Inefficient Degradation of Oxidized Regions of Protein Molecules

We have previously shown that the intracellular half-life of endocytosed oxidized albumin is much longer than that of native albumin. We now report that the regions of oxidized albumin which contain oxidation products (carbonyls and fluorophores), are less readily released as small degradation products by cell-free proteolysis than is the molecule overall. We deduce that oxidized moieties in the polypeptide chain can confer localized resistance to enzymatic proteolysis. Such resistance to proteolysis may account for the intracellular accumulation of some endocytosed oxidized protein which we have previously observed.     

Enhanced Enzymatic Degradation of Radical Damaged Mitochondrial Membrane Components

The location of a protein (soluble or membrane-bound) influences the extent of oxidative damage caused by free radicals. It has been established that after radical attack, soluble proteins can become more susceptible to hydrolysis by individual proteinases than native proteins.^1-4 We have now examined the hydrolytic susceptibility following radical attack of a protein that is located within a membrane environment, mitochondrial monoamine oxidase (MAO). After exposure to oxygen radicals generated by gamma irradiation, hydrolysis of sub-mitochondrial particles (SMP) containing MAO was increased in three respects. First, the generation of small fragments of MAO by the proteinases elastase and trypsin, was enhanced. Second, the generation by these enzymes and by phospholipase A2 of non-sedimentable membrane fragments containing MAO was also increased. Third, autolysis of SMP was enhanced. Hence, proteins located within membranes may become more susceptible to enzymatic degradation following oxidative damage.     

Autodegradation of Protein Disulfide Isomerase

Protein disulfide isomerase (PDI) and its degradation products were found in HepG2, COS-1, and CHO-K1 cells. Whether or not the products were formed through autodegradation of PDI was examined, since PDI contains the CGHC motif, which is the active center of proteolytic activity in ER-60 protease. Commercial bovine PDI was autodegraded to produce a trimmed PDI. In addition, human recombinant PDI also had autodegradation activity. Mutant recombinant PDIs with CGHC motifs of which cysteine residues were replaced with serine or alanine residues were prepared. However, they were not autodegraded, suggesting the cysteine residues of motifs are necessary for autodegradation.     

An in Vitro Analysis System Using a Fluorescence Protein Reporter for Evaluating Anti-Inflammatory Effects in Macrophages

Monitoring of inflammation in adipose tissues, which causes insulin resistance, is valuable in evaluating insulin resistance. We developed an in vitro analysis system using a fluorescence protein (FP) as a reporter gene driven by pro-inflammatory cytokine promoters such as monocyte chemoattractant protein-1 (MCP-1) and tumor necrosis factor-α (TNFα). In the reporter-transfected RAW264 cells, the protein expression levels of green fluorescence protein (GFP) were increased by inflammatory stimulations such as lipopolysaccharide (LPS), conditioned medium prepared using hypertrophied 3T3-L1 adipocytes, and a co-culture system. The changes in fluorescence intensity were equivalent to those of the mRNA and protein expression levels for each cytokine. Moreover, the effects of 15-deoxy-12,14Δ-prostaglandine J₂, a natural anti-inflammatory compound, were detectable in this system. These data indicate that the FP system developed here is an analysis system of low cost with simple procedures for evaluating inflammation, suggesting usability in the large-scale screening of anti-inflammatory compounds.     

Oxidized protein degradation and repair in ageing and oxidative stress

Cellular ageing is characterized by the accumulation of oxidatively modified proteins which may be due to increased protein damage and/or decreased elimination of oxidized protein. Since the proteasome is in charge of protein turnover and removal of oxidized protein, its fate during ageing and upon oxidative stress has received special attention, and evidence has been provided for an age-related impairment of proteasome function. However, proteins when oxidized at the level of sulfur-containing amino acids can also be repaired. Therefore, the fate of the methionine sulfoxide reductase system during ageing has also been addressed as well as its role in protection against oxidative stress.     

Protein trafficking and maturation regulate intramembrane proteolysis

Intramembrane-cleaving proteases (I-CLiPs) are membrane embedded proteolytic enzymes. All substrates identified so far are also membrane proteins, involving a number of critical cellular signaling as well as human diseases. After synthesis and assembly at the endoplasmic reticulum, membrane proteins are exported to the Golgi apparatus and transported to their sites of action. A number of studies have revealed the importance of the intracellular membrane trafficking in i-CLiP-mediated intramembrane proteolysis, not only for limiting the unnecessary encounter between i-CLiPs and their substrate but also for their cleavage site preference. In this review, we will discuss recent advances in our understanding of how each i-CLiP proteolysis is regulated by intracellular vesicle trafficking. This article is part of a Special Issue entitled: Intramembrane Proteases.     

Protein aggregated into bacterial inclusion bodies does not result in protection from proteolytic digestion

Proteolytic resistance, as conferred by protein aggregation into inclusion bodies, has not been explored in detail. We have investigated the eventual digestion of several closely-related proteins, namely six insertional and two fusion mutants of the homotrimeric bacteriophage P22 tailspike (TSP) protein. When over-produced in E. coli, all these polypeptides form inclusion bodies accompanied by only traces of soluble protein. The mutations introduced in TSP impaired its degradation and enhanced its half live up to ten-fold, without affecting protein solubility. This indicates that protein properties other than solubility, are the main determinants of susceptibility to proteolysis. In addition, the analysis of the degradation fragments strongly suggests that the aggregated TSP polypeptides undergo a site-limited proteolytic attack, and that their complete digestion occurs through an in situ cascade cleavage process.     

Degradation of C-terminal tag sequences on domain antibodies purified from E. coli supernatant

Expression of recombinant proteins often takes advantage of peptide tags expressed in fusion to allow easy detection and purification of the expressed proteins. However, as the fusion peptides most often are flexible appendages at the N- or C-terminal, proteolytic cleavage may result in removal of the tag sequence. Here, we evaluated the functionality and stability of 14 different combinations of commonly used tags for purification and detection of recombinant antibody fragments. The tag sequences were inserted in fusion with the c-terminal end of a domain antibody based on the HEL4 scaffold in a phagemid vector. This particular antibody fragment was able to refold on the membrane after blotting, allowing us to detect c-terminal tag breakdown by use of protein A in combination with detection of the tags in the specific constructs. The degradation of the c-terminal tags suggested specific sites to be particularly prone to proteolytic cleavage, leaving some of the tag combinations partially or completely degraded. This specific work illustrates the importance of tag design with regard to recombinant antibody expression in E. coli, but also aids the more general understanding of protein expression.     

巨噬细胞新型氧化低密度脂蛋白结合蛋白的研究

小鼠腹腔巨噬细胞（ＭＰＭ）膜上存在能结合氧化低密度脂蛋白（ｏｘ－ＬＤＬ）的Ａ类清道夫受体（ＳＲ－Ａ）,但用配体印迹技术研究制备ＭＰＭ膜蛋白,发现还存在一种新型ｏｘ－ＬＤＬ膜结合蛋白,其分子量低于ＳＲ－Ａ,为９２ｋＤ它不结合乙酰化低密度脂蛋白ａｃ－ＬＤＬ）,与配体的结合也不受还原剂的影响,但唾液酸酶处理则明显减弱其与ｏｘ－ＬＤＬ的结合,未标记ｏｘ－ＬＤＬ能竞争性抑制（＾１２５Ｉ）ｏｘ－ＬＤＬ与９２ｋ     

Degradation of C-terminal tag sequences on domain antibodies purified from E. coli supernatant

Expression of recombinant proteins often takes advantage of peptide tags expressed in fusion to allow easy detection and purification of the expressed proteins. However, as the fusion peptides most often are flexible appendages at the N- or C-terminal, proteolytic cleavage may result in removal of the tag sequence. Here, we evaluated the functionality and stability of 14 different combinations of commonly used tags for purification and detection of recombinant antibody fragments. The tag sequences were inserted in fusion with the c-terminal end of a domain antibody based on the HEL4 scaffold in a phagemid vector. This particular antibody fragment was able to refold on the membrane after blotting, allowing us to detect c-terminal tag breakdown by use of protein A in combination with detection of the tags in the specific constructs. The degradation of the c-terminal tags suggested specific sites to be particularly prone to proteolytic cleavage, leaving some of the tag combinations partially or completely degraded. This specific work illustrates the importance of tag design with regard to recombinant antibody expression in E. coli, but also aids the more general understanding of protein expression.     

Multiple Sequence Signals Direct Recognition and Degradation of Protein Substrates by the AAA+ Protease HslUV

Proteolysis is important for protein quality control and for the proper regulation of many intracellular processes in prokaryotes and eukaryotes. Discerning substrates from other cellular proteins is a key aspect of proteolytic function. The Escherichia coli HslUV protease is a member of a major family of ATP-dependent AAA+ degradation machines. HslU hexamers recognize and unfold native protein substrates and then translocate the polypeptide into the degradation chamber of the HslV peptidase. Although a wealth of structural information is available for this system, relatively little is known about mechanisms of substrate recognition. Here, we demonstrate that mutations in the unstructured N-terminal and C-terminal sequences of two model substrates alter HslUV recognition and degradation kinetics, including changes in V_max. By introducing N- or C-terminal sequences that serve as recognition sites for specific peptide-binding proteins, we show that blocking either terminus of the substrate interferes with HslUV degradation, with synergistic effects when both termini are obstructed. These results support a model in which one terminus of the substrate is tethered to the protease and the other terminus is engaged by the translocation/unfolding machinery in the HslU pore. Thus, degradation appears to consist of discrete steps, which involve the interaction of different terminal sequence signals in the substrate with different receptor sites in the HslUV protease.     

SARS冠状病毒核衣壳(N)蛋白不同区域的原核表达

利用大肠杆菌表达系统对SARS冠状病毒的核衣壳(N)蛋白全长及N末端或／和C末端缺失突变体进行了表达,共表达了39个重组蛋白,表达量在15％～30％之间。分别利用电洗脱或金属鳌合介质纯化重组蛋白,用蛋白印迹实验检测纯化蛋白对SARS病人恢复期血清的反应性,结果发现全长N蛋白活性最好,其余的末端缺失蛋白均无法达到同—：活性水平。由此说明N蛋白的完整性对于其优势表位的充分暴露是必要的。     

Structural Basis for the Recognition of Oxidized Phospholipids in Oxidized Low Density Lipoproteins by Class B Scavenger Receptors CD36 and SR-BI

Specific oxidized phospholipids (oxPC_CD36) accumulate in vivo at sites of oxidative stress and serve as high affinity ligands for scavenger receptors class B (CD36 and SR-BI). Recognition of oxPC_CD36 by scavenger receptors plays a role in several pathophysiological processes. The structural basis for the recognition of oxPC_CD36 by CD36 and SR-BI is poorly understood. A characteristic feature of oxPC_CD36 is an sn-2 acyl group that incorporates a terminal γ-hydroxy (or oxo)-α,β-unsaturated carbonyl. In the present study, a series of model oxidized phospholipids were designed, synthesized, and tested for their ability to serve as ligands for CD36 and SR-BI. We demonstrated that intact the sn-1 hydrophobic chain, the sn-3 hydrophilic phosphocholine or phosphatidic acid group, and the polar sn-2 tail are absolutely essential for high affinity binding. We further found that a terminal negatively charged carboxylate at the sn-2 position suffices to generate high binding affinity to class B scavenger receptors. In addition, factors such as polarity, rigidity, optimal chain length of sn-2, and sn-3 positions and negative charge at the sn-3 position of phospholipids further modulate the binding affinity. We conclude that all three positions of oxidized phospholipids are essential for the effective recognition by scavenger receptors class B. Furthermore, the structure of residues in these positions controls the affinity of the binding. The present studies suggest that, in addition to oxPC_CD36, other oxidized phospholipids observed in vivo may represent novel ligands for scavenger receptors class B.     

蛋白质表面氨基酸特性研究进展

分布在蛋白质分子表面的暴露于溶剂的氨基酸所具有的一些特性对蛋白质的折叠和聚合过程、蛋白质一蛋白质相互作用以及蛋白质的功能具有重要影响。本文分析了蛋白质表面氨基酸在疏水性、保守性、静电势及结构方面的一些特性,阐述了近年来国际上利用这些特性对蛋白质一蛋白质相互作用界面进行预测的方法,最后介绍了几款预测蛋白质表面氨基酸的软件。     

Recognition of Oxidized Thymine Base on the Single-Stranded DNA by Replication Protein A

Replication protein A (RAP) is a eukaryotic single-stranded DNA binding protein involved in DNA replication, repair, and recombination. Recent studies indicate that RPA preferentially binds the damaged sites rather than the undamaged sites. Therefore, RPA is thought to be a member of repair factories or a sensor of lesion on DNA. To obtain further information of behavior of RPA against the oxidized lesion, we studied the binding affinity of RPA for the single-stranded DNA containing 5-formyluracil, a major lesion of thymine base yielded by the oxidation, using several synthetic oligonucleotides. The affinity of RPA for oligonucleotides was determined by gel shift assay. Results suggest that the surrounding sequence of 5-formyluracil may affect the affinity for RPA, and that the 5-formyluracil on the purine stretch but not the pyrimidine stretch increases the affinity for RPA. Results of affinity labeling experiment of RPA with the oligonucleotides containing 5-formyluracil indicate that RPA1 subunit may directly recognize and bind to the 5-formyluracil on the single-stranded DNA.