面向同源蛋白质探测的一种新型混合深度学习模型

根据蛋白质氨基酸链探测其同源蛋白质,进而预测蛋白质的功能,是生物信息学研究领域的一个重要挑战,也是众多生物医学研究领域的基础研究内容,有着重要的科研价值和广泛的应用需求。其研究难点在于:(1)如何学习对同源蛋白质预测有效、有用的蛋白质特征信息;(2)如何更好地运用蛋白质特征信息,实现同源蛋白质的探测与识别。为了解决同源蛋白质探测与识别研究中的关键难点,本文提出一种基于混合深度学习架构的同源蛋白质探测与识别模型(HDLM-PHP)。通过采用统一的"管道式"深度学习架构,将蛋白质特征学习和探测识别统一为一个整体,提高同源蛋白质探测与识别的效能。采用多组并行的深度卷积神经网络,学习蛋白质的各种属性信息,以期获得丰富的待检测蛋白质和靶蛋白质的高级相关性特征,并通过全连接方式使用多层RBM结构融合和精炼这些相关性特征为全局相关性特征。通过统一的深度网络连接方式,以探测和识别任务为导向,学习到对于同源蛋白质预测最有效、最全面的蛋白质特征信息。在标准数据集SCOPe上,对所提模型进行性能与效率评测,结果表明:本文提出的模型能有效地学习到符合任务导向的蛋白质特征数据,提升同源蛋白质探测与识别的准确度和召回率,优于现有的模型和算法。     

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.     

不同蛋白质来源配合饲料对犬饲喂效果及养分消化率研究

用不同蛋白质饲料 (植物蛋白质饲料、动物蛋白质饲料和动植物混合蛋白质饲料 )的配合饲料饲喂实验比格犬。各组的采食积极性和采食量没有明显差异 ;蛋白质来源对生长犬增重没有明显的影响。动植物混合蛋白饲料组与植物蛋白饲料组蛋白质消化率相近 ,动物蛋白饲料组最低 ;动植物混合蛋白饲料组有机质消化率高于植物蛋白饲料组和动物蛋白饲料组 (P <0 0 5 ) ;钙磷消化率以植物蛋白饲料组最低。因此为控制饲料成本并在不能获得高品质动物性蛋白的情况下 ,用动植物混合蛋白饲料饲喂实验犬效果较好     

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.     

蛋白质芯片——蛋白质高表达及固定技术研究进展

就近年来国际上蛋白质芯片的高通量蛋白质生产及固定技术的研究进展进行了系统的总结和分析。蛋白质芯片是一种大规模、高通量的蛋白质组学研究技术,目前己广泛运用于基础研究(如蛋白质/蛋白质相互作用)和应用研究(如病理诊断,药物开发),而该技术的关键步骤是实现蛋白质高表达及固定。及时把握蛋白质高表达及固定技术的研究动向是开展蛋白质芯片研究的基础。     

Low pH-induced conformational changes in 33 kD protein of photosystem Ⅱ

33 kD protein, located on the lumen side ofthylakoid membranes, is one of three extrinsic proteins ofphotosystem Ⅱ (PS Ⅱ ). Previous study showed that NBSmodification of W241, the only tryptophan in 33 kD protein,is helpful for understanding the function of W241 in main-taining functional conformation of 33 kD protein. In thispaper, studies of both circular dichroism and fluorescencespectra showed that upon decreasing pH from 6.2 to 2.5, theconformation of soluble 33 kD protein changed significantly,with an increase or a decrease in percentage of random coilor (z-helix and turns. The changes in secondary structures ofthis protein are pH reversible. After NBS modification at pH2.5, the conformational change of 33 kD protein was keptfixed. The CD ellipticity at 200 nm for NBS-modified 33 kDprotein is much lower than that for control, indicating that the unfolding degree of 33 kD protein was enhanced after the NBS modification. Moreover, the conformational flexibility islost in NBS-modified 33 kD protein, and the conformationalchange becomes pH irreversible, indicating that NBS modi-fication blocked the reversibility of conformational change of33 kD protein. The specific binding capability of NBS-modi-fled 33 kD protein is much lower than that of low pH-treatedcontrol. Furthermore, the rebinding of modified protein on PS Ⅱ membranes cannot restore the activity of oxygen evo-lution. We suggest that it is low pH but not NBS modificationof W241 that leads to the conformational change of 33 kDprotein from one functional to another non-functional state.The significant capability of proton transport of 33 kD pro-tein is discussed.     

基于遗传算法的蛋白质折叠模拟系统

在模拟蛋白质折叠的遗传算法基础上，采用晶格模型，设计了一个用于蛋白质折叠模拟的软件系统，并举例说明该系统的用法。该蛋白质折叠模拟系统可用于蛋白质折叠预测和蛋白质进化研究，并可为蛋白质分子设计提供重要信息。     

使用差异定位SunTag组件实现对细胞质内高含量蛋白的活细胞观察

生物过程由数百万个蛋白质驱动.蛋白质结构和蛋白质定位是蛋白质行使功能的关键.在过去的研究中,快速发展的荧光显微镜成像技术使研究人员可以直接观察蛋白质在活细胞内的定位.然而,对细胞质内高含量蛋白的活细胞观察仍然存在技术障碍.我们通过改进SunTag标记技术,使用差异定位的SunTag组件:一方面,在研究目的蛋白(POI)上标记多个V4抗原;另一方面,将识别V4抗原的抗体GCN4融合的绿色荧光蛋白(GCN4-GFP)通过差异定位后限制其与抗原的结合量.我们的方法大大降低了背景荧光信号,实现了对dynamin膜上功能单位的直接可视化.     

一种测定大豆蛋白质水解度的简易方法

介绍了一种新的测定大豆蛋白质水解度的方法,G-25色谱层析法。该方法利用快速蛋白纯化系统将大豆蛋白水解多肽溶液进行G-25色谱层析,根据蛋白峰和肽峰面积计算蛋白质的水解度,并与甲醛滴定法进行了比较。结果表明,G-25色谱层析法测定的大豆蛋白水解度略低于甲醛滴定法。该方法快速、简便,可以普遍适用于各种蛋白质水解度的测定。     

蛋白质亚细胞定位预测研究进展

蛋白质的功能与其在细胞中的定位有着密切的联系,新合成的蛋白质必须处于适当的亚细胞位置才能正确的行使其功能．预测蛋白质的亚细胞定位,在确定一个未知蛋白质的功能,了解蛋白质相互作用等方面有着重要的意义．机器学习方法在蛋白质亚细胞定位研究中扮演着一个重要的角色．笔者从数据集的构建、蛋白质序列特征提取方法、蛋白质亚细胞定位预测算法以及预测算法的性能评估等四方面总结了过去十几年间机器学习方法在蛋白质亚细胞定位研究中的应用情况,系统阐述了蛋白质亚细胞定位预测研究的进展．     

小麦幼叶中小G蛋白的粗分离

对小麦幼苗叶片中的蛋白进行了粗提,聚丙烯酰胺凝胶电泳(SDS-PAGE)检测在20.1 KDa～31 KDa间呈现一条蛋白条带,经分析其分子量约为23.1 KDa,占所提取总蛋白的2.93%,推测其为小G蛋白家族中的成员.采用传统的硫酸铵盐析法对此目的蛋白进行粗分离.结果显示,30%的硫酸铵饱和度可将该蛋白分离,且所含杂蛋白量最少,其纯度和得率分别是22.96%和47.3%,是进一步细分离纯化的较好选择.     

冬蝶鱼皮肤型抗冻蛋白的克隆及表达

冬蝶鱼皮肤型抗冻蛋白（ｗ ｆｓ Ａ Ｆ Ｐ）的克隆和表达,是研究抗冻蛋白抗冻机制的重要步骤之一,有助于揭示抗冻蛋白分子结构与活力的关系．用 Ｐ Ｃ Ｒ 法获得 ｗ ｆｓ Ａ Ｆ Ｐ 基因片段,构建了分泌型表达载体 Ｐｌａｃ Ｉ Ｑｐａｒ８ｗ ｆｓ Ａ Ｆ Ｐ．用 Ｗ ｅｓｔｅｒｎ Ｂｌｏｔ 法测其表达水平,氨基酸组成分析及质谱分析证明表达的蛋白与天然蛋白完全一致,并具有天然蛋白相同的活力．     

Framework to Identify Protein Complexes Based on Similarity Preclustering

Proteins interact with each other to form protein complexes, and cell functionality depends on both protein interactions and these complexes. Based on the assumption that protein complexes are highly connected and correspond to the dense regions in Protein-protein Interaction Networks(PINs), many methods have been proposed to identify the dense regions in PINs. Because protein complexes may be formed by proteins with similar properties,such as topological and functional properties, in this paper, we propose a protein complex identification framework(KCluster). In KCluster, a PIN is divided into K subnetworks using a K-means algorithm, and each subnetwork comprises proteins of similar degrees. We adopt a strategy based on the expected number of common neighbors to detect the protein complexes in each subnetwork. Moreover, we identify the protein complexes spanning two subnetworks by combining closely linked protein complexes from different subnetworks. Finally, we refine the predicted protein complexes using protein subcellular localization information. We apply KCluster and nine existing methods to identify protein complexes from a highly reliable yeast PIN. The results show that KCluster achieves higher Sn and Sp values and f-measures than other nine methods. Furthermore, the number of perfect matches predicted by KCluster is significantly higher than that of other nine methods.     

GST融合蛋白包涵体纯化方法的探索

克隆结核分枝杆菌培养滤液蛋白CFP10基因,并在大肠杆菌中进行表达和纯化。用PCR方法从结核分枝杆菌H37Rv基因组扩增出CFP10基因片段,克隆至pMD18-T载体中,序列测定正确后,将其亚克隆到表达载体pGEX-4T-1并在大肠杆菌BL21中表达,表达蛋白经SDS-PAG及Western-blot分析后,亲和层析法纯化蛋白。成功克隆了CFP10基因,并对其在E.coli中进行了表达,SDS-PAGE及Western blot分析表明表达产物正确。通过GST纯化系统获得36kD纯化蛋白,与文献报道相符,该蛋白可与CFP10 mAb特异结合,并且同时与活动期结核病人血清发生反应。成功获得了纯化的CFP10蛋白,为进一步研究CFP10蛋白的致病机理提供了实验依据。     

东亚飞蝗消化系统蛋白质组双向电泳的分析

为了优化东亚飞蝗消化系统双向电泳技术,建立东亚飞蝗消化系统蛋白表达图谱,探讨雌、雄东亚飞蝗消化系统蛋白组分的差异,利用pH值为3~10和pH值为4~7的胶条分别对雌、雄东亚飞蝗消化系统进行双向电泳分析,进行蛋白组学分析.研究结果发现:雌性东亚飞蝗消化系统蛋白种类多于雄性,雌性东亚飞蝗消化系统特异蛋白中偏酸性蛋白数量与偏碱性蛋白相当,而雄性东亚飞蝗消化系统特异蛋白中酸性蛋白多于碱性蛋白.在雌、雄东亚飞蝗消化系统相匹配蛋白中,含量差异达3倍以上的蛋白约占总匹配蛋白的50;.可见,雌、雄东亚飞蝗消化系统蛋白组分存在差异.     

A homologue of the bacterial heat-shock gene DnaJ that alters protein sorting in yeast

Heat-shock proteins have been implicated in assembly of protein complexes, correct protein folding and uptake of proteins into organelles. In Escherichia coli, the heat-shock protein DnaJ and the Hsp70 homologue, DnaK, act together to disassemble a protein complex involved in bacteriophage lambda replication. We report the identification of SCJ1, a gene in the yeast Saccharomyces cerevisiae that encodes a homologue of the bacterial DnaJ protein. SCJ1 was identified by a genetic screen in which increased expression of candidate genes results in missorting of a nuclear-targeted test protein. The predicted amino-acid sequence of SCJ1 is 37% identical to the entire E. coli DnaJ protein. Hybridization experiments indicate that there is a family of yeast genes related to SCJ1. These findings suggest that the Hsp70 DnaK-DnaJ interaction is general to eukaryotes.     

Catalysis of guanine nucleotide exchange on Ran by the mitotic regulator RCC1

The product of the gene RCC1 (regulator of chromosome condensation) in a BHK cell line is involved in the control of mitotic events. Homologous genes have been found in Xenopus, Drosophila and yeast. A human genomic DNA fragment and complementary DNA that complement a temperature-sensitive mutation of RCC1 in BHK21 cells encode a protein of relative molecular mass 45,000 (Mr 45K) which is located in the nucleus and binds to chromatin. We have recently isolated a protein from HeLa cells that strongly binds an anti-RCC1 antibody and has the same molecular mass, DNA-binding properties, and amino-acid sequence as the 205 residues already identified. HeLa cell RCC1 is complexed to a protein of Mr 25K. We have shown that this 25K protein has a sequence homologous to the translated reading frame of TC4, a cDNA found by screening a human teratocarcinoma cDNA library with oligonucleotides coding for a ras consensus sequence, and that the protein binds GDP and GTP. We have referred to this protein as the Ran protein (ras-related nuclear protein). In addition to the fraction of Ran protein complexed to RCC1, a 25-fold molar excess of the protein over RCC1 was found in the nucleoplasm of HeLa cells. Here we show that RCC1 specifically catalyses the exchange of guanine nucleotides on the Ran protein but not on the protein c-Ha-ras p21 (p21ras).     

甲型流感病毒PB1-PA蛋白作用位点的发现与分析

 基于共进化理论,探究了甲型流感病毒PB1蛋白与PA蛋白上具有共同进化可能性的保守九聚片段 (C9MP)。结构信息显示PB1蛋白的第1-15位氨基酸与PA蛋白的第239-716位氨基酸具有相互作用域;对该区域变异分布的分析发现,PA蛋白第670位氨基酸Q所在的C9MP与PB1蛋白的第9位氨基酸F、第12位氨基酸V和第13位氨基酸P所在的C9MP在PB1-MP1相互作用面上具有最低的共进化值。结合DSSP程序的分析表明,由PA蛋白第670位氨基酸Q与PB1蛋白的第9位氨基酸F、第12位氨基酸V与第13位氨基酸P构成的区域可能成为潜在的相互作用位点。