甘肃东大山自然保护区夏季岩羊种群的初步调查

2004年7月和8月,通过样线调查、野外直接跟踪观察和瞬间取样的方法,首次对东大山自然保护区的岩羊种群进行了初步调查。东大山自然保护区夏季岩羊以小群为主,在观察到的720只岩羊中,719只组成了50个群,最大群82只,最小群2只,平均为14.38只,2～10只群占总群数的66%;雌性群占30%,雄性群占26%,混合群占44%,整个东大山的岩羊密度为34.8±19.2只/km2;岩羊的雌雄性比为1∶0.63,成年雌体、亚成体和幼体之比是1∶0.4∶0.24。研究结果表明,东大山近几年的狩猎对岩羊的种群并未造成大的影响。     

贺兰山岩羊的生命表和春夏季节社群结构的研究

利用６２架自然死亡的雄性岩羊角,初步探讨了贺兰山岩羊种群的生命表、年龄结构和存活曲线：贺兰山岩羊５．５龄和９．５龄死亡率明显增大,为两个死亡高峰;有一半以上的雄性个体年龄超过８岁;存活曲线基本接近Ａ型．此外,将春季调查的１３９群８０８只岩羊和夏季调查的６７群４４８只岩羊的社群结构进行比较,发现春季与夏季的雌幼比相似,雌雄比都是雄性大于雌性;春、夏季社群大小变化不显（Ｐ＞０．０５）,并且贺兰山岩羊     

春季岩羊种群生态学特征的初步研究

本文通过对贺兰山春季岩羊的研究得出,贺兰山的岩羊为晨昏性活动动物,两个活动高峰分别在５００～９００和１７００～２０００。在春季,岩羊群主要以小群为主,且主要是混合群,平均群大小为５．６头;整个贺兰山的岩羊密度为３．６头／ｋｍ２;岩羊的雌雄性比为１１．３６,并指出目前偷猎仍然影响着种群的性比;雄性岩羊的自然死亡年龄在６．５～１０．５岁,其中以９．５岁是其自然死亡的高峰时期。     

青海省玉树、果洛州岩羊的种群结构及生命表初探

本文根据野外发现的4470只岩羊,就其栖息地、种群大小和年龄组成进行分析。在已分辨性别的2168只岩羊中,成年雌雄性比为1：0.5。此外,我们还利用54架自然死亡的雄性岩羊头骨,初步探讨年龄分布、存活曲线和生命表。     

竹巴笼矮岩羊昼间行为节律和时间分配

2008年11月中旬至2009年1月中旬和2009年3月至8月,采用瞬时扫描取样法和目标取样法在竹巴笼自然保护区对矮岩羊的昼间行为节律和时间分配进行了研究,结果表明:矮岩羊的昼间行为活动有明显的节律性,活动高峰出现的时间与矮岩羊昼间取食高峰时间基本一致。取食和卧息是最主要的行为方式,分别占总观察频次的53.83%和27.76%,频次较少的是站立和移动,分别占总观察频次的9.93%和8.24%,其它行为所占频次最少,只有0.24%,昼间2个取食高峰(9:00-11:00, 17:00-19:00)和1个卧息高峰(11:00-16:00),呈现出取食-休息-取食的规律。Kruskal-Wallis H 检验表明,季节因素对矮岩羊取食(P <0.05)、卧息(P <0.05)和其它行为(P <0.05)所占时间影响显著,而对移动(P >0.05)和站立(P >0.05)行为影响不显著。各年龄段之间其它行为所占的时间比例差异显著(P<0.05),而取食(P>0.05)、移动(P>0.05)、卧息(P>0.05)和站立(P>0.05)所占时间比例差异不显著;对比分析不同性别矮岩羊昼间行为时间分配差异,雌性的取食、移动和卧息的时间略高于雄性,而站立和其他行为时间低于雄性;Mann-Whitney U 检验对不同性别矮岩羊昼间的各种行为差异进行分析表明:性别因素对矮岩羊昼间时间分配和行为节律产生一定程度的影响,但差异不显著(P>0.05)。     

贺兰山岩羊种群生态及保护

作者于1994年11月、1995年7～8月和9～10月在宁夏贺兰山对岩羊种群生态进行了初步研究,发现贺兰山岩羊的最适生态分布见于海拔1801～2000 m,岩羊每天有两个活动高峰,分别为早晨和下午。在观察到的448只岩羊中,发现平均群大小为5.5只,2～8只为一群的占总数的70.8%。岩羊种群的雌雄性比为1∶1.2,雌幼比为1∶0.44,贺兰山的岩羊处于增长趋势。目前在贺兰山,影响岩羊生存的主要因素是偷猎、人为干扰和家畜竞争。     

矮岩羊夏季活动节律、时间分配和集群行为

采用扫描取样法（每隔10 min进行一次扫描纪录,记录时间为5 min）对36只矮岩羊夏季昼间节律与时间分配进行了观察和研究,将矮岩羊行为划分为取食、移动、站立、卧息和其他行为等5类。结果表明,矮岩羊在夏季有3个取食高峰（6：00－9：00、10：00－11：00和16：00－20：00）;1个卧息高峰（11：00－15：00）。在时间分配上,用于取食的时间最多（30.14±3.32）%,其次是卧息（26.44±3.59）%,站立（24.90±4.27）%,移动（15.73±1.26）%,而用于其他行为的时间,仅占（2.82±1.00）%。通过不同个体的比较,发现成年雄性用于取食和站立的时间最多,幼体用于移动和其他行为的时间最多,成年雌性用于卧息的时间最多。在矮岩羊集群方面,其集群类型有：混合群、母仔群、雄性群、雌性群和独羊,在夏季集群平均大小为（7.81±8.42）只,2~8只的羊群,占总群数的54.05%;不同集群类型的大小差异极显著（χ2=13.197,d&#402;=3,P=0.004）,混合群群体最大,而雄性群最小;雌雄比为1∶0.54,雌幼比为1∶0.26,成幼比为1∶0.17。这些都说明矮岩羊这类独特的行为和种群特征是长期适应金沙江干热河谷的结果。     

丰容对圈养雌性岩羊活动时间分配的影响

为了探究环境丰容和食物丰容对岩羊行为和活动节律的影响,于2017年3月—7月,以上海动物园的5只雌性岩羊(Pseudois nayaur)为研究对象,设计环境丰容和食物丰容试验,利用瞬时扫描法对岩羊进行行为学观察,分析岩羊丰容前后昼间行为的变化。结果表明:经过环境丰容,岩羊的运动行为和反刍行为显著增加,卧息行为和其他行为显著减少,取食行为无明显变化。在环境丰容基础上,开展食物丰容后,运动行为明显减少,取食行为明显增加。卧息行为有所减少、反刍行为和其他行为有所增加,但变化均不明显。丰容后岩羊的昼间活动节律也发生了变化。取食行为呈现2个高峰期(8:00—11:00和15:00—18:00),取食行为普遍提高;运动行为在13:30—17:30时段较丰容前提前一个小时左右发生;卧息行为有相似的波动规律,但丰容后其昼间发生频次在16:00之前均降低;反刍行为波动最大,呈现出明显的2个高峰期(6:00—9:00和10:00—15:00)。试验表明,在进行环境和食物丰容后,岩羊的活动增加,优化了时间分配,福利状况得到了有效改善。     

冬春季矮岩羊集群特征比较

2007年10月至12月、2008年11月中旬至2009年1月中旬和2009年3月至5月,采用样线法对四川竹巴笼自然保护区矮岩羊冬春季的集群特征进行了研究,春季共观察到73群451只矮岩羊,冬季共观察到170群1036只矮岩羊。发现春季平均群大小为6.18±5.186,最大群34只;冬季平均集群大小为6.65±4.564,最大群24只;春冬两季矮岩羊集群大小季节性变化不显著(P0.05)。在观察到的矮岩羊中,冬春两季矮岩羊集群都以混合群为主,分别占57.20%和45.20%;与春季相比,冬季混合群和独羊出现频率增高,而春季雌性群和母仔群增多;2-8只的集群冬季109群,春季56群,分别占总群数的64.12%和76.71%;9只以上的集群冬季46群,春季15群,分别占总群数的20.06%和20.55%。说明矮岩羊主要以2-8只的小群为主。冬季雌雄比为1∶0.64;雌幼比为1∶0.77;春季雌雄比为1∶0.72;雌幼比为1∶0.81。     

发情交配期贺兰山岩羊的集群特征

2003 年和2004 年的11 ～12 月,采用样线法和全事件取样法研究了贺兰山岩羊的集群特征。共观察到岩羊715 群,共计2 473只。发情前期平均群大小3.5±2.8 只(n = 241),发情期平均群大小3.4±3.2 只(n =297)。发情前期与发情期雄性群、雌性群、雌雄群、混合群及母子群大小间均无显著差异。发情前期到发情期群类型组成差异极显著,发情期雌雄群、混合群和独羊比例显著上升;雄性群、雌性群和母子群比例显著下降。发情前期到发情期,雄性岩羊在雄性群、雌雄群、混合群和独羊中的分布差异极显著,成年雌性岩羊在雌性群、雌雄群、混合群、母子群和独羊中的分布差异极显著。发情期4 个年龄等级雄性在雄性群、雌雄群、混合群和独羊中分布差异极显著,4 个年龄等级雄性岩羊都倾向分布于混合群。
     

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.     

Extended secondary structures in proteins

Supersecondary structures of proteins have been systematically searched and classified, but not enough attention has been devoted to such large edifices beyond the basic identification of secondary structures. The objective of the present study is to show that the association of secondary structures that share some of their backbone residues is a commonplace in globular proteins, and that such deeper fusion of secondary structures, namely extended secondary structures (ESSs), helps stabilize the original secondary structures and the resulting tertiary structures. For statistical purposes, a set of 163 proteins from the protein databank was randomly selected and a few specific cases are structurally analyzed and characterized in more detail. The results point that about 30% of the residues from each protein, on average, participate in ESS. Alternatively, for the specific cases considered, our results were based on the secondary structures produced after extensive Molecular Dynamics simulation of a protein–aqueous solvent system. Based on the very small width of the time distribution of the root mean squared deviations, between the ESS taken along the simulation and the ESS from the mean structure of the protein, for each ESS, we conclude that the ESSs significantly increase the conformational stability by forming very stable aggregates. The ubiquity and specificity of the ESS suggest that the role they play in the structure of proteins, including the domains formation, deserves to be thoroughly investigated.     

Protein loop structure prediction with flexible stem geometries

The structure prediction of loops with flexible stem residues is addressed in this article. While the secondary structure of the stem residues is assumed to be known, the geometry of the protein into which the loop must fit is considered to be unknown in our methodology. As a consequence, the compatibility of the loop with the remainder of the protein is not used as a criterion to reject loop decoys. The loop structure prediction with flexible stems is more difficult than fitting loops into a known protein structure in that a larger conformational space has to be covered. The main focus of the study is to assess the precision of loop structure prediction if no information on the protein geometry is available. The proposed approach is based on (1) dihedral angle sampling, (2) structure optimization by energy minimization with a physically based energy function, (3) clustering, and (4) a comparison of strategies for the selection of loops identified in (3). Steps (1) and (2) have similarities to previous approaches to loop structure prediction with fixed stems. Step (3) is based on a new iterative approach to clustering that is tailored for the loop structure prediction problem with flexible stems. In this new approach, clustering is not only used to identify conformers that are likely to be close to the native structure, but clustering is also employed to identify far-from-native decoys. By discarding these decoys iteratively, the overall quality of the ensemble and the loop structure prediction is improved. Step (4) provides a comparative study of criteria for loop selection based on energy, colony energy, cluster density, and a hybrid criterion introduced here. The proposed method is tested on a large set of 3215 loops from proteins in the Pdb-Select25 set and to 179 loops from proteins from the Casp6 experiment.     

Sequence-similar, structure-dissimilar protein pairs in the PDB

It is often assumed that in the Protein Data Bank (PDB), two proteins with similar sequences will also have similar structures. Accordingly, it has proved useful to develop subsets of the PDB from which "redundant" structures have been removed, based on a sequence-based criterion for similarity. Similarly, when predicting protein structure using homology modeling, if a template structure for modeling a target sequence is selected by sequence alone, this implicitly assumes that all sequence-similar templates are equivalent. Here, we show that this assumption is often not correct and that standard approaches to create subsets of the PDB can lead to the loss of structurally and functionally important information. We have carried out sequence-based structural superpositions and geometry-based structural alignments of a large number of protein pairs to determine the extent to which sequence similarity ensures structural similarity. We find many examples where two proteins that are similar in sequence have structures that differ significantly from one another. The source of the structural differences usually has a functional basis. The number of such proteins pairs that are identified and the magnitude of the dissimilarity depend on the approach that is used to calculate the differences; in particular sequence-based structure superpositioning will identify a larger number of structurally dissimilar pairs than geometry-based structural alignments. When two sequences can be aligned in a statistically meaningful way, sequence-based structural superpositioning provides a meaningful measure of structural differences. This approach and geometry-based structure alignments reveal somewhat different information and one or the other might be preferable in a given application. Our results suggest that in some cases, notably homology modeling, the common use of nonredundant datasets, culled from the PDB based on sequence, may mask important structural and functional information. We have established a data base of sequence-similar, structurally dissimilar protein pairs that will help address this problem (http://luna.bioc.columbia.edu/rachel/seqsimstrdiff.htm).     

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.     

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.     

蛋白质二级结构指定

蛋白质二级结构是指蛋白质骨架结构中有规律重复的构象。由蛋白质原子坐标正确地指定蛋白质二级结构是分析蛋白质结构与功能的基础,二级结构的指定对于蛋白质分类、蛋白质功能模体的发现以及理解蛋白质折叠机制有着重要的作用。并且蛋白质二级结构信息广泛应用到蛋白质分子可视化、蛋白质比对以及蛋白质结构预测中。目前有超过20种蛋白质二级结构指定方法,这些方法大体可以分为两大类:基于氢键和基于几何,不同方法指定结果之间的差异较大。由于尚没有蛋白质二级结构指定方法的综述文献,因此,本文主要介绍和总结已有蛋白质二级结构指定方法。     

Structure alignment via Delaunay tetrahedralization

A novel protein structure alignment technique has been developed reducing much of the secondary and tertiary structure to a sequential representation greatly accelerating many structural computations, including alignment. Constructed from incidence relations in the Delaunay tetrahedralization, alignments of the sequential representation describe structural similarities that cannot be expressed with rigid-body superposition and complement existing techniques minimizing root-mean-squared distance through superposition. Restricting to the largest substructure superimposable by a single rigid-body transformation determines an alignment suitable for root-mean-squared distance comparisons and visualization. Restricted alignments of a test set of histones and histone-like proteins determined superpositions nearly identical to those produced by the established structure alignment routines of DaliLite and ProSup. Alignment of three, increasingly complex proteins: ferredoxin, cytidine deaminase, and carbamoyl phosphate synthetase, to themselves, demonstrated previously identified regions of self-similarity. All-against-all similarity index comparisons performed on a test set of 45 class I and class II aminoacyl-tRNA synthetases closely reproduced the results of established distance matrix methods while requiring 1/16 the time. Principal component analysis of pairwise tetrahedral decomposition similarity of 2300 molecular dynamics snapshots of tryptophanyl-tRNA synthetase revealed discrete microstates within the trajectory consistent with experimental results. The method produces results with sufficient efficiency for large-scale multiple structure alignment and is well suited to genomic and evolutionary investigations where no geometric model of similarity is known a priori.     

X-ray structure of Glu 53 human lysozyme.

The three-dimensional structure of a modified human lysozyme (HL), Glu 53 HL, in which Asp 53 was replaced by Glu, has been determined at 1.77 A resolution by X-ray analysis. The backbone structure of Glu 53 HL is essentially the same as the structure of wild-type HL. The root mean square difference for the superposition of equivalent C alpha atoms is 0.141 A. Except for the Glu 53 residue, the structure of the active site region is largely conserved between Glu 53 HL and wild-type HL. However, the hydrogen bond network differs because of the small shift or rotation of side chain groups. The carboxyl group of Glu 53 points to the carboxyl group of Glu 35 with a distance of 4.7 A between the nearest carboxyl oxygen atoms. A water molecule links these carboxyl groups by a hydrogen bond bridge. The active site structure explains well the fact that the binding ability for substrates does not significantly differ between Glu 53 HL and wild-type HL. On the other hand, the positional and orientational change of the carboxyl group of the residue 53 caused by the mutation is considered to be responsible for the low catalytic activity (ca. 1%) of Glu 53 HL. The requirement of precise positioning for the carboxyl group suggests the possibility that the Glu 53 residue contributes more than a simple electrostatic stabilization of the intermediate in the catalysis reaction.