use several alternative target-template alignments. Several methods can, at least in theory, utilize information from multiple templates, and many examples of improved model quality have been reported. However, to our knowledge, thus far no study has shown that automatic inclusion of multiple alignments is guaranteed to improve models without artifacts. Here, we have carried out a systematic investigation of the potential of multiple templates to improving homology model quality. We have used test sets consisting of targets from both recent CASP experiments and a larger reference set. In addition to Modeller and Nest, a new method (Pfrag) for multiple template-based modeling is used, based on the segment-matching algorithm from Levitt's SegMod program. Our results show that all programs can produce multi-template models better than any of the single-template models, but a large part of the improvement is simply due to extension of the models. Most of the remaining improved cases were produced by Modeller. The most important factor is the existence of high-quality single-sequence input alignments. Because of the existence of models that are worse than any of the top single-template models, the average model quality does not improve significantly. However, by ranking models with a model quality assessment program such as ProQ, the average quality is improved by approximately 5% in the CASP7 test set.