鹅膏毒肽与RNA聚合酶II相互作用的分子机制研究

研究鹅膏毒肽与RNA聚合酶II相互作用的分子机制,利用分子对接方法获得了9种鹅膏毒肽与RNA聚合酶II相互作用的结合模式、结合位点、对接能和抑制常数等信息,并对鹅膏毒肽的毒性与结构间的构效关系进行了考察。结果表明：利用分子对接方法获得的鹅膏毒肽与RNA聚合酶II相互作用的信息与实验结果相一致;不同R2取代基引起毒素与聚合酶II结合能力强弱不同,从而导致鹅膏毒肽分子间的毒性差异。结果证实了运用分子对接方法探索多肽分子与蛋白质相互作用的可行性,为在分子水平上研究多肽与蛋白质的相互作用开拓了新的思路。     

肽库及其在分子识别中的应用

肽库(peptide library)是利用基因克隆技术将合成的一组寡核苷酸混合物（小肽基因混合物）克隆至线性噬菌体基因组中,使之以融合蛋白的形式在噬菌体的外壳蛋白（Ⅲ或Ⅷ）的氨基端表达.肽库技术可以应用于与分子识别有关的许多领域,如：药物设计,疫苗设计,酶的抑制剂的筛选,蛋白质间的相互作用的研究等等.这是一项新兴的具有很高的实用价值和理论价值的技术.文中综述了其产生、发展和未来的应用前景.     

噬菌体展示肽库在细胞信号转导研究中的应用

细胞信号转导是一个由信号分子相互作用介导的生物信息传递的过程 ,蛋白质之间以及蛋白质与其他分子间的相互作用是信号转导的基础。近年来 ,利用噬菌体展示肽库技术研究细胞信号转导 ,取得了很多有意义的结果。1.鉴定信号蛋白识别结合位点信号蛋白之间特异性的识别结合主要通过一小段保守区实现 ,如ＳＨ2区 (Ｓｒｃ ｈｏｍｏｌｏｇｙｄｏｍａｉｎ)、ＳＨ3区、ＰＴＢ区 (ｐｈｏｓｐｈｏｔｙｒｏｓｉｎｅ ｂｉｎｄｉｎｇｄｏｍａｉｎ)等。用噬菌体展示肽库技术可以快速获得与这些保守区结合的配体的结构信息。用Ｓｒｃ酪氨酸激酶的ＳＨ3区筛…     

功能蛋白微阵列的作用

对蛋白质阵列的两大功能—分子识别和酶活测定进行了阐述.其中前者包括蛋白质-D N A间的相互作用、蛋白质-蛋白质复合体的相互作用、蛋白质-小分子之间的相互作用;后者包括阵列蛋白作为底物来测酶活、阵列蛋白作为酶的酶活.     

蛋白质相互作用研究的新技术与新方法

目前,蛋白质相互作用已成为蛋白质组学研究的热点. 新方法的建立及对已有技术的改进标志着蛋白质相互作用研究的不断发展和完善．在技术改进方面,本文介绍了弥补酵母双杂交的蛋白定位受限等缺陷的细菌双杂交系统;根据目标蛋白特性设计和修饰TAP标签来满足复合体研究要求的串联亲和纯化技术,以及在双分子荧光互补基础上发展的动态检测多个蛋白质间瞬时、弱相互作用的多分子荧光互补技术．还综述了近两年建立的新方法：与免疫共沉淀相比,寡沉淀技术直接研究具有活性的蛋白质复合体;减量式定量免疫沉淀方法排除了蛋白质复合体中非特异性相互作用的干扰;原位操作的多表位－配基绘图法避免了样品间差异的影响,以及利用多点吸附和交联加固研究弱蛋白质相互作用的固相蛋白质组学方法.     

促进或抑制α-synuclein蛋白异常聚集的相互作用蛋白质

α-synuclein蛋白的异常聚集在共核蛋白病的发病过程中起到了关键性作用。与α-synuclein相互作用的蛋白质对其异常聚集起着不同的调节作用,有的蛋白质(如:蛋白synphilin-1、微管蛋白、A-β肽等)会促进α-synuclein蛋白的异常聚集,而另外一些蛋白质(如:膜联蛋白A5、基于自识别元素设计的小肽等)却能够抑制α-synuclein蛋白的异常聚集。认识与α-synuclein相互作用的蛋白,并研究其作用位点,是从分子水平上理解α-synuclein蛋白质异常聚集、揭示共核蛋白病致病机制,以及设计新药物的基础。分子动力学模拟为开展这方面研究开辟了新的途径。文章对该领域的研究进展进行了综述。     

多元光学蛋白质芯片研究取得重要进展

蛋白质芯片技术是一种新型蛋白质分析技术,具有集成、并行、快速和自动化分析的优势。多元光学蛋白质芯片传感器,仅需微量生理或生物采样,即可以同时检测、识别和纯化不同的生物分子和研究分子间的相互作用。无需标记,可以直接测量像血浆、细胞裂解液等生理样品。     

双杂交和质谱技术在蛋白质-蛋白质相互作用研究中的应用

基因的功能是由蛋白质来执行的,而蛋白质要通过与其他生物分子相互作用来完成其各种生物功能。因此,如果能够快速做出蛋白质在不同时间、空间和不同环境中的相互作用图谱,就会帮助我们了解这些蛋白质的功能,进而了解许多生命活动的机制。目前,用于大规模研究蛋白质间相互作用的方法主要有酵母双杂交系统及其衍生系统、亲和纯化与质谱分析联用技术,前者用于研究蛋白分子间的两两相互作用,后者用于研究蛋白质复合物间的相互作用。本文主要阐述了酵母双杂交、细菌双杂交、哺乳动物细胞双杂交、亲和纯化与质谱联用技术在大规模蛋白质相互作用研究中的应用。     

分子内分子伴侣机制的研究进展

在原核生物、真核生物及病毒中,一些蛋白质的折叠不符合Anfinsen原则,即依靠自身的氨基酸序列是不够的,还需一段被称为分子内分子伴侣(IMC)的肽段来协助折叠．根据机制不同,IMC可分为两类：第一类IMC引导成熟肽折叠为具有空间结构的蛋白质;第二类IMC协助成熟肽的多聚化而使其获得生物学功能．IMC能提供比分子伴侣更契合的结构,更有效地引导成熟肽折叠,是一种更优的折叠策略．研究IMC分子机制,不仅能够确定IMC上哪些残基的协同作用引导成熟肽折叠,而且可通过改变或修饰其侧链来改造成熟肽,拓展传统的蛋白质工程．     

JACS：核酸与蛋白质相互作用机理研究获进展

近期来自吉林大学的研究人员分别与清华大学和中科院等处的研究人员在高分子结晶态分子间相互作用和RNA与蛋白质间相互作用研究方面取得重要进展。所获得的跨学科研究新成果公布在著名的国际期刊《美国化学会志》（J．Am．Chem．Soc．）上。获得了Nature Materials等多个杂志的推荐。     

Structures of designed armadillo repeat proteins binding to peptides fused to globular domains

Designed armadillo repeat proteins (dArmRP) are α‐helical solenoid repeat proteins with an extended peptide binding groove that were engineered to develop a generic modular technology for peptide recognition. In this context, the term “peptide” not only denotes a short unstructured chain of amino acids, but also an unstructured region of a protein, as they occur in termini, loops, or linkers between folded domains. Here we report two crystal structures of dArmRPs, in complex with peptides fused either to the N‐terminus of Green Fluorescent Protein or to the C‐terminus of a phage lambda protein D. These structures demonstrate that dArmRPs bind unfolded peptides in the intended conformation also when they constitute unstructured parts of folded proteins, which greatly expands possible applications of the dArmRP technology. Nonetheless, the structures do not fully reflect the binding behavior in solution, that is, some binding sites remain unoccupied in the crystal and even unexpected peptide residues appear to be bound. We show how these differences can be explained by restrictions of the crystal lattice or the composition of the crystallization solution. This illustrates that crystal structures have to be interpreted with caution when protein–peptide interactions are characterized, and should always be correlated with measurements in solution.     

Rate of loop formation in peptides: a simulation study

Experimental techniques with high temporal and spatial resolution extend our knowledge of how biological macromolecules self-organise and function. Here, we provide an illustration of the convergence between simulation and experiment made possible by techniques such as triplet-triplet energy transfer and fluorescence quenching with long-lifetime and fast-quenching fluorescent probes. These techniques have recently been used to determine the average time needed for two residues in a peptide or protein segment to form a contact. The timescale of this process is accessible to computer simulation, providing a microscopic interpretation of the data and yielding new insight into the disordered state of proteins. Conversely, such experimental data also provide a test of the validity of alternative choices for the molecular models used in simulations, indicating their possible deficiencies. We carried out simulations of peptides of various composition and length using several models. End-to-end contact formation rates and their dependence on peptide length agree with experimental estimates for some sequences and some force fields but not for others. The deviations are due to artefactual structuring of some peptides, which is not observed when an atomistic model for the solvation water is used. Simulations show that the observed experimental rates are compatible with considerably different distributions of the end-to-end distance; for realistic models, these are never Gaussian but indicative of a rugged energy landscape.     

A synthetic peptide forms voltage-gated porin-like ion channels in lipid bilayer membranes

Design of simple protein structures represents the essential first step toward novel macromolecules and understanding the basic principles of protein folding. Our work focuses on the ion channel formation and structure of peptides having a repeated pattern of glycine residues. Investigation of the ion channel properties of a glycine repeat peptide, VSLGLSIGFSVGVSIGWSFGRSRG revealed the formation of porin-like high conductance, multimeric, non-selective voltage-gated channels in phospholipid bilayer membranes. ATR-IR and CD spectroscopic studies showed an anti-parallel beta sheet structure in membranes. The formation of porin-like ion channels by a beta sheet peptide suggests spontaneous assembly into a beta barrel structure through oligomerization as in pore forming bacterial toxins. The present work is the first example of a short synthetic peptide mimicking the pore characteristics of a complex beta barrel protein and demonstrates that smaller peptides are capable of mimicking the complex functional properties of natural ion channels. This will have implications in understanding the folding of beta sheet proteins in membranes, the mechanism of two state voltage gating, and the role of glycine residues in beta barrel proteins.     

Membrane permeability commonly shared among arginine-rich peptides

Delivery of proteins and other macromolecules using membrane-permeable carrier peptides is a recently developed novel technology, which enables us to modulate cellular functions for biological studies with therapeutic potential. One of the most often used carrier peptides is the arginine-rich basic peptide derived from HIV-1 Tat protein [HIV-1 Tat (48-60)]. Using this peptide, efficient intracellular delivery of molecules including proteins, oligonucleic acids and liposomes has been achieved. We have demonstrated that these features were commonly shared among many arginine-rich peptides such as HIV-1 Rev (34-50) and octaarginine. Not only the linear peptides but also branched-chain peptides showed efficient internalization with an optimum number of arginines (approximately eight residues). The structural and mechanistic features of the translocation of these membrane-permeable arginine-rich peptides are reviewed.     

Basic amino acids in a distinct subset of signal peptides promote interaction with the signal recognition particle

Previous studies have demonstrated that signal peptides bind to the signal recognition particle (SRP) primarily via hydrophobic interactions with the 54-kDa protein subunit. The crystal structure of the conserved SRP ribonucleoprotein core, however, raised the surprising possibility that electrostatic interactions between basic amino acids in signal peptides and the phosphate backbone of SRP RNA may also play a role in signal sequence recognition. To test this possibility we examined the degree to which basic amino acids in a signal peptide influence the targeting of two Escherichia coli proteins, maltose binding protein and OmpA. Whereas both proteins are normally targeted to the inner membrane by SecB, we found that replacement of their native signal peptides with another moderately hydrophobic but unusually basic signal peptide (DeltaEspP) rerouted them into the SRP pathway. Reduction in either the net positive charge or the hydrophobicity of the DeltaEspP signal peptide decreased the effectiveness of SRP recognition. A high degree of hydrophobicity, however, compensated for the loss of basic residues and restored SRP binding. Taken together, the data suggest that the formation of salt bridges between SRP RNA and basic amino acids facilitates the binding of a distinct subset of signal peptides whose hydrophobicity falls slightly below a threshold level.     

Problems Associated with the Identification of Proteins in Homologous Families: The Wool Keratin Family as a Case Study

The keratin proteins from wool can be divided into two classes: the intermediate filament proteins (IFPs) and the matrix proteins. Using peptide mass spectral fingerprinting it was possible to match spots to the known theoretical sequences of some IFPs in web-based databases, as enzyme digestion generated sufficient numbers of peptides from each spot to achieve this. In contrast, it was more difficult to obtain good matches for some of the lower molecular weight matrix proteins. Relatively few peaks were generated from tryptic digests of high-sulfur proteins because of their lower molecular weight and the absence of basic residues in the first two-thirds of the sequence. Their high sequence homology also means that generally only a few of these peptides could be considered to be unique identifiers for each protein. Nevertheless, it was still possible to uniquely identify some of these proteins, while the presence of two peptides in the matrix-assisted laser desorption/ionization time-of-flight mass spectrum allowed classification of other protein spots as being members of this family. Only one major peptide peak was generated by the high-glycine tyrosine proteins (HGTPs) and there were relatively few sequences available in web-based databases, limiting their identification to one HGTP family.     

Effects of macromolecular crowding on the inhibition of virus assembly and virus-cell receptor recognition

Biological fluids contain a very high total concentration of macromolecules that leads to volume exclusion by one molecule to another. Theory and experiment have shown that this condition, termed macromolecular crowding, can have significant effects on molecular recognition. However, the influence of molecular crowding on recognition events involving virus particles, and their inhibition by antiviral compounds, is virtually unexplored. Among these processes, capsid self-assembly during viral morphogenesis and capsid-cell receptor recognition during virus entry into cells are receiving increasing attention as targets for the development of new antiviral drugs. In this study, we have analyzed the effect of macromolecular crowding on the inhibition of these two processes by peptides. Macromolecular crowding led to a significant reduction in the inhibitory activity of: 1), a capsid-binding peptide and a small capsid protein domain that interfere with assembly of the human immunodeficiency virus capsid, and 2), a RGD-containing peptide able to block the interaction between foot-and-mouth disease virus and receptor molecules on the host cell membrane (in this case, the effect was dependent on the conditions used). The results, discussed in the light of macromolecular crowding theory, are relevant for a quantitative understanding of molecular recognition processes during virus infection and its inhibition.     

Identifying Protein-protein Interaction Sites Using Peptide Arrays

Protein-protein interactions mediate most of the processes in the living cell and control homeostasis of the organism. Impaired protein interactions may result in disease, making protein interactions important drug targets. It is thus highly important to understand these interactions at the molecular level. Protein interactions are studied using a variety of techniques ranging from cellular and biochemical assays to quantitative biophysical assays, and these may be performed either with full-length proteins, with protein domains or with peptides. Peptides serve as excellent tools to study protein interactions since peptides can be easily synthesized and allow the focusing on specific interaction sites. Peptide arrays enable the identification of the interaction sites between two proteins as well as screening for peptides that bind the target protein for therapeutic purposes. They also allow high throughput SAR studies. For identification of binding sites, a typical peptide array usually contains partly overlapping 10-20 residues peptides derived from the full sequences of one or more partner proteins of the desired target protein. Screening the array for binding the target protein reveals the binding peptides, corresponding to the binding sites in the partner proteins, in an easy and fast method using only small amount of protein.In this article we describe a protocol for screening peptide arrays for mapping the interaction sites between a target protein and its partners. The peptide array is designed based on the sequences of the partner proteins taking into account their secondary structures. The arrays used in this protocol were Celluspots arrays prepared by INTAVIS Bioanalytical Instruments. The array is blocked to prevent unspecific binding and then incubated with the studied protein. Detection using an antibody reveals the binding peptides corresponding to the specific interaction sites between the proteins.     

The sequence dependence of fiber organization. A comparative molecular dynamics study of the islet amyloid polypeptide segments 22-27 and 22-29

Amyloid fiber formation and the possible polymorphism of molecular arrangements depend on the polypeptide length and composition. Here, we seek the chemical clues underlying these processes. Our starting point is based on the experimental observation that some short peptide segments are able to develop fibers that are very similar to those of their original parent proteins. We focus our study on the NFGAILSS peptide, derived from the human islet amyloid polypeptide (residues 22-29). This peptide turned out to be a perfect example, illustrating the fact that the amyloid microscopic organization is highly complex, rather than simply involving hydrogen bond formation. Furthermore, obtaining a reliable molecular model has allowed us to analyze the differences between the amyloid structure we have obtained for this peptide and that obtained for the previously studied, two residues shorter, segment (residues 22-27, NFGAIL). This comparative study yields some clues about chemical events that govern the aggregation of proteins into oriented fibers, such as molecular packing between sheets and the degree of interaction specificity. We characterize the important role played by the hydrophobic and aromatic residues in the inter-sheet association and present new approaches toward the understanding of the nature of events that are likely to take place during fibril formation. These include analysis of interaction patterns derived from specific sheet-associated packing.