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.     

An adaptable pentaloop defines a robust neomycin-B RNA aptamer with conditional ligand-bound structures

Aptamers can be highly specific for their targets, which implies precise molecular recognition between aptamer and target. However, as small polymers, their structures are more subject to environmental conditions than the more constrained longer RNAs such as those that constitute the ribosome. To understand the balance between structural and environmental factors in establishing ligand specificity of aptamers, we examined the RNA aptamer (NEO1A) previously reported as specific for neomycin-B. We show that NEO1A can recognize other aminoglycosides with similar affinities as for neomycin-B and its aminoglycoside specificity is strongly influenced by ionic strength and buffer composition. NMR and 2-aminopurine (2AP) fluorescence studies of the aptamer identified a flexible pentaloop and a stable binding pocket. Consistent with a well-structured binding pocket, docking analysis results correlated with experimental measures of the binding energy for most ligands. Steady state fluorescence studies of 2AP-substituted aptamers confirmed that A16 moves to a more solvent accessible position upon ligand binding while A14 moves to a less solvent accessible position, which is most likely a base stack. Analysis of binding affinities of NEO1A sequence variants showed that the base in position 16 interacts differently with each ligand and the interaction is a function of the buffer constituents. Our results show that the pentaloop provides NEO1A with the ability to adapt to external influences on its structure, with the critical base at position 16 adjusting to incorporate each ligand into a stable pocket by hydrophobic interactions and/or hydrogen bonds depending on the ligand and the ionic environment.     

Population genetics without intraspecific data

A central goal of computational biology is the prediction of phenotype from DNA and protein sequence data. Recent models of sequence change use in silico prediction systems to incorporate the effects of phenotype on evolutionary rates. These models have been designed for analyzing sequence data from different species and have been accompanied by statistical techniques for estimating model parameters when the incorporation of phenotype induces dependent change among sequence positions. A difficulty with these efforts to link phenotype and interspecific evolution is that evolution occurs within populations, and parameters of interspecific models should have population genetic interpretations. We show, with two examples, how population genetic interpretations can be assigned to evolutionary models. The first example considers the impact of RNA secondary structure on sequence change, and the second reflects the tendency for protein tertiary structure to influence nonsynonymous substitution rates. We argue that statistical fit to data should not be the sole criterion for assessing models of sequence change. A good interspecific model should also yield a clear and biologically plausible population genetic interpretation.     

Similarity between average distance maps of structurally homologous proteins

A similarity between average distance maps (Kikuchiet al., 1988a)—that is, predicted contact maps of two tertiary structurally homologous proteins—is examined. Comparisons of shapes of average distance maps (we refer to this as ADM) are made by superpositions of ADMs for two homologous proteins. Also, we compare shapes of actual contact maps for the pair of proteins. We search a optimal superposition mode of each pair of maps showing that two proteins are most similar. It is concluded that two ADMs are also similar when actual tertiary structures between two proteins show similarity. A criterion for similarity of maps is also proposed. The possibility of application of this method to detect weak homology between protein structures is discussed.     

Estimating the length of transmembrane helices using Z-coordinate predictions

Zpred2 is an improved version of ZPRED, a predictor for the Z-coordinates of alpha-helical membrane proteins, that is, the distance of the residues from the center of the membrane. Using principal component analysis and a set of neural networks, Zpred2 analyzes data extracted from the amino acid sequence, the predicted topology, and evolutionary profiles. Zpred2 achieves an average accuracy error of 2.18 A (2.17 A when an independent test set is used), an improvement by 15% compared to the previous version. We show that this accuracy is sufficient to enable the predictions of helix lengths with a correlation coefficient of 0.41. As a comparison, two state-of-the-art HMM-based topology prediction methods manage to predict the helix lengths with a correlation coefficient of less than 0.1. In addition, we applied Zpred2 to two other problems, the re-entrant region identification and model validation. Re-entrants were able to be detected with a certain consistency, but not better than with previous approaches, while incorrect models as well as mispredicted helices of transmembrane proteins could be distinguished based on the Z-coordinate predictions.     

一个可用于复杂大群体的可视化系谱绘制和分析软件

对于在遗传研究和家系研究中大的系谱结构图还很难分析。系谱的绘制通常是遗传性状的分析研究的第一步。系图可以反映整个群体的结构、每个个体之间的相互关系以及基因流的走向,便于理解遗传性状的本质。因为所用家系数目的增大和复杂性的增加,绘制1个清晰的系谱有时变得十分困难。因此开发了1种名为Pedigraph软件,可以解决这个问题。Pedigraph能够完成对于大的复杂的群体的系谱绘制工作,并能进行相应的系谱分析。初步的测试表明这个软件在研究动植物的遗传育种中是1个有用的工具,同时它也可以用于人类的群体和历史等方面的研究。     

Spectroscopic characterization of rhinoviral protease 2A: Zn is essential for the structural integrity.

Recently, protease 2A of human rhinovirus 2 (HRV2 2A) was shown to require a zinc ion for the formation of an active enzyme although zinc is not involved mechanistically. The data presented clearly show that the zinc ion bound to a picornaviral-specific motif represents an essential component of the native structure, probably representing a new Zn-binding motif. This structure, containing mostly beta-strand elements as shown by CD spectroscopy, changes drastically upon removal of zinc. The zinc-depleted form does represent an intermediate with mostly unchanged secondary structure, but not a fully denatured random coil as obtained by guanidinium hydrochloride. This is indicated by the blue-shifted fluorescence spectra and by CD. The native protein exhibited a cooperative phase transition at 53 degrees C. In contrast, the zinc-depleted form did not show any transition at all, again demonstrating the stabilizing role of the zinc ion. A structural intermediate was observed during thermal and pH denaturation that may represent a molten globule, as suggested by its ANS binding.     

High-resolution crystal structure of a truncated ColE7 translocation domain: implications for colicin transport across membranes

ColE7 is a nuclease-type colicin released from Escherichia coli to kill sensitive bacterial cells by degrading the nucleic acid molecules in their cytoplasm. ColE7 is classified as one of the group A colicins, since the N-terminal translocation domain (T-domain) of the nuclease-type colicins interact with specific membrane-bound or periplasmic Tol proteins during protein import. Here, we show that if the N-terminal tail of ColE7 is deleted, ColE7 (residues 63-576) loses its bactericidal activity against E.coli. Moreover, TolB protein interacts directly with the T-domain of ColE7 (residues 1-316), but not with the N-terminal deleted T-domain (residues 60-316), as detected by co-immunoprecipitation experiments, confirming that the N-terminal tail is required for ColE7 interactions with TolB. The crystal structure of the N-terminal tail deleted ColE7 T-domain was determined by the multi-wavelength anomalous dispersion method at a resolution of 1.7 angstroms. The structure of the ColE7 T-domain superimposes well with the T-domain of ColE3 and TR-domain of ColB, a group A Tol-dependent colicin and a group B TonB-dependent colicin, respectively. The structural resemblance of group A and B colicins implies that the two groups of colicins may share a mechanistic connection during cellular import.     

NMR of hydrogen bonding in cold-shock protein A and an analysis of the influence of crystallographic resolution on comparisons of hydrogen bond lengths

Hydrogen bonding in cold-shock protein A of Escherichia coli has been investigated using long-range HNCO spectroscopy. Nearly half of the amide protons involved in hydrogen bonds in solution show no measurable protection from exchange in water, cautioning against a direct correspondence between hydrogen bonding and hydrogen exchange protection. The N to O atom distance across a hydrogen bond, R(NO), is related to the size of the (3h)J(NC') trans hydrogen bond coupling constant and the amide proton chemical shift. Both NMR parameters show poorer agreement with the 2.0-A resolution X-ray structure of the cold-shock protein studied by NMR than with a 1.2-A resolution X-ray structure of a homologous cold-shock protein from the thermophile B. caldolyticus. The influence of crystallographic resolution on comparisons of hydrogen bond lengths was further investigated using a database of 33 X-ray structures of ribonuclease A. For highly similar structures, both hydrogen bond R(NO) distance and Calpha coordinate root mean square deviations (RMSD) show systematic increases as the resolution of the X-ray structure used for comparison decreases. As structures diverge, the effects of coordinate errors on R(NO) distance and Calpha coordinate root mean square deviations become progressively smaller. The results of this study are discussed with regard to the influence of data precision on establishing structure similarity relationships between proteins.     

重楼属系统发育探讨

重楼属是延龄草科一个特征鲜明的属,共约17—18种,分布于欧洲和亚洲,以中国为分布中心。在区别重楼属下各级类群时,最为有效的指标为:1.花基数(3-)4—10,花辫或萼片数与心皮数目相同;2.雄蕊2—6轮,其数目为心应数目(或萼片数,或花瓣数)的2—6倍;3.子房1室具(3-)4—10个侧膜胎座或数室而具中轴胎座,果为开裂的蒴果或不开裂的浆果;4.种子具多汁的假种皮、具不完全的假种皮或无假种皮;5.根状茎粗壮或细长匍匐.根据属内系统发育的趋势,可以确认:海南重楼Paris dunniana Levl．具粗厚根状茎、雄蕊4—6轮、子房1室具侧膜胎座、蒴果开裂、种于具完全的假种皮,是本属最原始的1个种。根据上述指标,本属划分为2个亚属7个组,其系统顺序如下.     

Comprehensively designed consensus of standalone secondary structure predictors improves Q3 by over 3%

Protein fold is defined by a spatial arrangement of three types of secondary structures (SSs) including helices, sheets, and coils/loops. Current methods that predict SS from sequences rely on complex machine learning-derived models andprovide the three-state accuracy (Q₃) at about 82%. Further improvements in predictive quality could be obtained with a consensus-based approach, which so far received limited attention. We perform first-of-its-kind comprehensive design of a SS consensus predictor (SScon), in which we consider 12 modern standalone SS predictors and utilize Support Vector Machine (SVM) to combine their predictions. Using a large benchmark data-set with 10 random training-test splits, we show that a simple, voting-based consensus of carefully selected base methods improves Q₃ by 1.9% when compared to the best single predictor. Use of SVM provides additional 1.4% improvement with the overall Q₃ at 85.6% and segment overlap (SOV₃) at 83.7%, when compared to 82.3 and 80.9%, respectively, obtained by the best individual methods. We also show strong improvements when the consensus is based on ab-initio methods, with Q₃ = 82.3% and SOV₃ = 80.7% that match the results from the best template-based approaches. Our consensus reduces the number of significant errors where helix is confused with a strand, provides particularly good results for short helices and strands, and gives the most accurate estimates of the content of individual SSs in the chain. Case studies are used to visualize the improvements offered by the consensus at the residue level. A web-server and a standalone implementation of SScon are available at http://biomine.ece.ualberta.ca/SSCon/.     

2．5分辨率单斜Al－（L－丙氨酸）胰岛素晶体结构研究

空间群为Ｐ２１的Ａ１－（Ｌ－丙氨酸）胰岛素晶胞内,一个不对称单位含有一个六聚体,应用差值Ｆｏｕｒｉｅｒ技术,立体化学制最小二来技术和Ｘ—ＰＬＯＲ程序并辅以电子密度图的人工拟合,解析了分辨率ＡＩ—（Ｌ－丙氨酸）胰岛素（Ａｌ－Ｌ－ＡｌａⅠ）的晶体结构。最终Ｒ因子为２０．６％,与标准键长与键角的均方根偏差分别为和４．１９°,从电子密度图与模型的拟合来看,六聚体中每条Ａ链的Ａｌ位置替换的Ｌ—Ａｌａ清晰可见,每条Ｂ链Ｎ端Ｂ１—Ｂ８伏段都为α螺旋构象,形成了Ｂ１—Ｂ１９的连续α螺旋段。     

Towards an understanding of the poliovirus replication complex: the solution structure of the soluble domain of the poliovirus 3A protein

Poliovirus is a positive-strand RNA virus and the prototypical member of the Picornaviridae family. Upon infection, the viral RNA genome is translated from a single open reading frame into a polypeptide which undergoes a series of cleavages to ultimately form four structural and seven non-structural proteins. A replication complex is then formed which replicates the viral genome into negative and positive strands for further translation, replication, and packaging into viral progeny. Poliovirus 3A protein (3A) is a critical component of the viral replication complex and is the putative target of enviroxime, an antiviral drug shown to block viral replication. 3A also inhibits host cell endoplasmic reticulum-to-Golgi apparatus transport, a function which may play a key role in viral evasion from the host immune response. 3A, an 87-residue protein consisting of a soluble N terminus and a hydrophobic C terminus, is formed by the cleavage of the precursor protein 3AB into 3A and 3B (VPg). Although they differ by only 22 residues, the precursor protein 3AB and its cleavage product 3A have distinct functions in viral replication. We have determined the structure of the soluble, N-terminal domain of 3A (3A-N) using NMR spectroscopy. We show that 3A-N exists as a symmetric dimer, and each monomer consists of an alpha-helical hairpin with unstructured, yet functional, N- and C termini. We also show that the 3A-N structure contains a negatively charged surface patch and provides a context for interpreting the biochemical characteristics of a number of previously reported 3A and 3AB mutants.     

红豆杉科、三尖杉科和罗汉松科植物叶片结构的比较观察

扫描电镜和光镜下的叶表皮特征以及叶片解剖结构的研究结果,支持在红豆杉科内建立白豆杉属的处理方式;赞同在三尖杉属内建立篦子三尖杉组,叶片解剖结构方面,三尖杉科和红豆杉科的穗花杉属的相似之处颇多。而叶表皮形态特征方面又表现为三尖杉科和罗汉松科更加接近。反映了出了红豆杉科、三尖杉科和罗汉松科之间的密切而又复杂的系统关系。     

A 3D building blocks approach to analyzing and predicting structure of proteins

A new approach is introduced for analyzing and ultimately predicting protein structures, defined at the level of C alpha coordinates. We analyze hexamers (oligopeptides of six amino acid residues) and show that their structure tends to concentrate in specific clusters rather than vary continuously. Thus, we can use a limited set of standard structural building blocks taken from these clusters as representatives of the repertoire of observed hexamers. We demonstrate that protein structures can be approximated by concatenating such building blocks. We have identified about 100 building blocks by applying clustering algorithms, and have shown that they can "replace" about 76% of all hexamers in well-refined known proteins with an error of less than 1 A, and can be joined together to cover 99% of the residues. After replacing each hexamer by a standard building block with similar conformation, we can approximately reconstruct the actual structure by smoothly joining the overlapping building blocks into a full protein. The reconstructed structures show, in most cases, high resemblance to the original structure, although using a limited number of building blocks and local criteria of concatenating them is not likely to produce a very precise global match. Since these building blocks reflect, in many cases, some sequence dependency, it may be possible to use the results of this study as a basis for a protein structure prediction procedure.     

Three-dimensional structure and substrate binding of Bacillus stearothermophilus neopullulanase

Crystal structures of Bacillus stearothermophilus TRS40 neopullulanase and its complexes with panose, maltotetraose and isopanose were determined at resolutions of 1.9, 2.4, 2.8 and 3.2A, respectively. Since the latter two carbohydrates are substrates of this enzyme, a deactivated mutant at the catalytic residue Glu357-->Gln was used for complex crystallization. The structures were refined at accuracies with r.m.s. deviations of bond lengths and bond angles ranging from 0.005A to 0.008A and 1.3 degrees to 1.4 degrees, respectively. The active enzyme forms a dimer in the crystalline state and in solution. The monomer enzyme is composed of four domains, N, A, B and C, and has a (beta/alpha)(8)-barrel in domain A. The active site lies between domain A and domain N from the other monomer. The results show that dimer formation makes the active-site cleft narrower than those of ordinary alpha-amylases, which may contribute to the unique substrate specificity of this enzyme toward both alpha-1,4 and alpha-1,6-glucosidic linkages. This specificity may be influenced by the subsite structure. Only subsites -1 and -2 are commonly occupied by the product and substrates, suggesting that equivocal recognition occurs at the other subsites, which contributes to the wide substrate specificity of this enzyme.     

Anatomy of the Pre-Parasitic Stage of Hydromermis conophaga (Mermithidae: Nematoda)

The anatomy of the preparasitic juvenile of Hydromermis conopophaga (Mermithidae: Nematoda) has been examined with the light and electron microscope. The alimentary tract consisted of an onchiostylet, pharyngeal tube, stichosome, and intestine. Paired penetration glands were associated with the anterior half of the stichosome. A total of 16 sensory papillae were found in this stage. Certain features, such as the character of the stylet and the attachment of the pharynx to the intestine, show that the preparasitic juvenile more than any other stage in its life cycle closely resembles a free-living dorylaimoid nematode.     

Porosity and tortuosity relations as revealed by a mathematical model of biofilm structure

A biofilm is assumed to be submerged in a fluid with given viscosity and low Reynolds number. The interaction between fluid and bacteria is modeled through streamlines. We use finite-difference and boundary element numerical schemes to predict streamlines within the biofilm. The results show that this approach can provide information about prior distribution and geometry of the biofilm structure. Theoretical values of porosity and tortuosity are computed and compared with published data.