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Meet the Editorial Board Member 认识编辑委员会成员
IF 0.8 4区 生物学 Q4 BIOCHEMICAL RESEARCH METHODS Pub Date : 2022-10-01 DOI: 10.2174/157016461905221208115443
S. Gonfloni
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引用次数: 0
Unraveling major proteins of Mycobacterium tuberculosis envelope 揭示结核分枝杆菌包膜的主要蛋白
IF 0.8 4区 生物学 Q4 BIOCHEMICAL RESEARCH METHODS Pub Date : 2022-09-08 DOI: 10.2174/1570164619666220908141130
D. Bisht, Rananjay Singh, D. Sharma, D. Sharma, S. Gautam, Mahendra K. Gupta
Although treatable, resistant form of tuberculosis has posed a major impediment to the effective TB control programme. As the Mycobacterium tuberculosis cell envelope is closely associated with its virulence and resistance, it is very important to understand the cell envelope for better treatment of causative pathogens. Cell membrane plays a crucial role in imparting various cell functions. Proteins being the functional moiety, it is impossible to characterize the functional properties based on genetic analysis alone. Proteomic based research has indicated mycobacterial envelope as a good source of antigens/proteins. Envelope/membrane and associated proteins have an anticipated role in biological processes which could be of vital importance to the microbe and hence could qualify as drug targets. This review provides an overview of the prominent and biologically important cell envelope and highlights the different functions offered by the proteins associated with it. Selective targeting of the mycobacterial envelope offers an untapped opportunity to address the problems associated with the current drugs regimen and also will lead to the development of more potent and safer drugs against all forms of tuberculous infections.
耐药结核病虽然可以治疗,但对有效的结核病控制规划构成了重大障碍。由于结核分枝杆菌的细胞包膜与其毒力和耐药性密切相关,因此了解细胞包膜对更好地治疗致病菌非常重要。细胞膜在赋予细胞各种功能中起着至关重要的作用。蛋白质作为功能片段,仅凭遗传分析是不可能表征其功能特性的。基于蛋白质组学的研究表明分枝杆菌包膜是抗原/蛋白质的良好来源。包膜/膜和相关蛋白在生物过程中具有预期的作用,这可能对微生物至关重要,因此可以作为药物靶点。本文综述了重要的生物学细胞包膜,并重点介绍了与之相关的蛋白质的不同功能。分枝杆菌包膜的选择性靶向为解决与当前药物方案相关的问题提供了一个尚未开发的机会,也将导致开发针对所有形式结核感染的更有效和更安全的药物。
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引用次数: 0
Meet the Editorial Board Member 认识编辑委员会成员
IF 0.8 4区 生物学 Q4 BIOCHEMICAL RESEARCH METHODS Pub Date : 2022-08-01 DOI: 10.2174/157016461904220907111423
A. Bairoch
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引用次数: 0
Heavy metal stress tolerance by Serratia nematodiphila sp. MB307: insights from mass spectrometry based proteomics 嗜线虫Serratia nematodiophila sp. MB307的重金属耐受性:基于质谱的蛋白质组学分析
IF 0.8 4区 生物学 Q4 BIOCHEMICAL RESEARCH METHODS Pub Date : 2022-06-17 DOI: 10.2174/1570164619666220617145437
Z. Basharat, K. Moon, L. Foster, A. Yasmin
Heavy metals impact living organism deleteriously when exceed the required limits. Their remediation by bacteria is a much pursued area of environmental research. In this study, we explored the quantitative changes for four heavy metals (Cadmium, Chromium, Zinc, Copper), on global and membrane proteome of gram negative S. nematodiphila MB307. This is a versatile bacterium, isolated from rhizosphere of heavy metal tolerating plant and equipped with characteristics ranging from useful biopeptide production to remediation of metals.We explored changes in its static end products of coding DNA sequences i.e. proteins after 24 incubation under metal stress, using LC-MS/MS. Data analysis was done using MaxQuant software coupled with Perseus package.Up and downregulated protein fractions consisted prominently of chaperones, membrane integrity proteins, mobility or transporter proteins. Comparative analysis with previously studied bacteria and functional contribution of these proteins in metal stress offers evidence for survival of S. nematodiphila under high concentrations of selected metals.The outcomes validate that this soil derived bacterium is well attuned to remove these metals from soil, water and may be additionally useful for boosting phytoremediation of metals. This study delivers interesting insights and overlays ground for further investigations into mechanistic activity of this bacterium under pollutant stress.
当重金属超过规定的限度时,会对生物体产生有害影响。细菌对它们的修复是环境研究的一个热门领域。本研究探讨了革兰氏阴性嗜线虫球菌MB307中四种重金属(镉、铬、锌、铜)在全局和膜蛋白质组中的定量变化。这是一种多用途细菌,从耐重金属植物的根际分离出来,具有从有用的生物肽生产到金属修复的特性。我们利用LC-MS/MS技术研究了金属胁迫24小时后其编码DNA序列的静态终产物(即蛋白质)的变化。使用MaxQuant软件和Perseus软件包进行数据分析。上调和下调的蛋白组分主要由伴侣蛋白、膜完整性蛋白、迁移蛋白或转运蛋白组成。与先前研究的细菌和这些蛋白质在金属胁迫下的功能贡献进行比较分析,为嗜线虫球菌在高浓度选定金属下的存活提供了证据。结果证实,这种土壤衍生的细菌可以很好地从土壤和水中去除这些金属,并且可能对促进金属的植物修复有用。这项研究提供了有趣的见解,并为进一步研究这种细菌在污染胁迫下的机制活性奠定了基础。
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引用次数: 0
Meet the Editorial Board Member 认识编辑委员会成员
IF 0.8 4区 生物学 Q4 BIOCHEMICAL RESEARCH METHODS Pub Date : 2022-06-01 DOI: 10.2174/157016461903220530111915
R. Abrol
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引用次数: 0
Identification of human protein subcellular location with multiple networks 基于多网络的人蛋白亚细胞定位鉴定
IF 0.8 4区 生物学 Q4 BIOCHEMICAL RESEARCH METHODS Pub Date : 2022-05-31 DOI: 10.2174/1570164619666220531113704
Rui Wang, Lei Chen
Protein function is closely related to its location within the cell. Determination of protein subcellular location is helpful to uncover its functions. However, traditional biological experiments to determine the subcellular location are of high cost and low efficiency, which cannot meet today’s needs. In recent years, lots of computational models have been set up to identify protein subcellular locations. Most models used features derived from protein sequences. Recently, features extracted from protein-protein interaction (PPI) network become popular to study various protein-related problems.A novel model with features derived from multiple PPI networks was proposed to predict protein subcellular location.Protein features were obtained by a new designed network embedding algorithm, Mnode2vec, which was a generalized version of the classic Node2vec algorithm. Two classic classification algorithms: support vector machine and random forest, were employed to build the model.Such model provided good performance and was superior to the model with features extracted by Node2vec. Also, this model outperformed some classic models. Furthermore, Mnode2vec can produce powerful features when the path length was small.The proposed model can be a powerful tool to determine protein subcellular location and Mnode2vec can efficiently extract informative features from multiple networks.
蛋白质的功能与其在细胞中的位置密切相关。确定蛋白质的亚细胞位置有助于揭示其功能。然而,传统的生物实验确定亚细胞位置成本高、效率低,已不能满足当今的需求。近年来,人们建立了许多计算模型来识别蛋白质亚细胞的位置。大多数模型使用来自蛋白质序列的特征。近年来,从蛋白质-蛋白质相互作用(PPI)网络中提取特征成为研究各种蛋白质相关问题的热点。提出了一种具有多个PPI网络特征的新模型来预测蛋白质亚细胞定位。蛋白质特征的获取采用了一种新的网络嵌入算法Mnode2vec,该算法是经典Node2vec算法的推广版本。采用支持向量机和随机森林两种经典分类算法建立模型。该模型具有良好的性能,优于Node2vec提取特征的模型。此外,这款机型的表现也优于一些经典机型。此外,当路径长度较小时,Mnode2vec可以产生强大的特征。该模型可以作为确定蛋白质亚细胞位置的有力工具,并且Mnode2vec可以有效地从多个网络中提取信息特征。
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引用次数: 10
Methanol and sorbitol affect the molecular dynamics of arginine deiminase: insights for improving its stability 甲醇和山梨醇影响精氨酸脱亚胺酶的分子动力学:提高其稳定性的见解
IF 0.8 4区 生物学 Q4 BIOCHEMICAL RESEARCH METHODS Pub Date : 2022-05-13 DOI: 10.2174/1570164619666220513123509
M. Zarei, S. Sabetian, M. Rahbar, M. Negahdaripour
Arginine deiminase enzyme of Mycoplasma arginini (MaADI) is a potential anti-cancer agent for treating arginine-auxotrophic cancers. Investigating the protein stability in the presence of osmolytes can help to increase protein stability under various stressed conditions.In this study, the stability and dynamics of MaADI were investigated in pure water and solutions of 1 M sorbitol, 10% (v/v) methanol, and 50% (v/v) methanol using molecular dynamics simulation.Sorbitol was found to stabilize the protein, whereas high-concentrated methanol destabilized it. Sorbitol molecules interacted with the protein through hydrogen bonding and reduced the protein fluctuations as well. At 50% methanol, the flexibility of regions 4-8, 195-201, 314-324, and 332-337 in the MaADI was increased; whereas residues 195-201 showed the highest variations.Thus, these regions of MaADI, especially 195-201, are the most sensitive regions in the presence of denaturing agents and can be subjected to protein engineering toward improving the stability of MaADI.
精氨酸支原体(Mycoplasma arginini, MaADI)的精氨酸脱亚胺酶(Arginine de亚胺酶)是一种治疗精氨酸营养不良癌症的潜在抗癌药物。研究渗透物存在下的蛋白质稳定性有助于提高蛋白质在各种应激条件下的稳定性。本研究通过分子动力学模拟研究了MaADI在纯水和1 M山梨醇、10% (v/v)甲醇和50% (v/v)甲醇溶液中的稳定性和动力学。山梨醇可以稳定蛋白质,而高浓度甲醇则会使其不稳定。山梨醇分子通过氢键与蛋白质相互作用,减少了蛋白质的波动。甲醇浓度为50%时,MaADI中4-8、195-201、314-324和332-337区的柔韧性增加;而残留195 ~ 201的变异最大。因此,MaADI的这些区域,特别是195-201,是变性剂存在时最敏感的区域,可以通过蛋白质工程来提高MaADI的稳定性。
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引用次数: 0
Proteomics, Peptidomics and Transcriptomic Analysis of the Venom from the Spider Macrothele yani (Mygalomorphae: Macrothelidae) 巨蛛毒液的蛋白质组学、肽组学和转录组学分析
IF 0.8 4区 生物学 Q4 BIOCHEMICAL RESEARCH METHODS Pub Date : 2022-04-30 DOI: 10.2174/1570164619666220430151150
X. Gu, Ying Wang, Chenggui Zhang, Xiu-Mei Wu, Huai Xiao, Yinnan Yang, Dasong Yang, Zhi-Bin Yang, Zijin Yang, Yu Zhao
Spider venom show abundant diversity in both peptides and proteins, which play essential roles in new drug development and agrochemistry. The venoms of Macrothele yani species have strong toxicity on the victims.Objective: The purpose of this study is to comprehensively characterize the profile of venom proteins and peptides of spider Macrothele yani mainly inhabiting in Yunnan province, China.Using a combination of RNA sequencing of the venom glands and venom proteomics based on Liquid Chromatography-Electrospray Ionization-Tandem Mass Spectrometry (LC-ESI-MS/MS), we provide the first overview of the peptides and proteins produced by Macrothele yani.A total of 116 peptide sequences were analyzed, and 43 homologous proteins were matched, of which 38.10% were toxin proteins. High-throughput sequencing by the HiSeq-2000 (Illumina), followed by de novo assembly. As a result, 301,024 similar protein sequences were annotated in the available databases. A total of 68 toxins-related sequences were identified, comparative sequence analyses of these sequences indicated the presence of different types of enzymes and toxin-like genes, including Acetylcholinesterase, Hyaluronidase, cysteine-rich secretory proteins (CRISP), Astacin metalloprotease and other venom components.The venom of spider is a very abundant resources in nature. They were analyzed in order to determine their function in pathophysiology. Molecular templates with potential application value in medical and biological fields were obtained by classifying and characterizing the presumed components about spider venom of Macrothele yani, which laid a foundation for further study of the venom in the future.
蜘蛛毒液具有丰富的多肽和蛋白质多样性,在新药开发和农化中发挥着重要作用。大腹蛇的毒液对受害者有很强的毒性。目的:对主要生活在云南的雅氏巨蛛(Macrothele yani)的毒液蛋白和肽谱进行全面研究。利用毒腺的RNA测序和基于液相色谱-电喷雾电离-串联质谱(LC-ESI-MS/MS)的毒液蛋白质组学,我们首次概述了Macrothele yani产生的肽和蛋白质。共分析116条多肽序列,匹配43个同源蛋白,其中38.10%为毒素蛋白。采用HiSeq-2000 (Illumina)进行高通量测序,然后进行从头组装。结果,在可用的数据库中注释了301,024个相似的蛋白质序列。共鉴定出68条毒素相关序列,序列比较分析表明,这些序列存在不同类型的酶和毒素样基因,包括乙酰胆碱酯酶、透明质酸酶、富含半胱氨酸的分泌蛋白(CRISP)、Astacin金属蛋白酶等毒液成分。蜘蛛毒液是自然界中非常丰富的资源。对其进行分析,以确定其在病理生理中的功能。通过对大蜘蛛毒液推定成分的分类和表征,获得了具有潜在医学和生物学应用价值的分子模板,为今后对大蜘蛛毒液的进一步研究奠定了基础。
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引用次数: 0
Proteomics and Computational Analysis of Cytosolic Proteome of a Thermoacidophilic Euryarchaeon Picrophilus torridus 嗜热嗜酸Euryarchaeon Picrophilus torridus的蛋白质组学和胞质蛋白质组学计算分析
IF 0.8 4区 生物学 Q4 BIOCHEMICAL RESEARCH METHODS Pub Date : 2022-04-29 DOI: 10.2174/1570164619666220429121247
N. Singhal, Anjali Garg, Nirpendra Singh, Manish Kumar, M. Goel
Picrophilus torridus is a thermoacidophilic archaeon which thrives in an extremely low pH (0-1) and high temperatures (50-60°C). Thus, it is a suitable organism to study microbial genetics and metabolic adaptations to extreme acidic and moderate thermal environment.In the present study we have conducted a global proteome analysis of P. torridus and discerned the cytosolic proteome of P. torridus using gel-free, liquid chromatography mass spectrometry (LC-MS/MS).The cytosolic proteins of P. torridus were extracted and identified using gel-free, LC-MS/MS. Gene Ontology based pathway analysis and protein-protein interaction studies were performed to understand the role of various cytosolic proteins in sustaining the thermoacidophilic environment. Also, domain analysis of hypothetical/uncharacterized proteins was performed.Using gel-free LC-MS/MS, 408 cytosolic proteins of P. torridus were identified, including 36 hypothetical/uncharacterized proteins. Thus, we could identify 26.58 % of the theoretical proteome of P. torridus. Majority of the cytosolic proteins were observed to be multi-functional and involved in activities related to microbial metabolism.Comparison with an earlier study which used gel-based LC-MS analysis to identify cytosolic proteins of P. torridus revealed that gel-free LC-MS was better in identifying more number of proteins and also, higher/lower molecular weight proteins. The information discerned in this study might add to the knowledge-base of P. torridus proteome and provide a useful basis for further proteomic studies on other thermoacidophilic archaea.
torridus是一种嗜热酸性古菌,在极低的pH值(0-1)和高温(50-60°C)下繁殖。因此,它是一种适合研究微生物遗传学和代谢适应极端酸性和中等热环境的生物。本研究采用无凝胶液相色谱质谱法(LC-MS/MS)对墨西哥纸虫的细胞质蛋白质组进行了分析。采用无凝胶液相色谱-质谱联用技术,提取并鉴定了torridus的胞质蛋白。通过基因本体通路分析和蛋白-蛋白相互作用研究,了解各种胞质蛋白在维持嗜热酸性环境中的作用。此外,还进行了假设/未表征蛋白的结构域分析。采用无凝胶LC-MS/MS技术,共鉴定出408种torridus胞质蛋白,其中36种为假设或未鉴定的蛋白。因此,我们可以鉴定出26.58%的torridus理论蛋白质组。大多数细胞质蛋白被观察到是多功能的,并参与与微生物代谢有关的活动。与之前采用凝胶- LC-MS方法鉴定番茄假单胞菌胞质蛋白的研究结果相比,无凝胶- LC-MS方法鉴定的蛋白数量更多,分子量更高或更低。本研究可为进一步研究其他嗜热酸古菌的蛋白质组学提供有益的基础,并为进一步研究其他嗜热酸古菌的蛋白质组学奠定基础。
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引用次数: 0
Analysis of membrane proteins of streptomycin resistant Mycobacterium tuberculosis isolates 耐链霉素结核分枝杆菌分离株膜蛋白分析
IF 0.8 4区 生物学 Q4 BIOCHEMICAL RESEARCH METHODS Pub Date : 2022-04-28 DOI: 10.2174/1570164619666220428082752
Rananjay Singh, D. Sharma, D. Sharma, Mahendra K. Gupta, D. Bisht
Drug resistant tuberculosis remains a health security threat and resistance to second-line drugs limits the options for treatment. Consequently, there is an utmost need for identifying and characterizing new biomarkers/drug targets of prime importance. Membrane proteins have an anticipated role in biological processes and could qualify as biomarkers/drug targets. Streptomycin (SM) is recommended as a second-line treatment regimen only when amikacin resistance has been confirmed. As extensively drug-resistant (XDR) isolates are frequently cross-resistant to second-line injectable drugs, an untapped potential for continued use of SM has been suggested.The study aimed to analyze the membrane proteins overexpressed in SM resistant isolates of Mycobacterium tuberculosis using proteomics approaches.Membrane proteins were extracted employing sonication and ultracentrifugation. Two-dimensional gel electrophoresis (2DGE) of membrane proteins was performed and identification of proteins was done by liquid chromatography-mass spectrometry (LCMS) and bioinformatics tools.On analyzing the two-dimensional (2D) gels, five protein spots were found overexpressed in the membrane of SM resistant isolates. Docking analysis revealed that SM might bind to the conserved domain of overexpressed proteins and Group-based prediction system-prokaryotic ubiquitin-like protein (GPS-PUP) predicted potential pupylation sites within them.These proteins might be of diagnostic importance for detecting the cases early and for exploring effective control strategies against drug-resistant tuberculosis, particularly SM.
耐药结核病仍然是一种卫生安全威胁,对二线药物的耐药性限制了治疗的选择。因此,迫切需要鉴定和表征新的生物标志物/药物靶点。膜蛋白在生物过程中具有预期的作用,可以作为生物标志物/药物靶点。只有在确认阿米卡星耐药时,才推荐链霉素(SM)作为二线治疗方案。由于广泛耐药(XDR)分离株经常对二线注射药物产生交叉耐药,因此建议继续使用SM的潜力尚未开发。本研究旨在利用蛋白质组学方法分析结核分枝杆菌SM耐药分离株膜蛋白的过表达情况。采用超声和超离心法提取膜蛋白。对膜蛋白进行双向凝胶电泳(2DGE),并通过液相色谱-质谱(LCMS)和生物信息学工具进行鉴定。在二维凝胶分析中,发现5个蛋白点在SM耐药菌株的膜上过表达。对接分析显示,SM可能与过表达蛋白的保守结构域结合,而基于群的预测系统原核泛素样蛋白(prokaryotic ubiquitin-like protein, GPS-PUP)预测了其中潜在的化蛹位点。这些蛋白可能对早期发现病例和探索针对耐药结核病(特别是SM)的有效控制策略具有诊断意义。
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引用次数: 0
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Current Proteomics
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