赖氨酸胍基化对蛋白质组分析的影响

赖氨酸胍基化在蛋白质组学定性和定量研究中起着重要作用,本文系统分析了胍基化前后,HeLa细胞蛋白质经胰蛋白酶酶解产生的3种不同类型肽段的质谱鉴定情况,并探讨了不同肽段质谱响应改变的内在原因。发现赖氨酸在侧链能选择性地发生胍基化反应（其选择性达到96.8%）,转化为高精氨酸,碱性增强。因此在正离子质谱模式下,C端为赖氨酸的肽段产生了更多的y离子,提供了许多新的离子碎片信息。在鉴定结果中,此类肽段所占总肽段的比例由原来的51.7%上升为57.3%,并且有1015条新的肽段被检测到。对于不含有赖氨酸的肽段,其鉴定结果在胍基化前后基本没有变化。结果表明,胍基化可以在一定程度上提高质谱鉴定的灵敏度和互补性,提高蛋白质分析的覆盖率。     

Leukocyte invasion of the brain after peripheral trauma in zebrafish (Danio rerio)

Despite well-known systemic immune reactions in peripheral trauma, little is known about their roles in posttraumatic neurological disorders, such as anxiety, sickness, and cognitive impairment. Leukocyte invasion of the brain, a common denominator of systemic inflammation, is involved in neurological disorders that occur in peripheral inflammatory diseases, whereas the influences of peripheral leukocytes on the brain after peripheral trauma remain largely unclear. In this study, we found that leukocytes, largely macrophages, transiently invaded the brain of zebrafish larvae after peripheral trauma through vasculature-independent migration, which was a part of the systemic inflammation and was mediated by interleukin-1b (il1b). Notably, myeloid cells in the brain that consist of microglia and invading macrophages were implicated in posttraumatic anxiety-like behaviors, such as hyperactivity (restlessness) and thigmotaxis (avoidance), while a reduction in systemic inflammation or myeloid cells can rescue these behaviors. In addition, invading leukocytes together with microglia were found to be responsible for the clearance of apoptotic cells in the brain; however, they also removed the nonapoptotic cells, which suggested that phagocytes have dual roles in the brain after peripheral trauma. More importantly, a category of conserved proteins between zebrafish and humans or rodents that has been featured in systemic inflammation and neurological disorders was determined in the zebrafish brain after peripheral trauma, which supported that zebrafish is a translational model of posttraumatic neurological disorders. These findings depicted leukocyte invasion of the brain during systemic inflammation after peripheral trauma and its influences on the brain through il1b-dependent mechanisms.Subject terms: Neuroimmunology, Acute inflammation     

Comprehensive profiling of lysine acetylome in Staphylococcus aureus

The Gram-positive bacterium Staphylococcus aureus(S.aureus)is a wide spread common opportunistic pathogen that causes a wide variety of infectious diseases,from benign skin infections to life-threatening diseases such as the methicillin-resistant Staphylococcus aureus(MRSA)infection.Although emerging evidence suggests that lysine acetylation may play critical roles in bacterial physiology,the atlas of acetylome in S.aureus has not been studied.To comprehensively profile protein lysine acetylation in S.aureus,we used an integrated approach that combined immune affinity peptide enrichment using anti-lysine acetylation antibody,high-pH HPLC fractionation,and HPLC/mass spectrometry analysis.This study led to the identification of 1361 non-redundant acetylation sites on 412 proteins found in a search of S.aureus protein database extracted from the Swiss-Prot database.We further performed bioinformatic analysis to characterize this modification,including gene ontology annotation,protein-protein interaction,and domain analysis of the acetylation sites.We found that the acetylated proteins were enriched in multiple biological pathways,such as ribosomal function and energy metabolism.Our data provides a rich source for functional studies of lysine acetylation in S.aureus.     

Time-course expression of DNA repair-related genes in hepatocytes of zebrafish (Danio rerio) after UV-B exposure

The objective of this study was to evaluate the time-course effects of UV-B exposure on expression of genes involved in the DNA repair system of zebrafish ( Danio rerio ) hepatocytes, a highly competent species in terms of damage repair induced by UV radiation. For gene expression analysis (RT-PCR), cells were exposed to 23.3 mJ cm⁻² UV-B, which was the dose that affected viable cell number (reduction of 30% when compared with the control group) and produced no visual alteration on cell morphology. The early response observed (6 h) showed induction in the expression of the CDKI gene (cyclin-dependent kinase inhibitor) and genes related to DNA damage repair (mainly XPC and DDB2 ), while the late response observed (24 h) was more related to up-regulation of p53 and genes involved in cell cycle arrest ( gadd45a , cyclinG1 ). In all times analyzed, the anti-apoptotic gene Bcl-2 was down-regulated. Another interesting result observed was the up-regulation of the Apex- 1 gene after UV-B exposure, which could indicate the induction of oxidative lesions in the DNA molecule. In conclusion, these results demonstrate an activation of the DNA repair system in hepatocytes of zebrafish exposed to UV-B radiation, mainly involving the participation of p53.     

Interrogating Substrate Selectivity and Composition of Endogenous Histone Deacetylase Complexes with Chemical Probes

Histone deacetylases (HDACs) regulate the function and activity of numerous cellular proteins by removing acetylation marks from regulatory lysine residues. We have developed peptide‐based HDAC probes that contain hydroxamate amino acids of various lengths to replace modified lysine residues in the context of known acetylation sites. The interaction profiles of all human HDACs were studied with three sets of probes, which derived from different acetylation sites, and sequence context was found to have a strong impact on substrate recognition and composition of HDAC complexes. By investigating K382 acetylation of the tumor suppressor p53 as an example, we further demonstrate that the interaction profiles reflect the catalytic activities of respective HDACs. These results underline the utility of the newly established probes for deciphering not only activity, but also substrate selectivity and composition of endogenous HDAC complexes, which can hardly be achieved otherwise.     

Specific rearrangement reactions of acetylated lysine containing peptide bn (n = 4–7) ion series

Characterization of ε‐N‐acetylated lysine containing peptides, one of the most prominent post‐translational modifications of proteins, is an important goal for tandem mass spectrometry experiments. A systematic study for the fragmentation reactions of b ions derived from ε‐N‐acetyllysine containing model octapeptides (K_AcYAGFLVG and YAK_AcGFLVG) has been examined in detail. Collision‐induced dissociation (CID) mass spectra of b_n (n = 4–7) fragments of ε‐N‐acetylated lysine containing peptides are compared with those of N‐terminal acetylated and doubly acetylated (both ε‐N and N‐terminal) peptides, as well as acetyl‐free peptides. Both direct and nondirect fragments are observed for acetyl‐free and singly acetylated (ε‐N or N‐terminal) peptides. In the case of ε‐N‐acetylated lysine containing peptides, however, specific fragment ions (m/z 309, 456, 569 and 668) are observed in CID mass spectra of b_n (n = 4–7) ions. The CID mass spectra of these four ions are shown to be identical to those of selected protonated C‐terminal amidated peptides. On this basis, a new type of rearrangement chemistry is proposed to account for the formation of these fragment ions, which are specific for ε‐N‐acetylated lysine containing peptides. Consistent with the observation of nondirect fragments, it is proposed that the b ions undergo head‐to‐tail macrocyclization followed by ring opening. The proposed reaction pathway assumes that b_n (n = 4–7) of ε‐N‐acetylated lysine containing peptides has a tendency to place the K_Ac residue at the C‐terminal position after macrocyclization/reopening mechanism. Then, following the loss of CO, it is proposed that the marker ions are the result of the loss of an acetyllysine imine as a neutral fragment. Copyright © 2014 John Wiley & Sons, Ltd.     

Evaluation of the toxic effect on zebrafish (Danio rerio) exposed to uranium mill tailings leaching solution

The objective of this study was to evaluate the potential ecological danger and toxic effect of uranium mill tailings leaching solution (UMTLS) on aquatic animals. UMTLS was identified to contain two radioactive elements, nine heavy metal elements, and five non-metallic materials. The acute toxicity test indicated that the 1, 12, 24, 48, 72, 96 h LC₅₀ values of UMTLS to the zebrafish were 12.1, 7.1, 4.4, 3.8, 3.4, and 2.9%, respectively. In sub-lethal toxicity tests, superoxide dismutase, catalase, Na⁺–K⁺–ATPase activities, and malondialdehyde content were respectively determined and analyzed in the zebrafish gill, gonad, muscle, and liver after exposed to four different concentration levels of UMTLS for 7 and 14 days, respectively. The result showed that the most sensitivity of the antioxidant system in zebrafish tissues in UMTLS was gill, and then decreased in gonad, muscle and liver respectively. Na⁺–K⁺–ATPase activity in the liver and gonad may be considered as a reference biomarker of UMTLS stress. The data in this study may be valuable that the toxicity of such as the leaching solution of potentially hazardous material was compared with that of each constituent.     

蛋白质甲基化修饰的蛋白质组学分析方法新进展

蛋白质的甲基化修饰是一类重要的翻译后修饰。但与磷酸化、糖基化和泛素化等翻译后修饰相比,甲基化修饰的蛋白质组学分析方法开发还是一个较新的研究领域。近几年,由于甲基化修饰在表观遗传调控中的重要作用,这一修饰类型得到了越来越多的关注,相关的分析技术和分析方法也取得了较多进展。其中,基于质谱的蛋白质组学分析方法在甲基化修饰中发挥着关键的作用,实现了这一甲基化修饰的高通量分析。该综述将从甲基化修饰的分离富集、假阳性率控制以及定量蛋白质组学等方面对一些蛋白质甲基化修饰的分析技术和方法的最新进展进行介绍。     

Enhancement of mass spectrometry performance for proteomic analyses using highfield asymmetric waveform ion mobility spectrometry (FAIMS)

Remarkable advances in mass spectrometry sensitivity and resolution have been accomplished over the past two decades to enhance the depth and coverage of proteome analyses. As these technological developments expanded the detection capability of mass spectrometers, they also revealed an increasing complexity of low abundance peptides, solvent clusters and sample contaminants that can confound protein identification. Separation techniques that are complementary and can be used in combination with liquid chromatography are often sought to improve mass spectrometry sensitivity for proteomics applications. In this context, high‐field asymmetric waveform ion mobility spectrometry (FAIMS), a form of ion mobility that exploits ion separation at low and high electric fields, has shown significant advantages by focusing and separating multiply charged peptide ions from singly charged interferences. This paper examines the analytical benefits of FAIMS in proteomics to separate co‐eluting peptide isomers and to enhance peptide detection and quantitative measurements of protein digests via native peptides (label‐free) or isotopically labeled peptides from metabolic labeling or chemical tagging experiments. Copyright © 2015 John Wiley & Sons, Ltd.     

Isotopically Labeled Desthiobiotin Azide (isoDTB) Tags Enable Global Profiling of the Bacterial Cysteinome

Rapid development of bacterial resistance has led to an urgent need to find new druggable targets for antibiotics. In this context, residue‐specific chemoproteomic approaches enable proteome‐wide identification of binding sites for covalent inhibitors. Described here are easily synthesized isotopically labeled desthiobiotin azide (isoDTB) tags that shortened the chemoproteomic workflow and allowed an increased coverage of cysteines in bacterial systems. They were used to quantify 59 % of all cysteines in essential proteins in Staphylococcus aureus and enabled the discovery of 88 cysteines that showed high reactivity, which correlates with functional importance. Furthermore, 268 cysteines that are engaged by covalent ligands were identified. Inhibition of HMG‐CoA synthase was verified and will allow addressing the bacterial mevalonate pathway through a new target. Overall, a broad map of the bacterial cysteinome was obtained, which will facilitate the development of antibiotics with novel modes‐of‐action.     

新型整体材料的制备及其在蛋白质组学中的应用

蛋白质组学是后基因时代生命科学研究的核心内容之一,其中发展高分辨、高灵敏度、高准确性和高通量的分析技术至关重要。整体材料具有制备简单、传质速度快、色谱柱反压低、表面易修饰等优点,因此已被广泛用于蛋白质组学研究中。本文对各种整体材料(包括有机聚合物整体材料、硅胶整体材料、有机-无机杂化整体材料)的制备方法及其在蛋白质组学研究(如蛋白质的酶解、蛋白质和肽段的分离以及在线酶解-分离-鉴定的高通量分析)中的应用进行了系统综述。     

Effect of degree of acetylation and solvent on the chiroptical properties of lyotropic (acetyl) (ethyl) cellulose solutions

(Acetyl) (ethyl) cellulose (AEC) polymers with an ethyl degree of substitution (DS) of 2.5 and acetyl DS ranging from 0 to 0.5 dissolve readily in a wide range of organic solvents and form chiral nematic liquid crystalline phases in concentrated solution. The chiroptical properties of these liquid crystals are strongly influenced by the acetyl content and solvent. In dichloromethane, dibromomethane, chloroform, bromoform, m-cresol, acetic acid, and aqueous phenol, the AEC lyotropic mesophases all show a handedness inversion as the acetyl DS of the polymers is increased, changing from left- to right-handed supermolecular helicoidal structures. The temperature dependence of the pitch for these mesophases is also reversed from negative to positive with increasing acetyl DS in all the above solvents except aqueous phenol, in which the corresponding AEC mesophases change from positive to negative. The optical microscopic, optical diffraction, and ORD evidence provide a unique indication that the reversal of the handedness and temperature dependence for the AEC mesophases occurs at a compensated degree of acetylation, DA^*. The corresponding compensated mesophases show an infinite pitch and behave optically like nematic mesophases. The value of the DA^* is dependent on solvent. In dichloroacetic acid, AEC liquid crystals remain right-handed, independent of the acetyl DS. At given concentration and temperature, the long pitch samples flow much more readily than short pitch samples. © 1994 John Wiley & Sons, Inc.     

Recent advances in computational analysis of mass spectrometry for proteomic profiling

The proteome, defined as an organism's proteins and their actions, is a highly complex end-effector of molecular and cellular events. Differing amounts of proteins in a sample can be indicators of an individual's health status; thus, it is valuable to identify key proteins that serve as 'biomarkers' for diseases. Since the proteome cannot be simply inferred from the genome due to pre- and posttranslational modifications, a direct approach toward mapping the proteome must be taken. The difficulty in evaluating a large number of individual proteins has been eased with the development of high-throughput methods based on mass spectrometry (MS) of peptide or protein mixtures, bypassing the time-consuming, laborious process of protein purification. However, proteomic profiling by MS requires extensive computational analysis. This article describes key issues and recent advances in computational analysis of mass spectra for biomarker identification.     

Biocompatibility Study of Curcumin-Loaded Pluronic F127 Nanoformulation (NanoCUR) against the Embryonic Development of Zebrafish (Danio rerio)

Curcumin (CUR) has been studied for its biomedical applications due to its active biological properties. However, CUR has limitations such as poor solubility, low bioavailability, and rapid degradation. Thus, CUR was nanoformulated with the application of polymeric micelle. Previous studies of CUR-loaded Pluronic F127 nanoformulation (NanoCUR) were generally prioritized toward cancer cells and its therapeutic values. There are reports that emphasize the toxicity of CUR, but reports on the toxicity of NanoCUR on embryonic developmental stages is still scarce. The present study aims to investigate the toxicity effects of NanoCUR on the embryonic development of zebrafish (Danio rerio). NanoCUR was synthesized via thin film hydration method and then characterized using DLS, UV-Vis, FTIR, FESEM, and XRD. The toxicity assessment of NanoCUR was conducted using zebrafish embryos, in comparison to native CUR, as well as Pluronic F127 (PF) as the controls, and ROS assay was further carried out. It was revealed that NanoCUR showed an improved toxicity profile compared to native CUR. NanoCUR displayed a delayed toxicity response and showed a concentration- and time-dependent toxicity response. NanoCUR was also observed to generate a significantly low reactive oxygen species (ROS) compared to native CUR in ROS assay. Overall, the results obtained highlight the potential of NanoCUR to be developed in clinical settings due to its improved toxicity profile compared to CUR.     

Synthesis and chiral recognition properties of poly(N‐propargylamide) gels derived from ornithine and lysine

Copolymerization of ornithine‐ and lysine‐derived N‐propargylamides, N‐α‐tert‐butoxycarbonyl‐N‐δ‐fluorenylmethoxycarbonyl‐L ‐ornithine N′‐propargylamide ( 1 ), N‐α‐tert‐butoxycarbonyl‐N‐ε‐fluorenylmethoxycarbonyl‐L ‐lysine N′‐propargylamide ( 2 ), N‐α‐fluorenylmethoxycarbonyl‐N‐δ‐tert‐butoxycarbonyl‐L ‐ornithine N′‐propargylamide ( 3 ), and N‐α‐fluorenylmethoxycarbonyl‐N‐ε‐tert‐butoxycarbonyl‐L ‐lysine N′‐propargylamide (4) with dipropargyl adipate was carried out using (nbd)Rh⁺[η⁶‐C₆H₅B^?(C₆H₅)₃] as a catalyst in THF to obtain polymer gels in 80–93% yields. The gels adsorbed N‐benzyloxycarbonyl L ‐alanine, N‐benzyloxycarbonyl L ‐alanine methyl ester, and (S)‐(+)‐1‐phenyl‐1,2‐ethanediol preferably than the corresponding optical isomers. The order of chiral discrimination was poly( 1 ) > poly( 4 ) > poly( 2 ), poly( 3 ) gels. The fluorenylmethoxycarbonyl groups of the gels could be partly removed by piperidine treatment, leading to increase of adsorptivity but decrease of chiral recognition ability. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 4175–4182, 2008     

超高效液相色谱-串联质谱法测定斑马鱼性腺中13种类固醇激素

建立了超高效液相色谱-串联质谱测定雌性斑马鱼性腺中13种类固醇激素的分析方法。雌鱼性腺分别经预冷的乙腈、乙酸乙酯浸提后,氨基(NH2)、亲水-亲脂平衡介质(HLB)固相萃取柱富集净化,ACQUITY UPLCBEH C18色谱柱进行梯度分离。采用多反应监测模式扫描,基质匹配外标法定量。研究了不同提取溶剂对13种类固醇激素的提取效果,考察了固相萃取柱的净化效果,并对斑马鱼性腺进行类固醇激素加标回收率实验,结果表明,13种分析物的平均加标回收率为74.8%~127.0%,相对标准偏差为3.9%~15.8%,方法检出限为0.006~0.300μg/kg。该方法简便、准确、灵敏,可应用于斑马鱼性腺类固醇激素生理水平的检测。     

微流控芯片技术在蛋白质分析中的应用进展

近年来,微流控芯片技术取得了显著的发展。随着微电子及微机械等制作技术的不断进步,高通量、高效、快速、低成本的微流控分析芯片在蛋白质和多肽分析方面获得了令人瞩目的成果。本文主要介绍了微流控芯片在蛋白质组学分析研究的应用和发展。引用文献52篇。     

Sweroside Ameliorated Memory Deficits in Scopolamine-Induced Zebrafish (Danio rerio) Model: Involvement of Cholinergic System and Brain Oxidative Stress

Sweroside is a secoiridoid glycoside and belongs to a large group of naturally occurring monoterpenes with glucose sugar attached to C-1 in the pyran ring. Sweroside can promote different biological activities such as antifungal, antibacterial, hepatoprotective, gastroprotective, sedative and antitumor, antioxidant, and neuroprotective activities. Zebrafish were given sweroside (12.79, 8.35, and 13.95 nM) by immersion once daily for 8 days, along with scopolamine (Sco, 100 μM) 30 min before the initiation of the behavioral testing to cause anxiety and memory loss. Employing the novel tank diving test (NTT), the Y-maze, and the novel object recognition test (NOR), anxiety-like reactions and memory-related behaviors were assessed. The following seven groups (n = 10 animals per group) were used: control, Sco (100 μM), sweroside treatment (2.79, 8.35, and 13.95 nM), galantamine (GAL, 2.71 μM as the positive control in Y-maze and NOR tests), and imipramine (IMP, 63.11 μM as the positive control in NTT test). Acetylcholinesterase activity (AChE) and the antioxidant condition of the brains were also evaluated. The structure of sweroside isolated from Schenkia spicata was identified. Treatment with sweroside significantly improved the Sco-induced decrease of the cholinergic system activity and brain oxidative stress. These results suggest that sweroside exerts a significant effect on anxiety and cognitive impairment, driven in part by the modulation of the cholinergic system activity and brain antioxidant action.