蛋白质残基相互作用网络在线服务及可视化分析

蛋白质残基相互作用网络对理解蛋白质的结构特征，生物学功能和结合位点预测等研究有重要的作用.然而，现有的蛋白质残基相互作用分析方法易用性较差，需要下载和安装程序，较少提供友好易用的网络可视化功能，极大限制了蛋白质结构、功能和药物设计的相关研究.建立了蛋白质残基相互作用网络在线服务及可视化计算平台(http：//renault.fun)，用户不需要下载和编写程序，仅需上传蛋白质结构数据和口袋相关信息即可搭建蛋白质残基相互作用网络，并实现度中心度(degree centrality)，接近中心度(closeness centrality)和中介中心度(betweenness centrality)等网络特征的计算.该计算平台可进一步实现蛋白质残基相互作用网络的可视化，分析蛋白质表面结合口袋的网络特性，对理解蛋白质结构和药物设计的相关应用研究有较大的帮助.     

蛋白质残基接触图预测

蛋白质是由多个氨基酸组成的长链,是生物体的必要组成成分,参与了生命活动的每一个进程。蛋白质结构决定了许多蛋白质的功能,准确预测蛋白质中氨基酸残基接触对于蛋白质结构预测具有重要意义,蛋白质残基接触问题已经成为当前生物信息领域的热点问题。该文首先给出了蛋白质残基接触图预测的相关背景知识及其重要意义;其次,总结了当前国内外研究的主流方法,包括基于局部相关性的方法、直接耦合分析法与其后处理的方法、以及基于有监督机器学习的方法,并对其中的代表性方法进行了阐述;结合国际蛋白质结构预测竞赛(Critical assessment of protein structure prediction,CASP)的结果对现有模型的性能做了对比和分析;在此基础上,探讨了残基接触图预测在蛋白质结构功能建模中的应用;最后,针对蛋白质接触图预测中存在的若干难点问题,给出了有望取得突破的若干研究方向。     

蛋白质组研究进展

蛋白质组学是在基因组研究由结构基因组学转入到功能基因组学的背景下产生的．蛋白质组是指一个有机物所有的全部蛋白质．蛋白质组研究中使用双向凝胶电泳技术分离蛋白质，质谱技术鉴定蛋白质．蛋白质组研究可应用于基础研究和应用研究，尤其在生物医学领域前景美好．蛋白质组研究将带来生命科学的巨大变化，并将深刻地影响和改变人类的生活．     

多肽链二级结构的氢键定义及氨基酸残基间的氢键分布

蛋白质的生物功能往往决定于它的三维结构，而二级结构是蛋白质的氨基酸顺序和三维构象之间的桥梁，决定了蛋白质折迭的框架，氢键是稳定二级结构的主要作用力。通过Kab—sch—Sander的二级结构的氢键定义，由氢键识别模式对二级结构及其氨基酸残基问的氢键作了统计分析，发现二级结构中的氨基酸残基的丰度与其提供氢键的能力没有统计关联，但氨基酸残基(除ser外)的CO基团形成氢键的能力越强，其NH基团形成氢键的能力越弱，反之亦然I同时给出了各种残基对在*螺旋中形成氢键能力的比较。     

植物组蛋白赖氨酸甲基化研究进展

组蛋白甲基化修饰在真核生物的表观遗传调控中具有重要作用．SET结构域蛋白质可以特异地甲基化修饰组蛋白的赖氨酸残基,进而促进或抑制基因的表达．有关SET结构域蛋白质和组蛋白赖氨酸甲基化的研究为深入了解染色质结构和功能提供了重要信息．文中综述了组蛋白赖氨酸甲基化修饰在植物中的最新进展,探讨了SET结构域蛋白质在植物生长发育调控中的重要作用．     

基于改进贝叶斯优化算法预测蛋白质残基可溶性

蛋白质的残基相对可溶性表征蛋白质残基在三级结构中与溶剂接触的程度,它反映蛋白质三级结构及功能位点的主要特征。文章通过引入免疫算法中的亲和度和浓度概念,提出了一种改进贝叶斯优化算法,形成了贝叶斯优化算法选择局部残基相对可溶性优化依据。利用改进贝叶斯优化算法对2148条蛋白链进行分类实验,分析了窗宽对结果的影响,计算了三组数据在最佳参数状态下平均预测精度为79.7%。与其它方法相比,从结果来看,改进贝叶斯优化算法具有更好分类预测性能。     

三肽基肽酶I的研究进展

三肽基肽酶I(Tripeptidyl Peptidase I，TPPI)是存在于溶酶体中蛋白酶，它能特异地降解寡肽和蛋白质N-末端而释放出三肽．TPPI的基因位于人的染色llpl5，含有13个外显子和12个内含子，全长为6．65Kb，编码563个氨基酸残基．TPP1是迟发型婴儿晚期神经元样脂褐质沉积症(Classical late infantile neuronal ceroid lipofuscinodid，CLN2)的病因蛋白质．由于TPP1的基因突变导致在CLN2患者的溶酶体中线粒体的ATP合成酶的亚单位C大量的堆积．现就TPP1的由来、理化性质及生物学功能加以叙述．     

新生肽链折叠的格子模型

由放置在简立方子上的１２５个以单位键长联接的残基模拟肽链，残基分为亲水和疏水两类．考虑每对非键联接的空间相邻疏水残基间相互吸引．新生肽链的折叠由两种算法模拟：生长算法模拟新生肽链的生长过程，类似于动力学生长行走（ＫＧＷ）．折叠算法采用Ｍｅｔｒｏｐｏｌｉｓ算法．在肽链生长过程中，两种算法交替使用，一旦生长完毕则只使用折叠算法．对３０个随机序列和４个真实蛋白序列的模拟结果表明，生长完毕时，即经过约１０３步模拟，肽链就已处于一种能量较低的状态，其后的折叠较缓慢，再经过约１０５模拟，无明显变化．Ｋａｒｐｌｕｓ小组的模拟结果表明，２７肽须经１０７步才能达到全局极小，这与蛋白体内折叠时标相差很多．提出ｒｏｂｕｓｔ极小的概念取代全局极小来描述蛋白质的生物活性状态．一个ｒｏｂｕｓｔ极小由一组能量足够低的、动力学可及的、几何结构相似的极小组成，系统进入ｒｏｂｕｓｔ极小就不会因热涨落而跃出．一个序列一般有多个ｒｏｂｕｓｔ极小，具体折叠到哪个则与折叠途径有关，据此提出将序列结构特异性推广为序列一途径一结构特异性．     

神经网络预测蛋白质二级结构的编码技术

考虑不同残基的物理化学性质,将其融入蛋白质二级结构的神经网络预测中,提出了一种新的归一化二进制编码技术,将各种残基不同的疏水值与体积大小归一化结果作为神经网络的二进制输入序列．与其他蛋白质二级结构预测的方法进行了比较,结果表明,该方法能充分利用蛋白质的一级结构信息,获得了很好的预测效果。     

新基因GIDRP88编码蛋白质电泳异常迁移的研究

通过制备GIDRP88蛋白质特异的多克隆抗体对GIDRP88基因体外翻译的样品进行检测,结果观察到GIDRP88蛋白质的电泳迁移率随凝胶中丙稀酰胺浓度的改变而发生改变,表明其存在异常迁移．生物信息学分析发现GIDRP88蛋白质一级结构电荷分布不均．为进一步研究电荷分布对其迁移率的影响,分别克隆了GIDRP88基因中电荷分布相对均匀的C端区段A(编码222个氨基酸残基),以及有多余负电荷的中部区段B(编码182个氨基酸残基),在大肠杆菌中诱导表达后,发现A区段表达肽段迁移正常而B区段表达肽段表观分子量比预期偏大32．9％．表明电荷分布不均影响了GIDRP88蛋白质在SDS-PAGE上的迁移．     

同源建模方法预测蛋白质突变结构的适用性分析

通过从Protein Data Bank(PDB)结构数据库中提取单氨基酸突变的晶体结构,构建了一组无冗余的测试数据集,对目前应用最广泛的两款同源建模预测软件(SWISS-MODEL和MODELLER)进行了测试分析,发现它们对蛋白质的整体结构预测效果良好,均方根偏差小于0.5埃(RMSD0.5),但在突变导致结构显著变化(RMSD1.5)的情况下却均不能得到准确结果.分类统计显示,发生在蛋白质结构内部和极性氨基酸之间的突变结构变化小,两款软件预测效果较好(RMSD1.0).突变导致结构显著变化的可能性不高(5%),但它对蛋白质功能的影响不可忽视,因此应用同源建模方法对于蛋白质突变的模拟并不完全适用,还需要开发新方法来提高准确性.     

Applying genetic algorithms to the study of protein mutation theory

Genetic algorithms were applied to the study of simulation of protein mutation carried out on two_dimensional lattice model; to the study of effects of single mutation and double mutation on protein folding and protein structure stability. It is found that in two_dimensional lattice models, replacement of inner core hydrophobic residue by hydrophilic residue will result in reduction of protein stability; at the same time the number of residues of protein surface relatively grows with increase of protein chain length; and most mutations occur in residues of protein surface, these mutations are all neutral and have no effects on protein natural structure. The two mutations of double mutation are interactive and related to each other.     

Three key residues form a critical contact network in a protein folding transition state

Determining how a protein folds is a central problem in structural biology. The rate of folding of many proteins is determined by the transition state, so that a knowledge of its structure is essential for understanding the protein folding reaction. Here we use mutation measurements--which determine the role of individual residues in stabilizing the transition state--as restraints in a Monte Carlo sampling procedure to determine the ensemble of structures that make up the transition state. We apply this approach to the experimental data for the 98-residue protein acylphosphatase, and obtain a transition-state ensemble with the native-state topology and an average root-mean-square deviation of 6 A from the native structure. Although about 20 residues with small positional fluctuations form the structural core of this transition state, the native-like contact network of only three of these residues is sufficient to determine the overall fold of the protein. This result reveals how a nucleation mechanism involving a small number of key residues can lead to folding of a polypeptide chain to its unique native-state structure.     

蛋白质折叠二维HP模型中的关联条件及其应用

蛋白质折叠是生物信息学中的一个重要问题，因为蛋白质是生物功能的主要承载者，几乎所有的生物功能都与蛋白质有关。在本文中，我们主要讨论了二维HP模型下蛋白质折叠中疏水核的关联关系，并利用关联关系避免了在求解蛋白质链的空间结构时陷入能量局部最小值，有效地找出了蛋白质的最低能量，同时，利用关联关系去除了大量的无效构象，进而提高搜索构象的收敛速度。     

禽流感病毒H5N1亚型RNA聚合酶蛋白表达纯化及晶体生长

通过使用原核表达载体大量表达H5N1病毒RNA聚合酶亚基PA-C257,PB1_N25,再经过GST亲和层析和Sephadex G-200层析柱纯化,获得了高纯度的蛋白复合体.采用悬滴气相扩散法筛选蛋白晶体,在1～1.5mol/L乙酸钠和pH7.9条件下获得了理想的晶体,为解析禽流感病毒RNA聚合酶三维结构并进一步认识其生物功能奠定了基础.     

Grafting of protein-protein binding sites

A strategy for grafting protein-protein binding sites is described. Firstly, key interaction residues at the interface of ligand protein to be grafted are identified and suitable positions in scaffold protein for grafting these key residues are sought. Secondly, the scaffold proteins are superposed onto the ligand protein based on the corresponding C_α and C_β atoms. The complementarity between the scaffold protein and the receptor protein is evaluated and only matches with high score are accepted. The relative position between scaffold and receptor proteins is adjusted so that the interface has a reasonable packing density. Then the scaffold protein is mutated to corresponding residues in ligand protein at each candidate position. And the residues having bad steric contacts with the receptor proteins, or buried charged residues not involved in the formation of any salt bridge are mutated. Finally, the mutated scaffold protein in complex with receptor protein is co-minimized by Charmm. In addition, we deduce a scoring function to evaluate the affinity between mutated scaffold protein and receptor protein by statistical analysis of rigid binding data sets.     

Protein functional-group 3D motif and its applications

Representing and recognizing protein active sites sequence motif (1D motif) and structural motif (3D motif) is an important topic for predicting and designing protein function. Prevalent methods for extracting and searching 3D motif always consider residue as the minimal unit, which have limited sensitivity. Here we present a new spatial representation of protein active sites, called "functional-group 3D motif ", based on the fact that the functional groups inside a residue contribute mostly to its function. Relevant algorithm and computer program are developed, which could be widely used in the function prediction and the study of structural-function relationship of proteins. As a test, we defined a functional-group 3D motif of the catalytic triad and oxyanion hole with the structure of porcine trypsin (PDB code: 1mct) as the template. With our motif-searching program, we successfully found similar sub-structures in trypsins, subtilisins and a/b hydrolases, which show distinct folds but share similar catalytic mechanism. Moreover, this motif can be used to elucidate the structural basis of other proteins with variant catalytic triads by comparing it to those proteins. Finally, we scanned this motif against a non-redundant protein structure database to find its matches, and the results demonstrated the potential application of functional group 3D motif in function prediction. Above all, compared with the other 3D-motif representations on residues, the functional group 3D motif achieves better representation of protein active region, which is more sensitive for protein function prediction.     

健康家兔晶状体激光拉曼光谱研究

激光拉曼光谱法被公认为是研究生物大分子的结构、动力学和功能的有效方法。对健康家兔晶状体的激光拉曼光谱进行研究,发现在710 cm-1到1 280 cm-1区域内,健康家兔晶状体表现为典型的蛋白质拉曼光谱区,说明健康家兔晶状体主要由α、β和γ-蛋白组成的,以β折叠结构为主。对家兔晶状体蛋白侧链中酪氨酸残基的微环境研究表明,晶状体中酪氨酸残基大部分处于"暴露"状态,而有一小部分处于"埋藏"状态。     

蛋白质二级结构预测的结构表达方法研究

蛋白质二级结构预测时,描述窗口内氨基酸残基序列的各种物理化学和分子结构参数的数量非常大,而且不能很好地直接体现氨基酸的连接顺序,这样就造成二级结构预测工作既费时效果又低下,因此,对这些数据预处理是非常必要的.研究发现,这些初始数据对应的变换矩阵的本征值谱与氨基酸残基序列情况无关,只与氨基酸的类别、数量性质有关,而其本征函数数据能够直接反映氨基酸残基的序列情况,利用有显著大小的本征值对应的本征函数作为描述参数,在进行蛋白质二级结构预测时,不但能够显著减少描述参数的个数,而且它体现了氨基酸顺序的变化,这将有效提高蛋白质二级结构预测研究效果.     

Sequence, structure, receptor-binding domains and internal repeats of human apolipoprotein B-100

Apolipoprotein (apo) B-100, the major protein component in low density lipoprotein (LDL), is the ligand that binds to the LDL receptor. It is important in the metabolism of LDL and elevated plasma levels of LDL-apo B are strongly associated with increased risk of coronary artery disease. Although apo B-100 is of great clinical and biological importance its primary structure has defied chemical elucidation, mainly because of its enormous size, insolubility, and tendency to aggregate. Less than 5% of the apo B-100 sequence has been reported, despite the efforts of many laboratories over the past twenty years. Here we report the complete amino acid sequence of human apo B-100 as deducted by sequence analysis of complementary DNA clones; 2,366 of the 4,536 residues were also confirmed by direct sequencing of apo B-100 tryptic peptides. The distribution of trypsin-accessible and -inaccessible peptides of the protein on LDL is non-random and they can be grouped into 5 hypothetical domains. Of 20 potential N-glycosylation sites identified in the sequence, 13 were found by direct peptide sequencing to be glycosylated, and 4 unglycosylated. Examination of the primary structure of apo B-100 reveals that it contains a large number of long (greater than 70 residues) internal repeats and an even larger number of shorter ones, suggesting that the apo B-100 sequence was derived largely from internal duplications. Finally, using synthetic peptides of a specific region of apo B-100, we have identified a potential LDL receptor-binding domain (residues 3,345-3,381) which can bind to the LDL receptor and suppress 3-hydroxy-3-methyl-glutaryl coenzyme A (HMG-CoA) reductase activities in cultured human fibroblasts.