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.     

植物炭疽病真菌金属硫蛋白的三级结构预测

根据实验测定的Ⅰ类金属硫蛋白(metallothionein, MT)三级结构的实验数据,给出该类蛋白质的两种特征结构(CXC、CXXC一级结构,半胱氨酸-金属络合簇三级结构)的原子间距离约束条件,然后运用距离几何算法计算出一系列可能的构象.从这些构象中经统计分析筛选出目标函数值显著较小的结构作为所预测蛋白质的三级结构模型.用已知结构的蓝蟹MT对方法进行检验证实其可行性后,对植物炭疽病真菌金属硫蛋白CAP3进行了三级结构预测.     

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。     

基于半胱氨酸排列方式的植物类金属硫蛋白的分类与命名法

随着植物基因组研究的进展,在基因库和蛋白库登录的植物类金属２硫蛋白基因已超过５０个,接近金属硫蛋白总数的１／３,而且有不断上升的趋势。鉴于目前植物类金属２硫蛋白命名与分灰随意性太大,很有必要建立一个统一合理的命名与分类法。对植物类金属２硫蛋白一级结构进行详细分析后,发现该蛋白两端富含半胱氨酸的区域内关胱氨酸的排列方式颇具规律性,进而提出了以半胱氨酸排列方式为基础的分类及命名法,并阐述了采用这种     

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。     

凡纳滨对虾MT基因序列及其在卵巢发育和低温胁迫中的表达分析

在低温处理仔虾全长cDNA文库的筛选测序中, 获得凡纳滨对虾(Litopenaeus vannmei)金属硫蛋白基因全长cDNA序列, 该序列含有425个碱基, 包含177 bp开放阅读框, 上游98 bp的非编码区及下游150 bp 的非编码区, 编码58个氨基酸, 其中半胱氨酸含量丰富, 富含金属硫蛋白典型的Cys-X(1-3)-Cys 结构。多序列比对表明, 凡纳滨对虾MT蛋白序列与美洲螯龙虾(Homarus americanus)MT蛋白序列具最高同源性72.4%。Real-time PCR结果表明, 凡纳滨对虾MT基因在卵巢组织中呈优势表达, 在不同发育期的卵巢中的表达量都很高, 在低温处理凡纳滨对虾肝胰腺组织中上调表达。实验所得结果为研究凡纳滨对虾金属硫蛋白基因在生殖发育和低温应激中的功能提供了参考。       

中华鳖肝金属硫蛋白的分离、纯化及鉴定（英文）

金属硫蛋白(metallothionein,MT)是一类低分子量、富含半胱氨酸的金属结合蛋白.MT几乎广泛分布于所有生物,包括哺乳动物、两栖动物、鱼、植物、真菌和蓝细菌.不同生物金属硫蛋白理化特性和其氨基酸序列及中心片段的比较研究,对研究MT的结构和生物功能及生物的分子进化提供重要依据.哺乳动物MT研究较多,爬行动物鳖MT的研究尚属空白,本文报道鳖肝的金属硫蛋白.中华鳖 (Pelodiscus sinensis) 分别经皮下注射ZnSO4、CuSO4和CdCl2 溶液诱导后,取乙醇沉淀的肝脏无细胞提取液再经Sephadex G-50、DEAE-SepharoseCL-6B 及SephadexG-25凝胶过滤和离子交换柱层析分离,自鳖肝脏中分别获得Zn-MT、Cu-MT和Cd-MT,未经诱导的鳖肝脏中无MT.质谱和HPLC分析其分子量约为6 300 dalton.根据氨基酸组成分析,鳖肝脏MT含61个氨基酸残基,其中MT的典型氨基酸Cys含量占17%.Lys、Glu和Asp含量较高,而芳香族氨基酸和组氨酸含量极低.从紫外光谱特性分析,Zn-MT、Cu-MT、Cd-MT紫外吸收肩分别在220 nm、270 nm和250 nm.表明确为鳖肝脏MT.从氨基酸残基数和分子量看,鳖肝脏MT与哺乳动物MT类似;而从氨基酸组成和结合金属离子的量看,又与低等生物蚯蚓及酵母菌的MT类似.鳖MT的特性介于哺乳动物MT与低等生物MT之间,体现了鳖这种生物进化的特点.     

林木金属硫蛋白研究进展

金属硫蛋白（metallothionein,MT）是一种低分子量、富含半胱氨酸残基的金属结合蛋白,广泛分布于自然界中。随着工业化的发展和环境污染的加重,导致土壤中重金属的积累加剧。林木的植物修复在清除环境污染中占有越来越重要的作用,林木金属硫蛋白的研究也越来越热,本文就其分类,功能,表达等特点进行综述,并对其研究前景进行展望。     

转小鼠金属硫蛋白-Ⅰ基因聚球藻7002的营养需求

金属硫蛋白(Metallothionein,MT)是一类低分子量、富含半胱氨酸的小分子蛋白。自1957年被发现以来,因其具有多种复杂多样的生理活性和功能,而受到广泛关注。研究表明,金属硫蛋白在生物体内,不仅参与必需金       

Sequence-based prediction of protein domains

Guessing the boundaries of structural domains has been an important and challenging problem in experimental and computational structural biology. Predictions were based on intuition, biochemical properties, statistics, sequence homology and other aspects of predicted protein structure. Here, we introduced CHOPnet, a de novo method that predicts structural domains in the absence of homology to known domains. Our method was based on neural networks and relied exclusively on information available for all proteins. Evaluating sustained performance through rigorous cross-validation on proteins of known structure, we correctly predicted the number of domains in 69% of all proteins. For 50% of the two-domain proteins the centre of the predicted boundary was closer than 20 residues to the boundary assigned from three-dimensional (3D) structures; this was about eight percentage points better than predictions by ‘equal split’. Our results appeared to compare favourably with those from previously published methods. CHOPnet may be useful to restrict the experimental testing of different fragments for structure determination in the context of structural genomics.     

Prediction of the location of structural domains in globular proteins

The location of structural domains in proteins is predicted from the amino acid sequence, based on the analysis of a computed contact map for the protein, the average distance map (ADM). Interactions between residues i and j in a protein are subdivided into several ranges, according to the separation |i-j| in the amino acid sequence. Within each range, average spatial distances between every pair of amino acid residues are computed from a data base of known protein structures. Infrequently occurring pairs are omitted as being statistically insignificant. The average distances are used to construct a predicted ADM. The ADM is analyzed for the occurrence of regions with high densities of contacts (compact regions). Locations of rapid changes of density between various parts of the map are determined by the use of scanning plots of contact densities. These locations serve to pinpoint the distribution of compact regions. This distribution, in turn, is used to predict boundaries of domains in the protein. The technique provides an objective method for the location of domains both on a contact map derived from a known three-dimensional protein structure, the real distance map (RDM), and on an ADM. While most other published methods for the identification of domains locate them in the known three-dimensional structure of a protein, the technique presented here also permits the prediction of domains in proteins of unknown spatial structure, as the construction of the ADM for a given protein requires knowledge of only its amino acid sequence.     

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。     

Rampant Exchange of the Structure and Function of Extramembrane Domains between Membrane and Water Soluble Proteins

Of the membrane proteins of known structure, we found that a remarkable 67% of the water soluble domains are structurally similar to water soluble proteins of known structure. Moreover, 41% of known water soluble protein structures share a domain with an already known membrane protein structure. We also found that functional residues are frequently conserved between extramembrane domains of membrane and soluble proteins that share structural similarity. These results suggest membrane and soluble proteins readily exchange domains and their attendant functionalities. The exchanges between membrane and soluble proteins are particularly frequent in eukaryotes, indicating that this is an important mechanism for increasing functional complexity. The high level of structural overlap between the two classes of proteins provides an opportunity to employ the extensive information on soluble proteins to illuminate membrane protein structure and function, for which much less is known. To this end, we employed structure guided sequence alignment to elucidate the functions of membrane proteins in the human genome. Our results bridge the gap of fold space between membrane and water soluble proteins and provide a resource for the prediction of membrane protein function. A database of predicted structural and functional relationships for proteins in the human genome is provided at sbi.postech.ac.kr/emdmp.     

蛋白质结构与功能中的结构域

结构域是蛋白质亚基结构中的紧密球状区域.结构域作为蛋白质结构中介于二级与三级结构之间的又一结构层次,在蛋白质中起着独立的结构单位、功能单位与折叠单位的作用.在复杂蛋白质中,结构域具有结构与功能组件与遗传单位的作用.结构域层次的研究将会促进蛋白质结构与功能关系、蛋白质折叠机制以及蛋白质设计的研究.     

Conservation of inter-residue interactions and prediction of folding rates of domain repeats

Domains are the main structural and functional units of larger proteins. They tend to be contiguous in primary structure and can fold and function independently. It has been observed that 10–20% of all encoded proteins contain duplicated domains and the average pairwise sequence identity between them is usually low. In the present study, we have analyzed the structural similarity between domain repeats of proteins with known structures available in the Protein Data Bank using structure-based inter-residue interaction measures such as the number of long-range contacts, surrounding hydrophobicity, and pairwise interaction energy. We used RADAR program for detecting the repeats in a protein sequence which were further validated using Pfam domain assignments. The sequence identity between the repeats in domains ranges from 20 to 40% and their secondary structural elements are well conserved. The number of long-range contacts, surrounding hydrophobicity calculations and pairwise interaction energy of the domain repeats clearly reveal the conservation of 3-D structure environment in the repeats of domains. The proportions of mainchain–mainchain hydrogen bonds and hydrophobic interactions are also highly conserved between the repeats. The present study has suggested that the computation of these structure-based parameters will give better clues about the tertiary environment of the repeats in domains. The folding rates of individual domains in the repeats predicted using the long-range order parameter indicate that the predicted folding rates correlate well with most of the experimentally observed folding rates for the analyzed independently folded domains.