植物类金属硫蛋白半胱氨酸富含区结构的建模

详细了解蛋白质的三级结构信息有助于理解其生物学功能.随着植物基因组研究的进展,已发现了50多个植物类金属硫蛋白(Metallothionein-Like, MT-L)基因.但至今只有少数几个MT-L蛋白得到了纯化,而其结构尚无报道,因此有必要建立分析这类蛋白结构特征的方法.本研究根据已知的哺乳动物MT的结构数据,分析得出了CXC、CXXC模式和金属-硫络合簇结构原子间的距离限制条件,并用距离几何算法计算得出预测蛋白可能的构象;然后通过统计分析筛选出目标函数值显著较小、构象能低的结构作为这些蛋白半胱氨酸富含区的预测结构,由此建成了适合于植物类金属硫蛋白半胱氨酸富含区的结构预测方法.从应用该方法正确地预测出了已知结构的蓝蟹MT的结构来看,该方法是可行的.并用该方法预测了油菜MT-L蛋白的半胱氨酸富含区的结构.     

植物类金属硫蛋白半胱氨酸富含区结构的建模

详细了解蛋白质的三级结构信息有助于理解其生物学功能。随着植物基因组研究的进展 ,已发现了 50多个植物类金属硫蛋白 (Metallothionein_Like ,MT_L)基因。但至今只有少数几个MT_L蛋白得到了纯化 ,而其结构尚无报道 ,因此有必要建立分析这类蛋白结构特征的方法。本研究根据已知的哺乳动物MT的结构数据 ,分析得出了CXC、CXXC模式和金属 硫络合簇结构原子间的距离限制条件 ,并用距离几何算法计算得出预测蛋白可能的构象 ;然后通过统计分析筛选出目标函数值显著较小、构象能低的结构作为这些蛋白半胱氨酸富含区的预测结构 ,由此建成了适合于植物类金属硫蛋白半胱氨酸富含区的结构预测方法。从应用该方法正确地预测出了已知结构的蓝蟹MT的结构来看 ,该方法是可行的。并用该方法预测了油菜MT_L蛋白的半胱氨酸富含区的结构。     

用距离几何算法和同源建模法对水稻类金属硫蛋白(rgMT)的三维结构建模

水稻类金属硫蛋白(rgMT)的两端是高度保守的半胱氨酸富含区的结构域(CR区),中间是不含半胱氨酸的间隔区,呈典型的三段式结构.本研究分别采用距离几何算法和同源建模相结合的方法对水稻类金属硫蛋白进行三级结构建模.在排列出CR区的所有可能的半胱氨酸-金属硫络合的组合方式,并对每一种组合方式给出一定的限制条件后各生成20个随机构象.根据生成的随机构象是否能形成金属硫络合结构,从900个随机构象中最终选出6个构象(N端4种,C端2种组合)作为可能的结构模型.另一方面,采用GOR方法对间隔区进行了二级结构预测,随后用同源建模法对其建模.将上述建成的三部分模型连接起来后形成rgMT的整体三维构象.结果表明rgMT能像哺乳动物MT蛋白一样,可形成两个独立的、在结构和能量上均没有障碍的金属-硫络合结构.介于所有植物类金属硫蛋白都具有典型的三段式结构,其中的一部分还具有与rgMT相同的半胱氨酸排列方式,所以rgMT三维结构模型的建立对于其他植物类金属硫蛋白的结构研究具有重要的参考价值.     

用距离几何算法和同源建模法对水稻类金属硫蛋白（rgMT）的三维结构建模

水稻类金属硫蛋白(rgMT)的两端是高度保守的半胱氨酸富含区的结构域(CR区),中间是不含半胱氨酸的间隔区,呈典型的三段式结构。本研究分别采用距离几何算法和同源建模相结合的方法对水稻类金属硫蛋白进行三级结构建模。在排列出CR区的所有可能的半胱氨酸-金属硫络合的组合方式,并对每一种组合方式给出一定的限制条件后各生成20个随机构象。根据生成的随机构象足否能形成金属硫络合结构,从900个随机构象中最终选出6个构象(N端4种,C端2种组合)作为可能的结构模型。另一方面,采用GOR方法对间隔区进行了二级结构预测,随后用同源建模法对其建模。将上述建成的三部分模型连接起来后形成rgMT的整体三维构象。结果表明rgMT能像哺乳动物MT蛋白一样,可形成两个独立的、在结构和能量上均没有障碍的金属-硫络合结构。介于所有植物类金属硫蛋白都具有典型的三段式结构,其中的一部分还具有与rgMT相同的半胱氨酸排列方式,所以rgMT三维结构模型的建立对于其他植物类金属硫蛋白的结构研究具有重要的参考价值。     

植物金属硫蛋白MT2的生物信息分析

用生物信息分析方法对已在GenBank上注册的拟南芥等13种植物金属硫蛋白MT2的氨基酸序列与组成、亚细胞定位、跨膜区与信号肽、疏水性／亲水性、蛋白质二、三级结构以及功能等进行分析与预测。结果表明,植物MT2主要位于叶绿体中,无信号肽,是非跨膜的亲水性蛋白,不规则卷曲是其蛋白质二级结构的主要结构元件,无功能结构域。这一结果可为植物MT2深入的结构与功能分析及利用提供进一步的信息与参考。     

金属硫蛋白与红细胞的相互作用

根据金属硫蛋白(MT)对标记在膜上的马来酰亚胺自旋标记物的ESR波谱的影响,研究了MT与红细胞膜的相互作用,发现不同种属的MT对膜构象的影响不同.体外实验表明,MT可以吸附在红细胞的表面,用CdCl₂诱导家兔,对血浆和红细胞溶血液中的MT组分进行色谱分离,发现血液中的MT主要存在于血细胞中.进而对血液MT的来源、分布及其重要的生物学意义进行了讨论.     

金属硫蛋白的结构模型

金属硫蛋白是一种低分子量(6,000—10,000),富含半胱氨酸(25—35％),并能结合重金属如Zn、Cd、Cu、Hg或Ag的蛋白质。因其含硫及金属故称为金属硫蛋白(Metallothionein,简称MT)。自1957年Margashes和Vallee在马的肾脏皮质中第一次分离出含有镉的蛋白质以来,在哺乳动物(包括人)、微生物、原核生物蓝绿藻及植物中已先后分离出金属硫蛋白。它是一种诱导性的蛋白质。在实验的动物和培养的细胞中(如Hela细胞、人的上皮细胞等)金属硫蛋白不仅能被重金属离子而且也能为皮质激素诱导而合成。并已证明二者诱导MT的合成是受转录水平调节。     

三穗麻鸭MT基因克隆与序列分析

目的:为三穗麻鸭金属硫蛋白(MT)的结构与功能研究提供基础材料。方法:应用MT特异引物,通过RT-PCR从三穗麻鸭肝组织总RNA中扩增目的基因,克隆测序后应用生物信息学软件对该编码蛋白二级结构、亚细胞定位、跨膜结构及信号肽进行预测。结果:三穗麻鸭MT基因全长185bp,可编码61个氨基酸,其中半胱氨酸19个,丝氨酸9个,不含芳香族氨基酸;该基因序列与绿头鸭MT基因的核苷酸同源性为99%,氨基酸同源性达100%;该蛋白为可溶性蛋白,可分布细胞核内和核外,不含信号肽。结论:首次克隆出三穗麻鸭金属硫蛋白基因。     

金属硫蛋白的结构模型

金属硫蛋白是一种低分子量(6,000—10,000),富含半胱氨酸(25—35％),并能结合重金属如Zn、Cd、Cu、Hg 或Ag的蛋白质。因其含硫及金属故称为金属硫蛋白(Metallothionein,简称MT)。自1957年Margashes和Vallee在马的肾脏皮质中第一次分离出含有镉的蛋白质以来,在哺乳动物(包括人)、微生物、原核生物蓝绿藻及植物中已先后分离出金属硫蛋白。它是一种诱导性的蛋白质。在实验的动物和培养的细胞中(如 Hela 细胞、人的上皮细胞等)金属硫蛋白不仅能被重金属离子而且也     

金属硫蛋白及其生物学功能

金属硫蛋白(metallothionein, MT) 是一类富含半胱氨酸的低分子质量蛋白质,已鉴定4种亚型：MT-1、MT-2、MT-3和MT-4,基于各亚型功能的相对异质性而使MT呈现其生物学作用的多样性。金属硫蛋白通过与金属离子结合而参与基因表达调控和机体的重金属解毒过程;金属硫蛋白通过抑制多种氧化应激途径而保护细胞免受损伤;金属硫蛋白通过参与细胞的增殖、分化和凋亡的调节而影响肿瘤及其他重大疾病的发生发展。本文在金属硫蛋白的结构和分类的基础上综述其生物学作用及其相关机制。     

CONFOLD: Residue‐residue contact‐guided ab initio protein folding

Predicted protein residue–residue contacts can be used to build three‐dimensional models and consequently to predict protein folds from scratch. A considerable amount of effort is currently being spent to improve contact prediction accuracy, whereas few methods are available to construct protein tertiary structures from predicted contacts. Here, we present an ab initio protein folding method to build three‐dimensional models using predicted contacts and secondary structures. Our method first translates contacts and secondary structures into distance, dihedral angle, and hydrogen bond restraints according to a set of new conversion rules, and then provides these restraints as input for a distance geometry algorithm to build tertiary structure models. The initially reconstructed models are used to regenerate a set of physically realistic contact restraints and detect secondary structure patterns, which are then used to reconstruct final structural models. This unique two‐stage modeling approach of integrating contacts and secondary structures improves the quality and accuracy of structural models and in particular generates better β‐sheets than other algorithms. We validate our method on two standard benchmark datasets using true contacts and secondary structures. Our method improves TM‐score of reconstructed protein models by 45% and 42% over the existing method on the two datasets, respectively. On the dataset for benchmarking reconstructions methods with predicted contacts and secondary structures, the average TM‐score of best models reconstructed by our method is 0.59, 5.5% higher than the existing method. The CONFOLD web server is available at http://protein.rnet.missouri.edu/confold/ . Proteins 2015; 83:1436–1449. © 2015 Wiley Periodicals, Inc.     

Adaptability of restrained molecular dynamics for tertiary structure prediction: application to Crotalus atrox venom phospholipase A2

In order to assess the adaptability and/or applicability of the restrained molecular dynamics (RMD) simulation for building a possible tertiary structure of a protein from the X-ray crystal structure of a family reference protein, the tertiary structure prediction of Crotalus atrox venom phospholipase A2 (PLA2) was attempted based on the X-ray crystal structure of bovine pancreatic PLA2. For the formation of secondary and tertiary structures from the fully extended starting structure, the RMD simulation with interatomic distance restraints and torsion angle restraints, which were derived from homologous amino acid sequence regions in the reference protein, was carried out until the molecular system was fully equilibrated. The predicted tertiary structure of C. atrox venom PLA2 was compared with its X-ray crystal structure, and furthermore the utility of this method was discussed by reference to the similar tertiary structure prediction of beta-trypsin from the X-ray crystal structure of an elastase.     

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.     

Ab initio fold prediction of small helical proteins using distance geometry and knowledge-based scoring functions.

The problem of protein tertiary structure prediction from primary sequence can be separated into two subproblems: generation of a library of possible folds and specification of a best fold given the library. A distance geometry procedure based on random pairwise metrization with good sampling properties was used to generate a library of 500 possible structures for each of 11 small helical proteins. The input to distance geometry consisted of sets of restraints to enforce predicted helical secondary structure and a generic range of 5 to 11 A between predicted contact residues on all pairs of helices. For each of the 11 targets, the resulting library contained structures with low RMSD versus the native structure. Near-native sampling was enhanced by at least three orders of magnitude compared to a random sampling of compact folds. All library members were scored with a combination of an all-atom distance-dependent function, a residue pair-potential, and a hydrophobicity function. In six of the 11 cases, the best-ranking fold was considered to be near native. Each library was also reduced to a final ab initio prediction via consensus distance geometry performed over the 50 best-ranking structures from the full set of 500. The consensus results were of generally higher quality, yielding six predictions within 6.5 A of the native fold. These favorable predictions corresponded to those for which the correlation between the RMSD and the scoring function were highest. The advantage of the reported methodology is its extreme simplicity and potential for including other types of structural restraints.     

A comparison of the restrained molecular dynamics and distance geometry methods for determining three-dimensional structures of proteins on the basis of interproton distances

A direct comparison of the metric matrix distance geometry and restrained molecular dynamics methods for determining three-dimensional structures of proteins on the basis of interproton distances is presented using crambin as a model system. It is shown that both methods reproduce the overall features of the secondary and tertiary structure (shape and polypeptide fold). The region of conformational space sampled by the converged structures generated by the two methods is similar in size, and in both cases the converged structures are distributed about mean structures which are closer to the X-ray structure than any of the individual structures. The restrained molecular dynamics structures are superior to those obtained from distance geometry as regards local backbone conformation, side chain positions and non-bonding energies.     

Secondary structural predictions for the clostridial neurotoxins

The primary structures of a family of ten clostridial. Neurotoxins have recently been deduced yet little information is presently available concerning their secondary or tertiary structures. Because the overall similarity percentage of multiply aligned sequences is high, the secondary structures of these metalloendopeptidases are also expected to be conserved. The neural net program, PHD (Rost and Sander, Proc. Natl. Acad. Sci. USA 90:7558–7562, 1993), predicted that the secondary structures of the neurotoxins were indeed conserved in both single and multiple sequence modes of analysis. Predictions for the amounts of helical, extended, and loop states from the single sequence analyses were consistent with previously published data from circular dichroism studies on some of these neurotoxins. In the single analysis mode, only the aligned regions were predicted to show conservation of the three-state structure. In contrast, the multiple sequence analysis predicted that a conserved state (variable loops) also exists in non-aligned regions. Alignments with the primary structure of the prototypic metalloendopeptidase thermolysin showed that about 25% of the residues within this enzyme are similar to those in the neurotoxins. A comparison of thermolysin's known secondary structure with the predictions from this study showed that about 80% of thermolysin's residues could be structurally aligned with those in the neurotoxins. These predictions provide the necessary. Framework to build a homologous low-resolution tertiary structure of the neurotoxin active site that will be essential in the development of synthetic inhibitors. © 1994 Wiley-Liss, Inc.     

Improving a consensus approach for protein structure selection by removing redundancy

In protein tertiary structure prediction, a crucial step is to select near-native structures from a large number of predicted structural models. Over the years, extensive research has been conducted for the protein structure selection problem with most approaches focusing on developing more accurate energy or scoring functions. Despite significant advances in this area, the discerning power of current approaches is still unsatisfactory. In this paper, we propose a novel consensus-based algorithm for the selection of predicted protein structures. Given a set of predicted models, our method first removes redundant structures to derive a subset of reference models. Then, a structure is ranked based on its average pairwise similarity to the reference models. Using the CASP8 data set containing a large collection of predicted models for 122 targets, we compared our method with the best CASP8 quality assessment (QA) servers, which are all consensus based, and showed that our QA scores correlate better with the GDT-TSs than those of the CASP8 QA servers. We also compared our method with the state-of-the-art scoring functions and showed its improved performance for near-native model selection. The GDT-TSs of the top models picked by our method are on average more than 8 percent better than the ones selected by the best performing scoring function.