化学生物学新前沿——化学蛋白质组学

随着包括人类在内的主要模式生物的基因组计划的完成,生命科学的研究重心转向蛋白质组的研究--在对应基因组的整体蛋白质水平上系统研究调控细胞生命活动的蛋白质.化学蛋白质组学是化学生物学在后基因组时代的最新发展:化学蛋白质组学利用化学小分子为工具和手段,以基于靶蛋白质功能的新战略探测体内蛋白质组,是新一代的功能蛋白质组学.本文综述了化学蛋白质组学的最新进展、有关技术及其在生物医学和药物研发等方面的应用,并对化学蛋白质组学的发展趋势和前景进行了讨论.     

The Ketamine Antidepressant Story: New Insights

Ketamine is a versatile agent primarily utilized as a dissociative anesthetic, which acts by blocking the excitatory receptor N-methyl-d-aspartate receptor (NMDA). It functions to inhibit the current of both Na⁺ and K⁺ voltage-gated channels, thus preventing serotonin and dopamine reuptake. Studies have indicated that administering a single subanesthetic dose of ketamine relieves depression rapidly and that the effect is sustained. For decades antidepressant agents were based on the monoamine theory. Although ketamine may not be the golden antidepressant, it has opened new avenues toward mechanisms involved in the pathology of treatment-resistant depression and achieving rapid antidepressant effects. Thus, preclinical studies focusing on deciphering the molecular mechanisms involved in the antidepressant action of ketamine will assist in the development of a new antidepressant. This review was conducted to elucidate the emerging pathways that can explain the complex dose-dependent mechanisms achieved by administering ketamine to treat major depressive disorders. Special attention was paid to reviewing the literature on hydroxynorketamines, which are ketamine metabolites that have recently attracted attention in the context of depression.     

比较蛋白质组学研究中的稳定同位素标记技术

比较蛋白质组学是指在蛋白质组学水平上研究正常和病理情况下细胞或组织中蛋白质表达变化,以期发现具有重要功能的生物标识物,为疾病的早期诊断提供依据。近年来它正成为蛋白质组学研究的热点和发展趋势。比较蛋白质组学的研究方法和策略有多种,本文就最近几年来稳定同位素标记技术(体内代谢标记技术和体外化学标记技术)在比较蛋白质组学研究中的进展进行综述。     

基于质谱技术蛋白质定量方法的研究进展

质谱技术已经成为目前蛋白质鉴定的重要工具。定量分析细胞内蛋白质组的动态变化,是当前研究蛋白质功能、揭示细胞生物机理、寻找疾病蛋白标记物和药物靶标的迫切需要。本文综述了基于质谱技术蛋白质定量的策略、方法和应用等方面近年来的进展,评述了几种蛋白质质谱定量方法的特点和应用潜力。     

Amorphous Silicon: New Insights into an Old Material

Amorphous silicon is synthesized by treating the tetrahalosilanes SiX₄ (X=Cl, F) with molten sodium in high boiling polar and non‐polar solvents such as diglyme or nonane to give a brown or a black solid showing different reactivities towards suitable reagents. With regards to their technical relevance, their stability towards oxygen, air, moisture, chlorine‐containing reaction partners RCl (R=H, Cl, Me) and alcohols is investigated. In particular, reactions with methanol are a versatile tool to deliver important products. Besides tetramethoxysilane formation, methanolysis of silicon releases hydrogen gas under ambient conditions and is thus suitable for a decentralized hydrogen production; competitive insertion into the MeO?H versus the Me?OH bond either yields H‐ and/or methyl‐substituted methoxy functional silanes. Moreover, compounds, such as Me_nSi(OMe)_4?n (n=0–3) are simply accessible in more than 75 % yield from thermolysis of, for example, tetramethoxysilane over molten sodium. Based on our systematic investigations we identified reaction conditions to produce the methoxysilanes Me_nSi(OMe)_4?n in excellent (n=0:100 %) to acceptable yields (n=1:51 %; n=2:27 %); the yield of HSi(OMe)₃ is about 85 %. Thus, the methoxysilanes formed might possibly open the door for future routes to silicon‐based products.     

理解量子效应的新视角

以一维势箱中的粒子为例,从直观的视角对量子效应及其之间的关联做了阐明。作为讨论一维势箱量子效应的补充材料,有助于学生进一步理解微观粒子基本特征。     

Comparative Proteomics of Potato Cultivars with a Variable Dormancy Period

The control of the duration of the dormancy phase is a significant challenge in the potato industry and for seed producers. However, the proteome landscape involved in the regulation of the length of the dormancy period over potato cultivars remains largely unexplored. In this study, we performed for the first time a comparative proteome profiling of potato cultivars with differential duration of tuber dormancy. More specifically, the proteome profiling of Agata, Kennebec and Agria commercial potato varieties with short, medium and medium-long dormancy, respectively, was assessed at the endodormancy stage using high-resolution two-dimensional electrophoresis (2-DE) coupled to reversed-phase liquid chromatography–tandem mass spectrometry (LC-TripleTOF MS/MS). A total of 11 proteins/isoforms with statistically significant differential abundance among cultivars were detected on 2-DE gels and confidently identified by LC-TripleTOF MS/MS. Identified proteins have known functions related to tuber development, sprouting and the oxylipins biosynthesis pathway. Fructokinase, a mitochondrial ADP/ATP carrier, catalase isozyme 2 and heat shock 70 kDa were the proteins with the strongest response to dormancy variations. To the best of our knowledge, this study reports the first candidate proteins underlying variable dormancy length in potato cultivars.     

HCV全基因组培养细胞的比较蛋白组学研究

利用比较蛋白质组技术研究了转染丙型肝炎病毒(Hepatitis C virus, HCV)全基因组的人肝癌细胞系Huh7细胞模型中蛋白质表达谱的变化, 建立了Huh7-HCV的双向凝胶电泳蛋白质表达图谱和数据库. 通过双向凝胶电泳分离和图像分析, 对表达差异2倍以上蛋白质点进行了胶内酶解和MALDI-TOF MS鉴定. 得到包括与细胞骨架蛋白、细胞周期、凋亡和信号转导等相关的14个蛋白质, 并且用Western blot验证了热休克蛋白70的蛋白质组研究结果. 利用HCV全基因组培养系统, 采用蛋白质组学技术, 为研究HCV病毒和宿主细胞相互作用提供了新的实验数据, 为深入研究HCV病毒复制和分子致病机理奠定了基础.     

基于不同裂解液的蛋白质组样品制备方法的比较研究

蛋白质组学研究所面临的首要问题就是蛋白质组的样品制备,而不同的样品制备方案针对细胞、组织等样品的裂解能力,以及对不同种类蛋白的溶解能力会有很大的差异.本研究以培养的293T细胞为对象,利用质谱分析鉴定蛋白的方法,比较了采用3种常用的蛋白质组样品制备方法(Triton X-100法、尿素法和TRIzol法)所提取蛋白种类的差异,并利用生物信息学工具对所得数据进行了分析.结果表明,Triton X-100法和尿素法所提取蛋白的鉴定数目接近,而TRIzol法所提取蛋白的鉴定数目比二者减少约8％.从所鉴定的蛋白种类来看,3种方法相差较大,仅约有32％的蛋白为3种方法所共有,生物学功能也不尽相同.本研究为评价各种蛋白质组样品制备方法提供了一种快速、有效、全面的研究方法.     

大鼠骨髓间充质干细胞分化过程的比较蛋白质组学研究

从蛋白质组学角度分析大鼠骨髓间充质干细胞(MSCs)体外定向分化为心肌细胞过程中蛋白表达情况, 采用二维电泳分离蛋白, 用PDQuest软件分析蛋白表达差异, 并采用质谱(MALDI-TOF-MS)进行鉴定, 得到了54个蛋白点, 对蛋白的生物功能分析表明, 部分蛋白通过不同的信号途径参与了MSCs的分化过程.     

Frustrated Radical Pairs: Insights from EPR Spectroscopy

Progress in frustrated Lewis pair (FLP) chemistry has revealed the importance of the main group elements in catalysis, opening new avenues in synthetic chemistry. Recently, new reactivities of frustrated Lewis pairs have been uncovered that disclose that certain combinations of Lewis acids and bases undergo single‐electron transfer (SET) processes. Here an electron can be transferred from the Lewis basic donor to a Lewis acidic acceptor to generate a reactive frustrated radical pair (FRP). This minireview aims to showcase the recent advancements in this emerging field covering the synthesis and reactivities of frustrated radical pairs, with extensive highlights of the results from Electron Paramagnetic Resonance (EPR) spectroscopy to explain the nature and stability of the different radical species observed.     

Methods for the Functionalisation of Nanoparticles: New Insights and Perspectives

In the field of nanometre‐sized drug‐delivery systems, a wide range of colloidal systems have been created in recent decades. All of the systems have a similar global structure, that is, an inner part and an external surface/interface. In several applications, the external interface is the support for desired properties and the basis of future developments. The engineering of the particle’s surface is an emerging step in the design of systems at the nanometre scale. This review presents and summarises the available techniques with a particular attention to recent advances. It is also a base for future works in this expanding area of research.     

Solubilization Site of Organic Perfume Molecules in Sodium Dodecyl Sulfate Micelles: New Insights from Proton NMR Studies

The site of incorporation of solubilizates in sodium dodecyl sulfate (SDS) micellar systems has been investigated by proton NMR spectroscopy. The solubilizate molecules chosen for the present study are phenol, 4-methylphenol, 4-allyl-2-methoxyphenol, anisole, 4-methylanisole, 4-propenylanisole, 1,8-cineole, and limonene. These molecules possess a wide variety of functional groups with different degrees of hydrophilic/hydrophobic character and are thereby solubilized at different micellar locations. Aromatic compounds, especially those having a phenolic-OH group, showed a large upfield shift of SDS methylene protons that are closely linked to the terminal sulfate groups. Additionally, in the case of phenolic compounds, the unresolved signals of the nine straight-chain bulk methylene protons of SDS are split into a broad doublet with uneven intensity. This splitting of methylene protons was found to be dependent on the concentration of the substrate. Based on these observations, probable solubilization sites and orientation of the substrate molecule within the micelles are discussed. Phenolic compounds, being the most hydrophilic among the present set, reside at the hydrophilic/hydrophobic boundary of micelle-water interface and thus influence the resonances of SDS protons the most. Aromatic methoxy and aliphatic compounds, being relatively more hydrophobic in nature, reside inside the micellar core and thereby result in smaller shifts. Copyright 2000 Academic Press.     

Proteomics: capacity versus utility

Until recently scientists studied genes or proteins one at a time. With improvements in technology, new tools have become available to study the complex interactions that occur in biological systems. Global studies are required to do this, and these will involve genomic and proteomic approaches. High-throughput methods are necessary in each case because the number of genes and proteins in even the simplest of organisms are immense. In the developmental phase of genomics, the emphasis was on the generation and assembly of large amounts of nucleic acid sequence data. Proteomics is currently in a phase of technological development and establishment, and demonstrating the capacity for high throughput is a major challenge. However, funding bodies (both in the public and private sector) are increasingly focused on the usefulness of this capacity. Here we review the current state of proteome research in terms of capacity and utility.     

Revisiting the Early History of Synthetic Polymers: Critiques and New Insights

This essay seeks to clarify existing confusion in terminology regarding the history of polymers, plastics, and macromolecules, and explores various factors that complicate the early history of macromolecules. It also suggests reasons why materials such as polyaniline, an early fully synthetic polymer that found widespread commercial application in dyes, have not previously been treated in accounts of polymer history.     

Aminoglycoside Antibiotics: New Insights into the Biosynthetic Machinery of Old Drugs

2‐Deoxystreptamine (2DOS) is the unique chemically stable aminocyclitol scaffold of clinically important aminoglycoside antibiotics such as neomycin, kanamycin, and gentamicin, which are produced by Actinomycetes. The 2DOS core can be decorated with various deoxyaminosugars to make structurally diverse pseudo‐oligosaccharides. After the discovery of biosynthetic gene clusters for 2DOS‐containing aminoglycoside antibiotics, the function of each biosynthetic enzyme has been extensively elucidated. The common biosynthetic intermediates 2DOS, paromamine and ribostamycin are constructed by conserved enzymes encoded in the gene clusters. The biosynthetic intermediates are then converted to characteristic architectures by unique enzymes encoded in each biosynthetic gene cluster. In this Personal Account, we summarize both common biosynthetic pathways and the pathways used for structural diversification.

     

Comparative Modelling of Organic Anion Transporting Polypeptides: Structural Insights and Comparison of Binding Modes

To better understand the functionality of organic anion transporting polypeptides (OATPs) and to design new ligands, reliable structural data of each OATP is needed. In this work, we used a combination of homology model with molecular dynamics simulations to generate a comprehensive structural dataset, that encompasses a diverse set of OATPs but also their relevant conformations. Our OATP models share a conserved transmembrane helix folding harbouring a druggable binding pocket in the shape of an inner pore. Our simulations suggest that the conserved salt bridges at the extracellular region between residues on TM1 and TM7 might influence the entrance of substrates. Interactions between residues on TM1 and TM4 within OATP1 family shown their importance in transport of substrates. Additionally, in transmembrane (TM) 1/2, a known conserved element, interact with two identified motifs in the TM7 and TM11. Our simulations suggest that TM1/2-TM7 interaction influence the inner pocket accessibility, while TM1/2-TM11 salt bridges control the substrate binding stability.     

Polyphenols for the Treatment of Ischemic Stroke: New Applications and Insights

Ischemic stroke (IS) is a leading cause of death and disability worldwide. Currently, the main therapeutic strategy involves the use of intravenous thrombolysis to restore cerebral blood flow to prevent the transition of the penumbra to the infarct core. However, due to various limitations and complications, including the narrow time window in which this approach is effective, less than 10% of patients benefit from such therapy. Thus, there is an urgent need for alternative therapeutic strategies, with neuroprotection against the ischemic cascade response after IS being one of the most promising options. In the past few decades, polyphenolic compounds have shown great potential in animal models of IS because of their high biocompatibility and ability to target multiple ischemic cascade signaling pathways, although low bioavailability is an issue that limits the applications of several polyphenols. Here, we review the pathophysiological changes following cerebral ischemia and summarize the research progress regarding the applications of polyphenolic compounds in the treatment of IS over the past 5 years. Furthermore, we discuss several potential strategies for improving the bioavailability of polyphenolic compounds as well as some essential issues that remain to be addressed for the translation of the related therapies to the clinic.     

Electrostatics of phosphatidic acid monolayers: Insights from computer simulations

In this paper, we argue that many of the fascinating electrostatic effects that take place in amphiphilic systems are strongly related to the particular organization of the oxygen atoms within each individual molecule. In particular, we focus on two effects: charge inversion and dielectric overscreening. For that purpose, we present molecular dynamics simulations of phosphatidic acid (DMPA²⁻) in the presence of divalent counterions. Our results show that the many oxygens present in DMPA²⁻ cooperatively create strong binding sites for counterions, which in some cases lead to charge inversion. We also present an analysis of the role of interfacial water and relate our analysis to the phenomenon of dielectric overscreening. Several experimental implications are discussed in the conclusions.