EB病毒编码的潜伏膜蛋白与泛素蛋白酶系统

EB病毒(Epstein-Barr virus,EBV)是人类疱疹病毒,与淋巴系统、上皮细胞肿瘤相关。其编码潜伏性膜蛋白(LMPl、LMP2A和LMP2B)特别是LMP1,由于它是众多EBV编码蛋白质中唯一被明确证明能恶性转化原代B细胞、鼠成纤维细胞和人上皮细胞的蛋白质,所以被列为癌基因。最近对潜伏膜蛋白的研究显示．潜伏膜蛋白与病毒利用泛素蛋白酶系统来达到逃避宿主免疫应答等机制有关,研究这个过程也许可以开发新的策略来防治EBV相关肿瘤。     

A Membrane Topology Model for Human Interferon Inducible Transmembrane Protein 1

InterFeron Inducible TransMembrane proteins 1–3 (IFITM1, IFITM2 and IFITM3) are a family of proteins capable of inhibiting the cellular entry of numerous human and animal viruses. IFITM1-3 are unique amongst the currently described viral restriction factors in their apparent ability to block viral entry. This restrictive property is dependant on the localisation of the proteins to plasma and endosomal membranes, which constitute the main portals of viral entry into cells. The topology of the IFITM proteins within cell membranes is an unresolved aspect of their biology. Here we present data from immunofluorescence microscopy, protease cleavage, biotin-labelling and immuno-electron microscopy assays, showing that human IFITM1 has a membrane topology in which the N-terminal domain resides in the cytoplasm, and the C-terminal domain is extracellular. Furthermore, we provide evidence that this topology is conserved for all of the human interferon-induced IFITM proteins. This model is consistent with that recently proposed for murine IFITM3, but differs from that proposed for murine IFITM1.     

小鼠肝质膜蛋白质的生物信息学研究

随着高通量蛋白质组研究技术的发展,使用生物信息学方法对鉴定出的蛋白质进行批量的物理化学性质和功能属性的研究显得越来越重要．对2-DE分离的小鼠肝质膜中鉴定的209个蛋白质运用生物信息学方法进行了一系列的功能属性分析,包括统计分析ProtParam软件计算出的209个蛋白质的理论相对分子质量、等电点以及疏水值的分布情况,使用TMHMM预测蛋白质的跨膜区数目,运用系统发生谱方法预测蛋白质相互作用网络,根据其相互作用网络预测部分未知蛋白质的功能．     

Membrane Protein Profiling of Human Islets of Langerhans Using Several Extraction Methods

Introduction  

Proteomic characterization of the human pancreatic islets, containing the insulin producing beta-cells, is likely to be of great importance for improved treatment and understanding of the pathophysiology of diabetes mellitus.     

The Major Aeromonas veronii Outer Membrane Protein: Gene Cloning and Sequence Analysis

The gene encoding the major outer membrane protein (OMP) from Aeromonas veronii, Omp38, was cloned and characterized. Sequence analysis revealed an open reading frame of 1,047 nucleotides coding for a primary protein of 349 amino acids with a 20–amino-acid signal peptide at the N-terminal and the consensus sequence Ala-X-Ala (Ala-Asn-Ala) as the signal peptidase I recognition site. The mature protein is composed of 329 amino acids with a calculated molecular mass of 36,327 Da. The degree of identity of the deduced Omp38 amino acid sequence to porins from enteric bacteria (OmpF, PhoE, and OmpC) was only 30%. Nevertheless, Omp38 possesses typical features of Gram-negative porins, including acidic pI, high glycine and low proline content, no cysteine residues, and a carboxy-terminal Phe. On the basis of PhoE-OmpF three-dimensional structure and the Kyte-Doolittle hydrophobicity analysis, it seems likely that Omp38 secondary structure consists of 16 antiparallel β-strands and 8 loops. Phylogenetic analyses among Omp38 and related porins from Gram-negative bacteria originate well-defined clusters that agree with the taxonomy of the corresponding organisms.     

人红细胞膜带3蛋白的提纯与鉴定

提出了一种分离纯化人红细胞膜带3蛋白的不含血型糖蛋白制剂的改良方法:先后用0.89％NaCl、20mM pH8.0磷酸钠和0.05％TritonX-100处理膜除去膜骨骼蛋白类和血型糖蛋白,再用自行设计的凝胶制备电泳装置进一步纯化。冰冻干燥的制剂是均质的,得率为18.5±2.85％,它的分子量、氨基酸组成和紫外吸收光谱与文献报道基本相同。     

ESCRT系统： 一个多功能的蛋白转运及膜剪切机器

转运必需内体分选复合物（endosomal sorting complex required for transport, ESCRT）系统是真核细胞中完成内体（endosome）膜内陷以形成多囊泡体（multi-vesicular body, MVB）的分子机器.其主要功能是促进被泛素（ubiquitin）标记的膜蛋白的降解, 还与细胞分裂、病毒出芽、细胞自噬以及真菌pH感知相关. ESCRT系统包括ESCRT-0,-Ⅰ,-Ⅱ,-Ⅲ和Vps4-Vta1共5个蛋白 蛋白复合物.晶体学研究已经解析了大部分复合物的结构. 其促使膜内陷的分子机理一般认为分3步. 首先是ESCRT-Ⅰ和-Ⅱ在内体膜上结合并促使内体膜内陷形成初始芽体. 之后,ESCRT-Ⅲ在芽体颈部聚合并导致芽体的剪切,从而将内腔囊泡（intralumenal vesicles, ILVs）释放到内体腔内,形成MVB. 最后,Vps4/Vta1复合物则以水解ATP提供能量将聚合的ESCRT-Ⅲ解聚以循环使用,完成更多的出芽过程.本文将对ESCRT系统的结构、出芽机理和生物功能几方面做一个综述.     

膜蛋白的表达：在无细胞体系中实现功能性表达、折叠和组装

膜蛋白在人类和其他物种的生命活动中都起着至关重要的作用.在已完成测序的基因组中,膜蛋白占据30%.药物作用靶向位点、细胞之间的信号传递以及对外界环境的探测等功能,大多是通过生物膜上的特殊膜受体蛋白实现的.膜蛋白研究在工业、环境、国防、医学等领域具有重大意义.嗅觉受体蛋白是一类典型的膜蛋白,属于G蛋白偶联受体家族.嗅觉受体蛋白调控着生物的食物寻找、危险趋避和求偶行为.其主要分布于脊椎动物鼻腔和昆虫触角.嗅觉受体蛋白可以直接识别气味分子,将生物信号转化为电信号,最终传递至神经中枢,进而做出相关应答.膜蛋白的获取并不容易.天然组织中的膜蛋白含量太低不足以支撑学术研究.异源表达难以实现膜蛋白整合上膜,这给膜蛋白的结构和功能研究带来很大挑战.无细胞蛋白质合成系统是一个开放体系,且不依赖细胞活性,是体外表达蛋白质的有效方法.通过无细胞蛋白合成体系,在体外实现膜蛋白二聚体的自组装,将为膜蛋白研究带来全新突破.本文总结了用于无细胞表达的膜蛋白研究进展.     

人Transgelin蛋白家族生物信息学分析

本研究通过对人Transgelin蛋白家族(Transgelins)3位成员(Transgelin,-2,-3)的生物信息学预测分析,显示Transgelin和-2等电点分别为8.87和8.41,Transgelin-3等电点为6.84,3位成员均为非分泌型蛋白,且极有可能是跨膜型蛋白.蛋白质稳定性分析结果显示,除Tr...     

酵母双杂交系统在膜蛋白相互作用研究中的应用

膜相关蛋白约占细胞总蛋白质中的1/3,它们大都参与了细胞的诸多生理、病理过程和药物反应机理。研究膜蛋白的相互作用对于揭示细胞的生命活动规律及寻找药物作用靶标都有重要的意义。由于膜蛋白本身的特性及其难以进入核内等原因,经典的酵母双杂交技术并不适用于检测膜蛋白间的相互作用。针对在活细胞中研究膜蛋白相互作用的需要,近年来国际上先后发展了一系列用于膜蛋白相互作用研究的酵母双杂交新系统,并取得了许多重要发现。     

Quantitative Microscopy: Protein Dynamics and Membrane Organisation

The mobility of membrane proteins is a critical determinant of their interaction capabilities and protein functions. The heterogeneity of cell membranes imparts different types of motion onto proteins; immobility, random Brownian motion, anomalous sub-diffusion, 'hop' or confined diffusion, or directed flow. Quantifying the motion of proteins therefore enables insights into the lateral organisation of cell membranes, particularly membrane microdomains with high viscosity such as lipid rafts. In this review, we examine the hypotheses and findings of three main techniques for analysing protein dynamics: fluorescence recovery after photobleaching, single particle tracking and fluorescence correlation spectroscopy. These techniques, and the physical models employed in data analysis, have become increasingly sophisticated and provide unprecedented details of the biophysical properties of protein dynamics and membrane domains in cell membranes. Yet despite these advances, there remain significant unknowns in the relationships between cholesterol-dependent lipid microdomains, protein-protein interactions, and the effect of the underlying cytoskeleton. New multi-dimensional microscopy approaches may afford greater temporal and spatial resolution resulting in more accurate quantification of protein and membrane dynamics in live cells.     

Membrane Protein Frustration: Protein Incorporation into Hydrophobic Mismatched Binary Lipid Mixtures

Bacteriophage M13 major coat protein was reconstituted in different nonmatching binary lipid mixtures composed of 14:1PC and 22:1PC lipid bilayers. Challenged by this lose-lose situation of hydrophobic mismatch, the protein-lipid interactions are monitored by CD and site-directed spin-label electron spin resonance spectroscopy of spin-labeled site-specific single cysteine mutants located in the C-terminal protein domain embedded in the hydrophobic core of the membrane (I39C) and at the lipid-water interface (T46C). The CD spectra indicate an overall α-helical conformation irrespective of the composition of the binary lipid mixture. Spin-labeled protein mutant I39C senses the phase transition in 22:1PC, in contrast to spin-labeled protein mutant T46C, which is not affected by the transition. The results of both CD and electron spin resonance spectroscopy clearly indicate that the protein preferentially partitions into the shorter 14:1PC both above and below the gel-to-liquid crystalline phase transition temperature of 22:1PC. This preference is related to the protein tilt angle and energy penalty the protein has to pay in the thicker 22:1PC. Given the fact that in Escherichia coli, which is the host for M13 bacteriophage, it is easier to find shorter 14 carbon acyl chains than longer 22 carbon acyl chains, the choice the M13 coat protein makes seems to be evolutionary justified.     

Phosphoproteome Analysis of Functional Mitochondria Isolated from Resting Human Muscle Reveals Extensive Phosphorylation of Inner Membrane Protein Complexes and Enzymes

Mitochondria play a central role in energy metabolism and cellular survival, and consequently mitochondrial dysfunction is associated with a number of human pathologies. Reversible protein phosphorylation emerges as a central mechanism in the regulation of several mitochondrial processes. In skeletal muscle, mitochondrial dysfunction is linked to insulin resistance in humans with obesity and type 2 diabetes. We performed a phosphoproteomics study of functional mitochondria isolated from human muscle biopsies with the aim to obtain a comprehensive overview of mitochondrial phosphoproteins. Combining an efficient mitochondrial isolation protocol with several different phosphopeptide enrichment techniques and LC-MS/MS, we identified 155 distinct phosphorylation sites in 77 mitochondrial phosphoproteins, including 116 phosphoserine, 23 phosphothreonine, and 16 phosphotyrosine residues. The relatively high number of phosphotyrosine residues suggests an important role for tyrosine phosphorylation in mitochondrial signaling. Many of the mitochondrial phosphoproteins are involved in oxidative phosphorylation, tricarboxylic acid cycle, and lipid metabolism, i.e. processes proposed to be involved in insulin resistance. We also assigned phosphorylation sites in mitochondrial proteins involved in amino acid degradation, importers and transporters, calcium homeostasis, and apoptosis. Bioinformatics analysis of kinase motifs revealed that many of these mitochondrial phosphoproteins are substrates for protein kinase A, protein kinase C, casein kinase II, and DNA-dependent protein kinase. Our results demonstrate the feasibility of performing phosphoproteome analysis of organelles isolated from human tissue and provide novel targets for functional studies of reversible phosphorylation in mitochondria. Future comparative phosphoproteome analysis of mitochondria from healthy and diseased individuals will provide insights into the role of abnormal phosphorylation in pathologies, such as type 2 diabetes.Mitochondria are the primary energy-generating systems in eukaryotes. They play a crucial role in oxidative metabolism, including carbohydrate metabolism, fatty acid oxidation, and urea cycle, as well as in calcium signaling and apoptosis (1, 2). Mitochondrial dysfunction is centrally involved in a number of human pathologies, such as type 2 diabetes, Parkinson disease, and cancer (3). The most prevalent form of cellular protein post-translational modifications (PTMs),1 reversible phosphorylation (4–6), is emerging as a central mechanism in the regulation of mitochondrial functions (7, 8). The steadily increasing numbers of reported mitochondrial kinases, phosphatases, and phosphoproteins imply an important role of protein phosphorylation in different mitochondrial processes (9–11).Mass spectrometry (MS)-based proteome analysis is a powerful tool for global profiling of proteins and their PTMs, including protein phosphorylation (12, 13). A variety of proteomics techniques have been developed for specific enrichment of phosphorylated proteins and peptides and for phosphopeptide-specific data acquisition techniques at the MS level (14). Enrichment methods based on affinity chromatography, such as titanium dioxide (TiO₂) (15–17), zwitterionic hydrophilic interaction chromatography (ZIC-HILIC) (18), immobilized metal affinity chromatography (IMAC) (19, 20), and ion exchange chromatography (strong anion exchange and strong cation exchange) (21, 22), have shown high efficiencies for enrichment of phosphopeptides (14). Recently, we demonstrated that calcium phosphate precipitation (CPP) is highly effective for enriching phosphopeptides (23). It is now generally accepted that no single method is comprehensive, but combinations of different enrichment methods produce distinct overlapping phosphopeptide data sets to enhance the overall results in phosphoproteome analysis (24, 25). Phosphopeptide sequencing by mass spectrometry has seen tremendous advances during the last decade (26). For example, MS/MS product ion scanning, multistage activation, and precursor ion scanning are effective methods for identifying serine (Ser), threonine (Thr), and tyrosine (Tyr) phosphorylated peptides (14, 26).A “complete” mammalian mitochondrial proteome was reported by Mootha and co-workers (27) and included 1098 proteins. The mitochondrial phosphoproteome has been characterized in a series of studies, including yeast, mouse and rat liver, porcine heart, and plants (19, 28–31). To date, the largest data set by Deng et al. (30) identified 228 different phosphoproteins and 447 phosphorylation sites in rat liver mitochondria. However, the in vivo phosphoproteome of human mitochondria has not been determined. A comprehensive mitochondrial phosphoproteome is warranted for further elucidation of the largely unknown mechanisms by which protein phosphorylation modulates diverse mitochondrial functions.The percutaneous muscle biopsy technique is an important tool in the diagnosis and management of human muscle disorders and has been widely used to investigate metabolism and various cellular and molecular processes in normal and abnormal human muscle, in particular the molecular mechanism underlying insulin resistance in obesity and type 2 diabetes (32). Skeletal muscle is rich in mitochondria and hence a good source for a comprehensive proteomics and functional analysis of mitochondria (32, 33).The major aim of the present study was to obtain a comprehensive overview of site-specific phosphorylation of mitochondrial proteins in functionally intact mitochondria isolated from human skeletal muscle. Combining an efficient protocol for isolation of skeletal muscle mitochondria with several different state-of-the-art phosphopeptide enrichment methods and high performance LC-MS/MS, we identified 155 distinct phosphorylation sites in 77 mitochondrial phosphoproteins, many of which have not been reported before. We characterized this mitochondrial phosphoproteome by using bioinformatics tools to classify functional groups and functions, including kinase substrate motifs.     

人A1AT蛋白的生物信息学分析

通过生物信息学预测分析程序发现,人A1AT(alpha-1 antitrypsin)蛋白是由418个氨基酸组成的外分泌蛋白质,其等电点为5.37。同源性分析推断,在其第73~93位和第351~372位氨基酸间存在两个重要的功能区域。此外,A1AT蛋白二级结构中存在13个较大的α螺旋区域,占总蛋白质的42.58%。高级结构的分析发现,RCL结构域的存在对A1AT的结构和功能具有重要的影响。GO和KEGG分析发现,A1AT参与机体抗炎症反应、凝血反应以及细胞的迁移、侵袭、增殖过程。分析所得的A1AT生物信息学数据为其在疾病诊断和治疗方面的研究提供了重要的理论数据。     

Global Membrane Protein Interactome Analysis using In vivo Crosslinking and Mass Spectrometry-based Protein Correlation Profiling

We present a methodology using in vivo crosslinking combined with HPLC-MS for the global analysis of endogenous protein complexes by protein correlation profiling. Formaldehyde crosslinked protein complexes were extracted with high yield using denaturing buffers that maintained complex solubility during chromatographic separation. We show this efficiently detects both integral membrane and membrane-associated protein complexes,in addition to soluble complexes, allowing identification and analysis of complexes not accessible in native extracts. We compare the protein complexes detected by HPLC-MS protein correlation profiling in both native and formaldehyde crosslinked U2OS cell extracts. These proteome-wide data sets of both in vivo crosslinked and native protein complexes from U2OS cells are freely available via a searchable online database (www.peptracker.com/epd). Raw data are also available via ProteomeXchange (identifier PXD003754).Proteins rarely work as monomers to carry out all the biological processes needed for cells to function. An estimate of the total number of protein-protein interactions within the human proteome, based on currently available data sets, is ∼650,000 (1). This is likely an underestimate, given that many proteins form either transient, or weak interactions within intact cells that may not yet have been detected. This suggests that the majority of human proteins can participate in protein complex formation, at least under some conditions. This includes the many well-studied soluble protein complexes in the cytoplasm, exemplified by the proteasome, ribosomes and cytoskeletal network. It also includes many membrane-associated complexes, for example receptor tyrosine kinase signaling complexes, integrin networks and transmembrane transporters (2). To characterize the many roles of multi-protein complexes in biological regulatory mechanisms, it is important to have convenient methods for the rapid and efficient analysis of their composition and dynamics (3). Ideally, such methods should be applicable to system-wide studies and allow the analysis of endogenous proteins, rather than exclusively use tagged and/or over-expressed baits.The methods available for the proteome-wide analysis of protein interactions have developed swiftly over the last ten years. This field is dominated by affinity-enrichment based approaches, using either tagged constructs, or antibodies specific for endogenous proteins. Another approach is in vivo proximity labeling, based, for example, on the exogenous expression of a protein of interest, fused either to a promiscuous biotin-ligase (BioID) (4), or to a peroxidase enzyme that activates biotin-phenol (APEX) (5). While these data sets have proved very useful, there are some downsides. For example, a large expense in terms of both time and money to generate the thousands of individual “bait” proteins required for global interaction analyses. In addition, each of these affinity enrichments will be performed in only one type of buffer system, which is unlikely to be compatible with the maintenance of all protein-protein interactions. Another dimension to the analytical problem is that many proteins are expressed as different sized isoforms and/or in different post-translationally modified forms, resulting in formation of multiple, related, but functionally distinct complexes, with different combinations of interaction partners (6). Using affinity-enrichment/pull-down methods alone makes it difficult to resolve such mixtures of different forms of related protein complexes, complicating a detailed understanding of biological response mechanisms.An alternative strategy involves protein correlation profiling-MS, i.e. correlating similarities in the fractionation profiles of proteins detected by mass spectrometry, assuming that proteins in a common complex will cofractionate. This approach was previously applied to the analysis of subcellular organelle proteomes (7, 8), and subsequently extended to analyze soluble protein complexes. Thus, recent studies have shown that chromatography-based separation of soluble protein complexes, combined with fraction collection and high-throughput liquid chromatography-tandem mass spectrometry (LC-MS/MS)¹, facilitates analysis of many hundreds of soluble complexes from a single experiment (6, 9–11). A limitation of all of these studies, however, is that the native extraction conditions used to preserve protein-protein interactions isolates predominantly stable, soluble complexes. For example, many proteins that are integral to membranes are not recovered (12). Similarly, soluble protein complexes that have weakly bound protein subunits can dissociate upon cell lysis and the inevitable dilution associated with extraction. Thus, the potential value of this approach for the system-wide analysis of protein complexes is limited without a covalent tether to hold protein-protein interactions intact during extraction and subsequent chromatographic separation (13).Covalent protein crosslinking has been used extensively to stabilize protein complexes, cultured cells and tissues for subsequent analysis, either by microscopy, nucleotide sequencing or mass spectrometry. The agents employed to crosslink proteins to each other include various chemical groups able to react with the side-chains of either amino acids, nucleotides, carbohydrates or lipids (14). These crosslinking agents vary in the efficiency with which they perfuse into unbroken cells/tissues and the speed of their reaction when in proximity to a suitable chemical group. One of the most widely used crosslinkers is formaldehyde, which can reversibly form a covalent crosslink to stabilize both protein-protein and protein-nucleotide interactions (15–21). One of the main benefits of using formaldehyde is that because of its small size, it readily permeates intact cells and tissues. Another benefit of using formaldehyde is the easy reversal of the crosslinks by heating and subsequent compatibility with mass spectrometry-based proteome analysis.Here, we describe a mass spectrometry-based proteomic approach for the efficient global analysis of protein complexes, including membrane proteins, using in vivo protein crosslinking combined with denaturing extraction. Using high-resolution, size-exclusion chromatography (SEC) to separate crosslinked complexes under denaturing conditions and MS analysis of fractionated proteins, we could identify membrane bound and membrane associated complexes not accessible in native extracts. We present a detailed comparison of the sets of protein complexes that can be identified using protein correlation profiling MS analysis in conjunction with both formaldehyde crosslinked and native extracts from U2OS cells. We provide access to the entire proteome-wide data sets of both in vivo crosslinked and native U2OScell protein complexes via a searchable online database (http://www.peptracker.com/epd/).     

Human Protein Cluster Analysis Using Amino Acid Frequencies

The paper focuses on the development of a software tool for protein clustering according to their amino acid content. All known human proteins were clustered according to the relative frequencies of their amino acids starting from the UniProtKB/Swiss-Prot reference database and making use of hierarchical cluster analysis. Results were compared to those based on sequence similarities. Results: Proteins display different clustering patterns according to type. Many extracellular proteins with highly specific and repetitive sequences (keratins, collagens etc.) cluster clearly confirming the accuracy of the clustering method. In our case clustering by sequence and amino acid content overlaps. Proteins with a more complex structure with multiple domains (catalytic, extracellular, transmembrane etc.), even if classified very similar according to sequence similarity and function (aquaporins, cadherins, steroid 5-alpha reductase etc.) showed different clustering according to amino acid content. Availability of essential amino acids according to local conditions (starvation, low or high oxygen, cell cycle phase etc.) may be a limiting factor in protein synthesis, whatever the mRNA level. This type of protein clustering may therefore prove a valuable tool in identifying so far unknown metabolic connections and constraints.