蛋白质骨架库的构建及其在功能蛋白质设计中的应用

利用活性位点嫁接设计新的功能蛋白质的方法需要功能模体和蛋白质骨架两种构件。出于活性位点嫁接的需要,我们构建了一个蛋白质骨架库,且提供搜索与功能模体相配骨架的工具及其评估方法。并用两个活性位点的嫁接进行了检验。     

分子设计:用多拷贝分子动力学模拟方法搜索HIV蛋白酶活性中心的官能团结合位点

为了进行不受数据库局限的,基于蛋白质分子结构的药物设计,可以将设计过程分为三步：搜索各类官能团最可能的结合位点;连接各位点得到候选化合物;评价各候选化合物。官能团结合位点的搜索可利用多拷贝分子动力学模拟方法进行。用该方法在ＨＩＶ蛋白酶的活性中心搜索三种重要官能团可能结合位点的计算机模拟结果表明：该方法能搜索到有限数目,与受体有特异性相互作用的官能团结合位点;这些结合位点中包括了与晶体结构中相应官能团结合位置一致的位点。     

羧肽酶Y标记蛋白质羧基端方法的优化及应用（英文）

蛋白质水解是一种重要的翻译后修饰,它在许多生化过程(如细胞凋亡和肿瘤细胞转移等)中起着极其重要的作用。鉴定蛋白质水解位点可以进一步加深我们对这些生化过程的认识。尽管蛋白质氨基端标记方法和蛋白质组学在复杂生物体系中鉴定获得了许多蛋白质的水解位点,但这种方法存在固有的缺陷。羧基端标记方法是另一种可行的鉴定蛋白质水解位点的方法。本文优化了蛋白质羧基端生物酶标记方法,提高了亲和标记效率,从而可以更好地利用正向分离方法对蛋白质羧基端多肽进行分离并用质谱鉴定。我们用优化后的羧基端标记方法来标记大肠杆菌Escherichia coli复杂蛋白样品后鉴定到了120多个蛋白质羧基端多肽和内切多肽。在其所鉴定的蛋白质水解位点中,我们发现了许多已知和未知的位点,这些新的水解位点有可能在正常生化过程的调控中发挥着重要的作用。该研究提供了一个可以与蛋白质氨基端组学互为补充、可在复杂体系中鉴定蛋白质水解的方法。     

羧肽酶Y标记蛋白质羧基端方法的优化及应用

蛋白质水解是一种重要的翻译后修饰,它在许多生化过程 (如细胞凋亡和肿瘤细胞转移等) 中起着极其重要的作用。鉴定蛋白质水解位点可以进一步加深我们对这些生化过程的认识。尽管蛋白质氨基端标记方法和蛋白质组学在复杂生物体系中鉴定获得了许多蛋白质的水解位点,但这种方法存在固有的缺陷。羧基端标记方法是另一种可行的鉴定蛋白质水解位点的方法。本文优化了蛋白质羧基端生物酶标记方法,提高了亲和标记效率,从而可以更好地利用正向分离方法对蛋白质羧基端多肽进行分离并用质谱鉴定。我们用优化后的羧基端标记方法来标记大肠杆菌Escherichia coli复杂蛋白样品后鉴定到了120多个蛋白质羧基端多肽和内切多肽。在其所鉴定的蛋白质水解位点中,我们发现了许多已知和未知的位点,这些新的水解位点有可能在正常生化过程的调控发挥着重要的作用。该研究提供了一个可以与蛋白质氨基端组学互为补充、可在复杂体系中鉴定蛋白质水解的方法。     

基因的推理设计与改造—体外分子进化的捷径

体外分子进化是改造基因、获得新的功能蛋白质重要手段之一,已经取得了令人瞩目的成就。推理设计是利用序列和结构的比较信息创造新的基因和蛋白质,是研究改造蛋白质功能的有效方法。文章着重介绍了基因推理设计在基因体外分子进化中的应用,从简单实用的基因密码偏爱设计,结合多个不同性状相关功能基因信息的基因推理设计,关键功能区域的简并引物设计,位点直接蛋白质重组4个方面进行描述,并综述了该方法近年来的应用。     

DNA足纹步移作图法

一种以PCR介导的、可对任意长度靶DNA片段上的核蛋白结合位点进行DNA足纹作图分析的新方法.原理是：采用被随机降解靶DNA分子作为模板,用标记的跨越整个模板的足够多条特异性引物进行单链扩增.首先,利用某种化学试剂或酶如DNaseⅠ对已与蛋白质结合或未结合的双链靶DNA进行随机降解,在一定条件下使每一个DNA分子恰好只有一个位点被切割.然后,这些被随机降解DNA分子即可作为模板,用同位素标记的跨越整个模板的足够多条特异性引物（正向或反向）进行单链扩增.最后,扩增的单链产物通过变性聚丙烯酰胺凝胶电泳和放射自显影形成DNA片段梯队,而被蛋白质保护的位点则在DNA片段梯队中形成位置缺口,从而确定DNA与蛋白质相结合的精确位点.该方法被应用对人干细胞因子基因5′旁侧－1190～－273区域的DNA足纹部分作图.     

不依赖天然外显子的蛋白质内含子定向进化筛选系统

蛋白质剪接技术为在蛋白质水平上直接对蛋白质进行修饰和加工提供了一种全新的解决方案,因而在蛋白质工程及相关领域具有非常广阔的应用前景。现阶段,大部分天然的蛋白质内含子在异源蛋白质中剪接活性非常低,极大限制了蛋白质内含子的开发和应用。为了开发一个可以同时对蛋白质内含子通用性和剪接活性进行筛选的系统,利用Bsa I限制性内切酶识别位点和切割不重合的特性,将Ter ThyX内含子(不含外显子序列)插入到卡那霉素抗性蛋白基因的多个位点。并且摒弃了以往需要结合天然外显子以实现剪接的方法,可以同时对蛋白质内含子的剪接活性和通用性进行筛选。Western blot结果和卡那霉素平板生长结果表明,通过卡那霉素筛选系统可以精确的将蛋白质内含子剪接反应与卡那霉素抗性结合起来,仅从卡那霉素平板上的菌落生长情况即可完成蛋白质内含子剪接活性阳性突变的筛选,是一个快速,稳定的定向进化筛选系统。     

葡萄果实中脱落酸结合蛋白的存在及其性质

葡萄果实微粒体上存在高亲和力的脱落酸（ＡＢＡ）结合位点,这些位点与ＡＢＡ的结合具有饱和性,高亲和力及低容量。胰蛋白酶或ＤＴＴ处理可以使该位点的特异结合活性下降约９０％,表明此结合位点是一种蛋白质,故称为ＡＢＡ结合蛋白,它含有维系蛋白质特定构象的二硫键。该蛋白与ＡＢＡ反应的最适ｐＨ为６．０,说明与配基结合部位可能存在带有正电荷的氨基酸残基,结合活性在２５℃高于０℃,结合反应达到动态平衡需要３０ｍｉｎ     

蛋白质复合物结构预测的集成分子对接方法

蛋白质分子间相互作用与识别是当前生命科学研究的热点,分子对接方法是研究这一问题的有效手段．为了推进分子对接方法的发展,欧洲生物信息学中心组织了国际蛋白质复合物结构预测（CAPRI）竞赛．通过参加CAPRI竞赛,逐步摸索出了一套用于蛋白质复合物结构预测的集成蛋白质一蛋白质分子对接方法HoDock,它包括结合位点预测、初始复合物结构采集、精细复合物结构采集、结构成簇和打分排序以及最终复合物结构挑选等主要步骤．本文以最近的CAPRI Target 39为例,具体说明该方法的主要步骤和应用．该方法在CAPRI Target 39竞赛中取得了比较好的结果,预测结构Model 10是所有参赛小组提交的366个结构中仅有的3个正确结构之一,其配体均方根偏差（L_Rmsd）为0．25nm．在对接过程中,首先用理论预测和实验信息相结合的方法来寻找蛋白质结合位点残基,确认CAPRI Target 39A链的A31TRP和A191HIS,B链的B512ARG和B531ARG为可能结合位点残基．同时,用ZDock程序做不依赖结合位点的初步全局刚性对接．然后,根据结合位点信息进行初步局部刚性对接,从全局和局部对接中挑出了11个初始对接复合物结构．进而,用改进的Rosetta Dock程序做精细位置约束对接,并对每组对接中打分排序前200的结构进行成簇聚类．最后,综合分析打分、成簇和结合位点三方面的信息,得到10个蛋白质复合物结构．竞赛结果表明,A191HIS,B512ARG和B531ARG三个结合位点残基预测正确,提交的10个蛋白质复合物结构中有5个复合物受体一配体界面残基预测成功率较高．与其他参赛小组的对接结果比较,表明HoDock方法具有一定优势．这些结果说明我们提出的集成分子对接方法有助于提高蛋白质复合物结构预测的准确率．     

iSucc-PseAAC:基于集成机器学习的赖氨酸琥珀酰化修饰位点预测

赖氨酸琥珀酰化是一种新型的翻译后修饰,在蛋白质调节和细胞功能控制中发挥重要作用,所以准确识别蛋白质中的琥珀酰化位点是有必要的。传统的实验耗费物力和财力。通过计算方法预测是近段时间以来提出的一种高效的预测方法。本研究中,我们开发了一种新的预测方法iSucc-PseAAC,它是通过使用多种分类算法结合不同的特征提取方法。最终发现,基于耦合序列(PseAAC)特征提取下,使用支持向量机分类效果是最好的,并结合集成学习解决了数据不平衡问题。与现有方法预测效果对比,iSucc-PseAAC在区分赖氨酸琥珀酰化位点方面,更具有意义和实用性。     

Chloramine T-mediated radioiodination of proteins on intact polyacrylamide slab gels

A simple, inexpensive method is described here for the radioiodination of proteins on intact, developed polyacrylamide gels. The method is based on the chloramine T iodination procedure which yields proteins containing ¹²⁵I label specifically in tyrosine residues. When employed with intact polyacrylamide gels, our method allows detection of proteins in amounts too small to be observed by chemical stains, including Coomassie blue. The procedure should, therefore, be useful for analyzing protein mixtures where only a small amount of material is available or for assaying trace contaminants in purified protein preparations. Proteins radioactively labeled by our method are suitable for further analysis by proteolytic cleavage followed by peptide mapping or “fingerprinting.”     

Folding in lipid membranes (FILM): a novel method for the prediction of small membrane protein 3D structures

We present the results of applying a novel knowledge-based method (FILM) to the prediction of small membrane protein structures. The basis of the method is the addition of a membrane potential to the energy terms (pairwise, solvation, steric, and hydrogen bonding) of a previously developed ab initio technique for the prediction of tertiary structure of globular proteins (FRAGFOLD). The method is based on the assembly of supersecondary structural fragments taken from a library of highly resolved protein structures using a standard simulated annealing algorithm. The membrane potential has been derived by the statistical analysis of a data set made of 640 transmembrane helices with experimentally defined topology and belonging to 133 proteins extracted from the SWISS-PROT database. Results obtained by applying the method to small membrane proteins of known 3D structure show that the method is able to predict, at a reasonable accuracy level, both the helix topology and the conformations of these proteins.     

Predicting the helix packing of globular proteins by self-correcting distance geometry.

A new self-correcting distance geometry method for predicting the three-dimensional structure of small globular proteins was assessed with a test set of 8 helical proteins. With the knowledge of the amino acid sequence and the helical segments, our completely automated method calculated the correct backbone topology of six proteins. The accuracy of the predicted structures ranged from 2.3 A to 3.1 A for the helical segments compared to the experimentally determined structures. For two proteins, the predicted constraints were not restrictive enough to yield a conclusive prediction. The method can be applied to all small globular proteins, provided the secondary structure is known from NMR analysis or can be predicted with high reliability.     

Reconstitution of membrane proteins. Spontaneous association of integral membrane proteins with preformed unilamellar lipid bilayers

We have developed a simple method for reconstituting pure, integral membrane proteins into phospholipid-protein vesicles. The method does not depend on use of detergents or sonication. It has been used successfully with three different types of integral membrane proteins: UDPglucuronosyltransferase (EC 2.4.1.17) from pig liver microsomes, cytochrome oxidase (EC 1.9.3.1) from pig heart, and bacteriorhodopsin from Halobacterium halobium. The method depends on preparing unilamellar vesicles of dimyristoylphosphatidylcholine (DMPC) that contain a small amount of myristate as fusogen. Under conditions that the vesicles of DMPC have the property of fusing, all of the above proteins incorporated into bilayers. Two events appear to be involved in forming the phospholipid-protein complexes. The first is a rapid insertion of all proteins into a small percentage of total vesicles. The second is slower but continued fusion of the remaining phospholipid-protein vesicles, or proteoliposomes, with small unilamellar vesicles of DMPC. This latter process was inhibited by conditions under which vesicles of DMPC themselves would not fuse. On the basis of proton pumping by bacteriorhodopsin and negative staining, the vesicles were unilamellar and large. The data suggest that insertion of the above integral membrane proteins into vesicles occurred independently of fusion between vesicles.     

Small-molecule reagents for cellular pull-down experiments

Affinity purification of interacting proteins from cellular extracts is a powerful technique for identifying the cellular targets of small molecules. Affinity matrix-based small-molecule reagents are usually prepared by conjugating small molecules of interest to a solid support such as agarose. This protocol describes an efficient and robust method to immobilize small molecules containing a primary alcohol, a common functional group in small molecules, especially in small molecules prepared using diversity-oriented synthesis. This method comprises one element of a systematic approach to the target identification problem in chemical biology.     

Robust and Systematic Drug Screening Method Using Chemical Arrays and the Protein Library: Identification of Novel Inhibitors of Carbonic Anhydrase II

The identification of specific interactions between small molecules and human proteins of interest is a fundamental step in chemical biology and drug development. Here we describe an efficient method to obtain novel binding ligands of human proteins by a chemical array approach. Our method includes large-scale ligand screening with two libraries, proteins and chemicals, the use of cell lysates that express proteins of interest fused with red fluorescent protein, and high-throughput screening by merged display analysis, which removes false positive signals from array experiments. Using our systematic platform, we detected novel inhibitors of carbonic anhydrase II. It is suggested that our systematic platform is a rapid and robust approach to screen novel ligands for human proteins of interest.     

Iodination of proteins on nitrocellulose blotting paper

A procedure is described for radioiodination to a high specific activity of proteins immobilized on nitrocellulose membranes. After radioiodination, the proteins can be removed from the nitrocellulose to perform such structural analyses as proteolytic mapping. This method allows the detection of small amounts of protein recognized by immunoblotting and may be used to compare the structure of immunologically related proteins.     

Yeast ribosomal proteins: V. Correlation of several nomenclatures and proposal of a standard nomenclature

Summary A tentative nomenclature (YP number) for yeast (Saccharomyces cerevisiae) cytoplasmic ribosomal proteins, which is used in our laboratory (Otaka and Kobata 1978; Higo and Otaka 1979), has been correlated with those of Warner and Gorenstein (1978) and several others. Our nomenclature is based on the two-dimensional gel electrophoretic pattern of proteins as analyzed by a modified method of Mets and Bogorad (1974), while others have used various modifications of Kaltschmidt and Wittmann's two-dimensional gel electrophoresis (1970). The method of correlation involved the examination in our twodimensional electrophoresis system of each protein spot excised from gel patterns prepared by Kaltschmidt and Wittmann's method or vice versa.The numbers of protein species recognized in this paper are 29 for small subunit, and 44 for large subunit. Based on these results, we propose a standard nomenclature for yeast ribosomal proteins, in which the designations YS1–YS29 and YL1–YL44 have been given to the small subunit proteins and the large subunit proteins respectively.     

Robust and systematic drug screening method using chemical arrays and the protein library: identification of novel inhibitors of carbonic anhydrase II

The identification of specific interactions between small molecules and human proteins of interest is a fundamental step in chemical biology and drug development. Here we describe an efficient method to obtain novel binding ligands of human proteins by a chemical array approach. Our method includes large-scale ligand screening with two libraries, proteins and chemicals, the use of cell lysates that express proteins of interest fused with red fluorescent protein, and high-throughput screening by merged display analysis, which removes false positive signals from array experiments. Using our systematic platform, we detected novel inhibitors of carbonic anhydrase II. It is suggested that our systematic platform is a rapid and robust approach to screen novel ligands for human proteins of interest.     

Characterisation of eukaryotic ribosomal proteins.

A simple method of two-dimensional polyacrylamide gel electrophoresis is described which affords: (1) high resolution of eukaryotic ribosomal proteins; (2) good recovery of protein in the transfer from first to second dimension; and (3) characterisation of the separated proteins in terms of molecular weights and other electrophoretic properties. Using this method, we have characterised 70 proteins in rabbit reticulocyte ribosomes, 30 from the small subunit and 40 from the large subunit. The molecular weight distribution is compared with those obtained by other authors after fractionation of the proteins in two dimensions.