Glutamate Receptor-interacting Protein 1 Protein Binds to the Microtubule-associated Protein

To identify the interaction proteins for the α-amino-3-hydroxy-5-methyl-4-isoxazole propionate (AMPA) receptor subunit glutamate receptor-interacting protein 1 (GRIP1), GRIP1 interactions with microtubule-associated protein (MAP)-1B light chain (LC) were investigated. GRIP1 interacts with MAP-1A and MAP-1B in the yeast two-hybrid assay, as is indicated also by glutathione S-transferase (GST) pull-down and coimmunoprecipitation with MAP-1B LC antibody in brain fractions. These results suggest a novel mechanism for localizing AMPA receptors to synaptic sites.     

蛋白质间相互作用技术的研究近况

蛋白质间相互作用技术的研究近况黄翠芬叶棋浓（军事医学科学院生物工程研究所,北京１００８５０关键词：蛋白质,相互作用,技术ＲｅｃｅｎｔＡｄｖａｎｃｅｓｉｎｔｈｅＴｅｃｈｎｉｑｕｅｓｏｆＰｒｏｔｅｉｎ┐ＰｒｏｔｅｉｎＩｎｔｅｒａｃｔｉｏｎｓＨｕａｎｇＣｕ...     

Structure of the Non-Catalytic Domain of the Protein Disulfide Isomerase-Related Protein (PDIR) Reveals Function in Protein Binding

Protein disulfide isomerases comprise a large family of enzymes responsible for catalyzing the proper oxidation and folding of newly synthesized proteins in the endoplasmic reticulum (ER). Protein disulfide isomerase-related (PDIR) protein (also known as PDIA5) is a specialized member that participates in the folding of α₁-antitrypsin and N-linked glycoproteins. Here, the crystal structure of the non-catalytic domain of PDIR was determined to 1.5 Å resolution. The structure adopts a thioredoxin-like fold stabilized by a structural disulfide bridge with a positively charged binding surface for interactions with the ER chaperones, calreticulin and ERp72. Crystal contacts between molecules potentially mimic the interactions of PDIR with misfolded substrate proteins. The results suggest that the non-catalytic domain of PDIR plays a key role in the recognition of protein partners and substrates.     

Involvement of the Transmembrane Protein p23 in Biosynthetic Protein Transport

Here, we report the localization and characterization of BHKp23, a member of the p24 family of transmembrane proteins, in mammalian cells. We find that p23 is a major component of tubulovesicular membranes at the cis side of the Golgi complex (estimated density: 12,500 copies/μm² membrane surface area, or ≈30% of the total protein). Our data indicate that BHKp23-containing membranes are part of the cis-Golgi network/intermediate compartment . Using the G protein of vesicular stomatitis virus as a transmembrane cargo molecule, we find that p23 membranes are an obligatory station in forward biosynthetic membrane transport, but that p23 itself is absent from transport vesicles that carry the G protein to and beyond the Golgi complex. Our data show that p23 is not present to any significant extent in coat protein (COP) I-coated vesicles generated in vitro and does not colocalize with COP I buds and vesicles. Moreover, we find that p23 cytoplasmic domain is not involved in COP I membrane recruitment. Our data demonstrate that microinjected antibodies against the cytoplasmic tail of p23 inhibit G protein transport from the cis-Golgi network/ intermediate compartment to the cell surface, suggesting that p23 function is required for the transport of transmembrane cargo molecules. These observations together with the fact that p23 is a highly abundant component in the intermediate compartment, lead us to propose that p23 contributes to membrane structure, and that this contribution is necessary for efficient segregation and transport.     

Segmented Transition Pathway of the Signaling Protein Nitrogen Regulatory Protein C

Recent advances in experimental methods provide increasing evidence that proteins sample the conformational substates that are important for function in the absence of their ligands. An example is the receiver domain of nitrogen regulatory protein C, a member of the phosphorylation-mediated signaling family of “two-component systems.” The receiver domain of nitrogen regulatory protein C samples both inactive conformation and the active conformation before phosphorylation. Here we determine a possible pathway of interconversion between the active state and the inactive state by targeted molecular dynamics simulations and quasi-harmonic analysis; these methods are used because the experimental conversion rate is in the high microsecond range, longer than those that are easily accessible to atomistic molecular dynamics simulations. The calculated pathway is found to be composed of four consecutive stages described by different progress variables. The lowest quasi-harmonic principal components from unbiased molecular dynamics simulations on the active state correspond to the first stage, but not to the subsequent stages of the transition. The targeted molecular dynamics pathway suggests that several transient nonnative hydrogen bonds may facilitate the transition.     

YidC Protein,a Molecular Chaperone for LacY Protein Folding via the SecYEG Protein Machinery

To understand how YidC and SecYEG function together in membrane protein topogenesis, insertion and folding of the lactose permease of Escherichia coli (LacY), a 12-transmembrane helix protein LacY that catalyzes symport of a galactoside and an H⁺, was studied. Although both the SecYEG machinery and signal recognition particle are required for insertion of LacY into the membrane, YidC is not required for translocation of the six periplasmic loops in LacY. Rather, YidC acts as a chaperone, facilitating LacY folding. Upon YidC depletion, the conformation of LacY is perturbed, as judged by monoclonal antibody binding studies and by in vivo cross-linking between introduced Cys pairs. Disulfide cross-linking also demonstrates that YidC interacts with multiple transmembrane segments of LacY during membrane biogenesis. Moreover, YidC is strictly required for insertion of M13 procoat protein fused into the middle cytoplasmic loop of LacY. In contrast, the loops preceding and following the inserted procoat domain are dependent on SecYEG for insertion. These studies demonstrate close cooperation between the two complexes in membrane biogenesis and that YidC functions primarily as a foldase for LacY.     

The Relationship of the Feces Protein Particles to Rice Protein Bodies

Feces protein particles (FPP), spherical or oval in shape, 1.0~3.5 μ in diameter, which were observed in the fresh feces of the Japanese, in an average density of 5 × 10⁹/g, resembled the rice protein bodies (RPB) in electron-microscopical fine structure. The FPP decreased in the feces of the man who had been given a rice-free diet consisting of steamed sweet potato; when boiled rice had been fed, the FPP increased, and reached the level of the original density within 5 days. The FPP were concluded to be derived from an indigestible fraction of the RPB which were supplied to the Japanese with the daily intake of rice.     

Crystal Structure of the YcjX Stress Protein Reveals a Ras-Like GTP-Binding Protein

Stress proteins promote cell survival by monitoring protein homeostasis in cells and organelles. YcjX is a conserved protein of unknown function, which is highly upregulated in response to acute and chronic stress. Notably, heat shock induction of ycjX exceeded even levels observed for major stress-induced chaperones, including GroEL, ClpB, and HtpG, which use ATP as energy source. YcjX features a Walker-type nucleotide-binding domain indicating that YcjX might function as a molecular chaperone. Here, we present the first crystal structure of YcjX from Shewanella oneidensis solved at 1.9-Å resolution by SAD phasing. We show that YcjX is a GTP-binding protein that shares at its core the canonical alpha-beta domain of p21^ras (Ras). However, unlike Ras, YcjX features several unique insertions, including an entirely α-helical domain not previously observed in Ras-like GTPases. We note that this helical domain is reminiscent of a similar domain in the Gα subunit of heterotrimeric G proteins, supporting a potential role for YcjX as a signal transducer of stress responses. To elucidate the mechanism of GTP hydrolysis, we determined crystal structures of YcjX bound to GDP and GDPCP, respectively, which crystallized in three different nucleotide switch conformations. Supported by targeted mutagenesis experiments, we show that YcjX utilizes a non-canonical switch 2′ motif not previously observed in Ras-like GTPases. Together, our structures provide atomic snapshots of YcjX in different functional states, illustrating the structural determinants for stress signaling.     

重组标签蛋白在蛋白质纯化中的研究进展

重组蛋白的表达纯化是研究蛋白质结构与功能的重要环节之一,表达重组蛋白宿主细胞的监测筛选和重组蛋白低水平可溶性表达、低回收率以及不稳定易水解等问题一直是蛋白质高通量纯化工艺中的难题。近年来,将多肽或蛋白质作为标签,与目标蛋白共表达的方法已经很大程度地解决了这一问题。因此,针对不同特性的蛋白质选择合适的标签纯化策略在重组蛋白纯化研究中是相当关键的环节。本文回顾了几种传统标签蛋白的研究概况(His-tag,Arg-tag,Flag-tag,GST-tag,MBP-tag等),着重对近年来新开发的了几种标签蛋白(Si-tag,Halo-tag,Intein-CBD-tag,ELPs-tag等)进行了深入探讨,并对新标签蛋白在蛋白质纯化中的应用前景作以展望。     

Protein Orientation Affects the Efficiency of Functional Protein Transplantation into the Xenopus Oocyte Membrane

Xenopus oocytes incorporate into their plasma membrane nicotinic acetylcholine receptors (nAChRs) after intracellular injection of lipid vesicles bearing this protein. The advantage of this approach over the classical oocyte expression system lies in the transplantation of native, fully processed proteins, although the efficiency of functional incorporation of nAChRs is low. We have now studied the incorporation into the oocyte membrane of the Torpedo chloride channel (ClC-0), a minor contaminant protein in some nAChR preparations. nAChR-injected oocytes incorporated functional ClC-0: i) in a higher number than functional nAChRs; ii) retaining their original properties; and iii) with a right-side-out orientation in the oocyte membrane. In an attempt to elucidate the reasons for the low efficiency in the functional incorporation of nAChRs into the oocyte membrane, we combined electrophysiological and [125I]alpha-bungarotoxin-binding experiments. Up to 3% of injected nAChRs were present in the oocyte plasma membrane at a given time. Thus, fusion of lipoproteosome vesicles to the oocyte plasma membrane is not the limiting factor for an efficient functional transplantation of foreign proteins. Accounting for the low rate of functional transplantation of nAChRs is their backward orientation in the oocyte membrane, since about 80% of them adopted an out-side-in orientation. Other factors, including differences in the susceptibility of the transplanted proteins to intracellular damage should also be considered.     

Protein Array Identification of Substrates of the Epstein-Barr Virus Protein Kinase BGLF4

A conserved family of herpesvirus protein kinases plays a crucial role in herpesvirus DNA replication and virion production. However, despite the fact that these kinases are potential therapeutic targets, no systematic studies have been performed to identify their substrates. We generated an Epstein-Barr virus (EBV) protein array to evaluate the targets of the EBV protein kinase BGLF4. Multiple proteins involved in EBV lytic DNA replication and virion assembly were identified as previously unrecognized substrates for BGLF4, illustrating the broad role played by this protein kinase. Approximately half of the BGLF4 targets were also in vitro substrates for the cellular kinase CDK1/cyclin B. Unexpectedly, EBNA1 was identified as a substrate and binding partner of BGLF4. EBNA1 is essential for replication and maintenance of the episomal EBV genome during latency. BGLF4 did not prevent EBNA1 binding to sites in the EBV latency origin of replication, oriP. Rather, we found that BGLF4 was recruited by EBNA1 to oriP in cells transfected with an oriP vector and BGLF4 and in lytically induced EBV-positive Akata cells. In cells transfected with an oriP vector, the presence of BGLF4 led to more rapid loss of the episomal DNA, and this was dependent on BGLF4 kinase activity. Similarly, expression of doxycycline-inducible BGLF4 in Akata cells led to a reduction in episomal EBV genomes. We propose that BGLF4 contributes to effective EBV lytic cycle progression, not only through phosphorylation of EBV lytic DNA replication and virion proteins, but also by interfering with the EBNA1 replication function.Herpesviruses encode two families of serine/threonine protein kinases, one of which, the BGLF4 (Epstein-Barr virus [EBV])/UL97 (human cytomegalovirus)/UL13 (herpes simplex virus)/ORF36 (Kaposi''s sarcoma-associated herpesvirus)/ORF47 (varicella-zoster virus) family, is the sole protein kinase encoded by beta and gamma herpesviruses. The protein kinases phosphorylate both viral and host proteins (16, 21, 42) and are necessary for efficient virus lytic replication. Consequently, these kinases have been of interest as potential targets for antiviral drug development (37), and the compound 1263W94 (maribavir), which inhibits the cytomegalovirus UL97 protein (3), has been used in phase I clinical trials (27, 31, 47).EBV infection is prevalent worldwide, and primary infection in adolescence or early adulthood is associated in 30 to 40% of cases with infectious mononucleosis. EBV efficiently infects B cells in the lymphoid tissues of the Waldeyer ring (43). EBV infection of B cells is biased toward establishment of latency with limited viral-gene expression (49). During latent infection, EBV genomes are maintained as extrachromosomal episomes. Replication of episomal genomes utilizes the latency origin of replication, oriP. The only EBV-encoded protein required is the origin binding protein EBNA1. All other essential replication factors are provided by the cell. Expression of the EBV replicative cycle and production of progeny virus take place in terminally differentiated plasma B cells (11, 29), and epithelial cells may also contribute to the cycle of virus replication and spread that is an important component of both persistent infection of the individual and transmission of virus from one individual to the next (4, 22). Lytic DNA replication initiates at separate origins, oriLyt. EBV encodes a set of six core lytic replication proteins, along with ancillary proteins, such as thymidine kinase (TK), that are involved in nucleotide metabolism (13, 44).Several substrates have been described for the EBV BGLF4 protein kinase, including the core lytic EBV replication protein BMRF1, the polymerase processivity factor (8, 17). BGLF4 has also been found to locate to sites of lytic viral replication (46), to be required for efficient lytic DNA replication and release of nucleocapsids from the nucleus (18), and to contribute to the compaction of cell chromatin seen in cells undergoing lytic replication (32). Protein chip technology provides a new tool for global analysis of activities for biologically important enzymes, such as ubiquitin ligases, DNA repair enzymes, and kinases (7, 19, 36, 38, 52). Using an EBV protein array for unbiased screening, we identified multiple new BGLF4 substrates involved in lytic DNA replication, capsid assembly, and DNA packaging. Unexpectedly, we also identified EBNA1 as a substrate and binding partner for BGLF4. The data suggest that the contribution of BGLF4 to the EBV lytic cycle extends beyond the previously recognized contributions to lytic DNA replication and virion production and includes facilitating the switch from latent to lytic DNA replication by downregulating the EBNA1 replication function.     

Mapping of the Coronavirus Membrane Protein Domains Involved in Interaction with the Spike Protein

The coronavirus membrane (M) protein is the key player in virion assembly. One of its functions is to mediate the incorporation of the spikes into the viral envelope. Heterotypic interactions between M and the spike (S) protein can be demonstrated by coimmunoprecipitation and by immunofluorescence colocalization, after coexpression of their genes in eukaryotic cells. Using these assays in a mutagenetic approach, we have mapped the domains in the M protein that are involved in complex formation between M and S. It appeared that the 25-residue luminally exposed amino-terminal domain of the M protein is not important for M-S interaction. A 15-residue deletion, the insertion of a His tag, and replacement of the ectodomain by that of another coronavirus M protein did not affect the ability of the M protein to associate with the S protein. However, complex formation was sensitive to changes in the transmembrane domains of this triple-spanning protein. Deletion of either the first two or the last two transmembrane domains, known not to affect the topology of the protein, led to a considerable decrease in complex formation, but association was not completely abrogated. Various effects of changes in the part of the M protein that is located at the cytoplasmic face of the membrane were observed. Deletions of the extreme carboxy-terminal tail appeared not to interfere with M-S complex formation. However, deletions in the amphipathic domain severely affected M-S interaction. Interestingly, changes in the amino-terminal and extreme carboxy-terminal domains of M, which did not disrupt the interaction with S, are known to be fatal to the ability of the protein to engage in virus particle formation (C. A. M. de Haan, L. Kuo, P. S. Masters, H. Vennema, and P. J. M. Rottier, J. Virol. 72:6838-6850, 1998). Apparently, the structural requirements of the M protein for virus particle assembly differ from the requirements for the formation of M-S complexes.     

Phosphorylation of the Conditioning-Associated GTP-Binding Protein cp20 by Protein Kinase C

Abstract: The phosphorylation state of cp20, a low molecular weight membrane-associated GTP-binding protein, was previously shown to increase two- to threefold 24 h after associative conditioning. Here, cp20 is shown to be phosphorylated by protein kinase C (PKC) in vitro. Pronounced differences in activity were observed with the three major isoforms of PKC, whereas casein kinase, calcium/calmodulin-dependent protein kinase II, and cyclic AMP-dependent protein kinase produced no detectable phosphorylation of cp20. Phosphorylation of cp20 had no effect on its GTPase or GTP-binding activity but caused a translocation of cp20 from cytosol to the nuclei/mitochondrial particulate fraction. These results suggest that the increase in phosphorylation of cp20 after conditioning may be due to PKC.     

基于蛋白质序列的泛素化位点预测研究进展

泛素化是目前广受关注的一种翻译后修饰过程,对蛋白质降解、DNA修复等多种细胞过程都具有重要的调控作用。本文根据国内外蛋白质泛素化位点预测的研究,分析了预测泛素化位点的特征属性,总结了对这些特征进行优化的特征选择方法,并对预测过程中所使用的各种机器学习分类器进行了概述。     

Targeting the Unfolded Protein Response in Glioblastoma Cells with the Fusion Protein EGF-SubA

Rapidly growing tumors require efficient means to allow them to adapt to fluctuating microenvironments consisting of hypoxia, nutrient deprivation, and acidosis. The unfolded protein response (UPR) represents a defense mechanism allowing cells to respond to these adverse conditions. The chaperone protein GRP78 serves as a master UPR regulator that is aberrantly expressed in a variety of cancers, including glioma. Therefore, cancer cells may be particularly reliant upon the adaptive mechanisms offered by the UPR and targeting GRP78 may represent a unique therapeutic strategy. Here we report that diffuse expression of GRP78 protein is present in Grade III-IV, but not Grade I-II glioma. To determine the role GRP78 plays in glioblastoma tumorigenesis, we explored the anti-tumor activity of the novel fusion protein EGF-SubA, which combines EGF with the cytotoxin SubA that has been recently shown to selectively cleave GRP78. EGF-SubA demonstrated potent tumor-specific proteolytic activity and cytotoxicity in glioblastoma lines and potentiated the anti-tumor activity of both temozolomide and ionizing radiation. To determine if the tumor microenvironment influences EGF-SubA activity, we maintained cells in acidic conditions that led to both UPR activation and increased EGF-SubA induced cytotoxicity. EGF-SubA was well tolerated in mice and led to a significant tumor growth delay in a glioma xenograft mouse model. The UPR is emerging as an important adaptive pathway contributing to glioma tumorigenesis. Targeting its primary mediator, the chaperone protein GRP78, through specific, proteolytic cleavage with the immunotoxin EGF-SubA represents a novel and promising multi-targeted approach to cancer therapy.     

Identification of the Vesicular Stomatitis Virus Large Protein as a Unique Viral Protein

Previous studies have noted the existence of a 190,000-dalton vesicular stomatitis virus (VSV) protein called the large (L) protein. To determine whether this protein is a nonspecific aggregate, a precursor to the other VSV proteins, or a unique viral protein, its synthesis relative to the other VSV proteins was studied under conditions of inhibition of initiation of protein synthesis. Also, its tryptic peptides were compared to those of the other VSV proteins. In both cases the results were consistent with the identification of the large protein as a unique viral protein.     

Interplay between Chaperones and Protein Disorder Promotes the Evolution of Protein Networks

Evolution is driven by mutations, which lead to new protein functions but come at a cost to protein stability. Non-conservative substitutions are of interest in this regard because they may most profoundly affect both function and stability. Accordingly, organisms must balance the benefit of accepting advantageous substitutions with the possible cost of deleterious effects on protein folding and stability. We here examine factors that systematically promote non-conservative mutations at the proteome level. Intrinsically disordered regions in proteins play pivotal roles in protein interactions, but many questions regarding their evolution remain unanswered. Similarly, whether and how molecular chaperones, which have been shown to buffer destabilizing mutations in individual proteins, generally provide robustness during proteome evolution remains unclear. To this end, we introduce an evolutionary parameter λ that directly estimates the rate of non-conservative substitutions. Our analysis of λ in Escherichia coli, Saccharomyces cerevisiae, and Homo sapiens sequences reveals how co- and post-translationally acting chaperones differentially promote non-conservative substitutions in their substrates, likely through buffering of their destabilizing effects. We further find that λ serves well to quantify the evolution of intrinsically disordered proteins even though the unstructured, thus generally variable regions in proteins are often flanked by very conserved sequences. Crucially, we show that both intrinsically disordered proteins and highly re-wired proteins in protein interaction networks, which have evolved new interactions and functions, exhibit a higher λ at the expense of enhanced chaperone assistance. Our findings thus highlight an intricate interplay of molecular chaperones and protein disorder in the evolvability of protein networks. Our results illuminate the role of chaperones in enabling protein evolution, and underline the importance of the cellular context and integrated approaches for understanding proteome evolution. We feel that the development of λ may be a valuable addition to the toolbox applied to understand the molecular basis of evolution.     

Zinc Modulates the Interaction of Protein C and Activated Protein C with Endothelial Cell Protein C Receptor

Zinc is an essential trace element for human nutrition and is critical to the structure, stability, and function of many proteins. Zinc ions were shown to enhance activation of the intrinsic pathway of coagulation but down-regulate the extrinsic pathway of coagulation. The protein C pathway plays a key role in blood coagulation and inflammation. At present there is no information on whether zinc modulates the protein C pathway. In the present study we found that Zn²⁺ enhanced the binding of protein C/activated protein C (APC) to endothelial cell protein C receptor (EPCR) on endothelial cells. Binding kinetics revealed that Zn²⁺ increased the binding affinities of protein C/APC to EPCR. Equilibrium dialysis with ⁶⁵Zn²⁺ revealed that Zn²⁺ bound to the Gla domain as well as sites outside of the Gla domain of protein C/APC. Intrinsic fluorescence measurements suggested that Zn²⁺ binding induces conformational changes in protein C/APC. Zn²⁺ binding to APC inhibited the amidolytic activity of APC, but the inhibition was reversed by Ca²⁺. Zn²⁺ increased the rate of APC generation on endothelial cells in the presence of physiological concentrations of Ca²⁺ but did not further enhance increased APC generation obtained in the presence of physiological concentrations of Mg²⁺ with Ca²⁺. Zn²⁺ had no effect on the anticoagulant activity of APC. Zn²⁺ enhanced APC-mediated activation of protease activated receptor 1 and p44/42 MAPK. Overall, our data show that Zn²⁺ binds to protein C/APC, which results in conformational changes in protein C/APC that favor their binding to EPCR.     

Protein function prediction using the Protein Link EXplorer (PLEX)

We introduce the Protein Link EXplorer (PLEX), a web-based environment that allows the construction of a phylogenetic profile for any given amino acid sequence, and its comparison with profiles of approximately 350,000 predicted genes from 89 genomes, as a means of interactively identifying functionally linked genes and predicting protein function. PLEX can be searched iteratively and also enables searches for chromosomal gene neighbors and Rosetta Stone linkages. PLEX search results are accompanied by quantitative estimates of linkage confidence, enabling users to take advantage of coinheritance, operon and gene fusion-based methods for inferring gene function and reconstructing cellular systems and pathways. AVAILABILITY: http://bioinformatics.icmb.utexas.edu/plex