Molecular BioSystems最新文献

{"title":"Correction: Dynamic properties of dipeptidyl peptidase III from Bacteroides thetaiotaomicron and the structural basis for its substrate specificity – a computational study","authors":"M. Tomin and S. Tomić","doi":"10.1039/C7MB90042B","DOIUrl":"https://doi.org/10.1039/C7MB90042B","url":null,"abstract":"<p >Correction for ‘Dynamic properties of dipeptidyl peptidase III from <em>Bacteroides thetaiotaomicron</em> and the structural basis for its substrate specificity – a computational study’ by M. Tomin <em>et al.</em>, <em>Mol. BioSyst.</em>, 2017, <strong>13</strong>, 2407–2417.</p>","PeriodicalId":90,"journal":{"name":"Molecular BioSystems","volume":" 12","pages":" 2729-2730"},"PeriodicalIF":3.743,"publicationDate":"2017-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1039/C7MB90042B","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"3868197","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Pharmacology of predatory and defensive venom peptides in cone snails","authors":"Jutty Rajan Prashanth, Sebastien Dutertre and Richard James Lewis","doi":"10.1039/C7MB00511C","DOIUrl":"https://doi.org/10.1039/C7MB00511C","url":null,"abstract":"<p >Cone snails are predatory gastropods whose neurotoxic venom peptides (conotoxins) have been extensively studied for pharmacological probes, venom evolution mechanisms and potential therapeutics. Conotoxins have a wide range of structural and functional classes that continue to undergo accelerated evolution that underlies the rapid expansion of the genus over their short evolutionary history. A number of pharmacological classes, driven by separately evolved defensive and predatory venoms, have been hypothesised to facilitate shifts in prey that exemplify the adaptability of cone snails. Here we provide an overview of these pharmacological families and discuss their ecological roles and evolutionary impact.</p>","PeriodicalId":90,"journal":{"name":"Molecular BioSystems","volume":" 12","pages":" 2453-2465"},"PeriodicalIF":3.743,"publicationDate":"2017-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1039/C7MB00511C","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"3784095","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Staphylococcus aureus extracellular vesicles (EVs): surface-binding antagonists of biofilm formation†","authors":"Hansol Im, Sujin Lee, Steven A. Soper and Robert J. Mitchell","doi":"10.1039/C7MB00365J","DOIUrl":"https://doi.org/10.1039/C7MB00365J","url":null,"abstract":"<p >The prevalence of <em>Staphylococcus aureus</em> worldwide as a nosocomial infectious agent is recognized but the reason behind the spread of this bacterium has remained elusive. Here, we hypothesized that the communication of <em>S. aureus</em> might benefit from it blocking other bacteria from establishing themselves on the surface. This was found to be the case for several pathogens as the <em>S. aureus</em> supernatant curtailed their ability to form biofilms. Subsequent analyses using Acinetobacter baumannii as a model found this effect is primarily mediated by <em>S. aureus</em>’ extracellular vesicles (EVs), which bound to the polystyrene surface. We found the EV-treated surfaces were significantly more hydrophilic after EV treatment, a condition that made it difficult for <em>A. baumannii</em> to initially adhere to the polystyrene surface and reduced its resulting biofilm by up to 93%. Subsequent tests found this also extended to several other bacterial pathogens, with a 40–70% decrease in their biofilm mass. The <em>S. aureus</em> EVs and their activity still remained after the surface was washed with 10% bleach, while the use of ethylenediaminetetraacetic acid (EDTA) removed both the EVs from the surface and their activity.</p>","PeriodicalId":90,"journal":{"name":"Molecular BioSystems","volume":" 12","pages":" 2704-2714"},"PeriodicalIF":3.743,"publicationDate":"2017-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1039/C7MB00365J","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"3868195","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mechanism of the formation of the RecA–ssDNA nucleoprotein filament structure: a coarse-grained approach","authors":"Goutam Mukherjee, Arumay Pal and Yaakov Levy","doi":"10.1039/C7MB00486A","DOIUrl":"https://doi.org/10.1039/C7MB00486A","url":null,"abstract":"<p >In prokaryotes, the RecA protein catalyzes the repair and strand exchange of double-stranded DNA. RecA binds to single-stranded DNA (ssDNA) and forms a presynaptic complex in which the protein polymerizes around the ssDNA to form a right-handed helical nucleoprotein filament structure. In the present work, the mechanism for the formation of the RecA–ssDNA filament structure is modeled using coarse-grained molecular dynamics simulations. Information from the X-ray structure was used to model the protein itself but not its interactions; the interactions between the protein and the ssDNA were modeled solely by electrostatic, aromatic, and repulsive energies. For the present study, the monomeric, dimeric, and trimeric units of RecA and 4, 8, and 11 NT-long ssDNA, respectively, were studied. Our results indicate that monomeric RecA is not sufficient for nucleoprotein filament formation; rather, dimeric RecA is the elementary binding unit, with higher multimeric units of RecA facilitating filament formation. Our results reveal that loop region flexibility at the primary binding site of RecA is essential for it to bind the incoming ssDNA, that the aromatic residues present in the loop region play an important role in ssDNA binding, and that ATP may play a role in guiding the ssDNA by changing the electrostatic potential of the RecA protein.</p>","PeriodicalId":90,"journal":{"name":"Molecular BioSystems","volume":" 12","pages":" 2697-2703"},"PeriodicalIF":3.743,"publicationDate":"2017-10-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1039/C7MB00486A","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"3868194","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Conformational heterogeneity in tails of DNA-binding proteins is augmented by proline containing repeats†","authors":"Harshavardhan Khare, Debayan Dey, Chilakapati Madhu, Dillip Senapati, Srinivasarao Raghothama, Thimmaiah Govindaraju and Suryanarayanarao Ramakumar","doi":"10.1039/C7MB00412E","DOIUrl":"https://doi.org/10.1039/C7MB00412E","url":null,"abstract":"<p >A cationic terminal extension or tail is a common feature of many DNA-binding proteins. We show that a particular type of tail rich in proline, alanine and lysine belongs to the class of ‘flexible disorder’ and consists of characteristic pentapeptide repeats. Our designed peptides, (AAKKA)<small>_1–4</small> and (PAKKA)<small>_1–4</small>, represent the tails of several bacterial DNA-binding proteins. Enhanced conformational sampling of these representative peptides using accelerated molecular dynamic simulations supported by circular dichroism spectroscopy and nuclear magnetic resonance studies demonstrates the role of frequent and interspersed prolines in augmenting conformational heterogeneity of the peptide backbone. Analysis of circular variance of backbone dihedral angles indicates alternating regions of relative rigidity and flexibility along the peptide sequence due to prolines. Preferred placement of lysines in the regions of higher backbone flexibility might improve DNA-binding by conformational selection. Our results could be relevant for rational <em>de novo</em> design of disordered peptides.</p>","PeriodicalId":90,"journal":{"name":"Molecular BioSystems","volume":" 12","pages":" 2531-2544"},"PeriodicalIF":3.743,"publicationDate":"2017-10-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1039/C7MB00412E","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"3784103","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Development of an AlphaLISA high throughput technique to screen for small molecule inhibitors targeting protein arginine methyltransferases†","authors":"Lakshmi Prabhu, Lan Chen, Han Wei, Özlem Demir, Ahmad Safa, Lifan Zeng, Rommie E. Amaro, Bert H. O’Neil, Zhon-Yin Zhang and Tao Lu","doi":"10.1039/C7MB00391A","DOIUrl":"https://doi.org/10.1039/C7MB00391A","url":null,"abstract":"<p >The protein arginine methyltransferase (PRMT) family of enzymes comprises nine family members in mammals. They catalyze arginine methylation, either monomethylation or symmetric/asymmetric dimethylation of histone and non-histone proteins. PRMT methylation of its substrate proteins modulates cellular processes such as signal transduction, transcription, and mRNA splicing. Recent studies have linked overexpression of PRMT5, a member of the PRMT superfamily, to oncogenesis, making it a potential target for cancer therapy. In this study, we developed a highly sensitive (<em>Z</em>′ score = 0.7) robotic high throughput screening (HTS) platform to discover small molecule inhibitors of PRMT5 by adapting the AlphaLISA? technology. Using biotinylated histone H4 as a substrate, and <em>S</em>-adenosyl-<small>L</small>-methionine as a methyl donor, PRMT5 symmetrically dimethylated H4 at arginine (R) 3. Highly specific acceptor beads for symmetrically dimethylated H4R3 and streptavidin-coated donor beads bound the substrate, emitting a signal that is proportional to the methyltransferase activity. Using this powerful approach, we identified specific PRMT5 inhibitors P1608K04 and P1618J22, and further validated their efficacy and specificity for inhibiting PRMT5. Importantly, these two compounds exhibited much more potent efficacy than the commercial PRMT5 inhibitor EPZ015666 in both pancreatic and colorectal cancer cells. Overall, our work highlights a novel, powerful, and sensitive approach to identify specific PRMT5 inhibitors. The general principle of this HTS screening method can not only be applied to PRMT5 and the PRMT superfamily, but may also be extended to other epigenetic targets. This approach allows us to identify compounds that inhibit the activity of their respective targets, and screening hits like P1608K04 and P1618J22 may serve as the basis for novel drug development to treat cancer and/or other diseases.</p>","PeriodicalId":90,"journal":{"name":"Molecular BioSystems","volume":" 12","pages":" 2509-2520"},"PeriodicalIF":3.743,"publicationDate":"2017-10-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1039/C7MB00391A","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"3784101","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Imbalance in amino acid and purine metabolisms at the hypothalamus in inflammation-associated depression by GC-MS†","authors":"Yu Wu, Yonghong Li, Yanjuan Jia, Chaojun Wei, Hui Xu, Rui Guo, Yuanting Li, Jing Jia, Xiaoming Qi and Xiaoling Gao","doi":"10.1039/C7MB00494J","DOIUrl":"https://doi.org/10.1039/C7MB00494J","url":null,"abstract":"<p >Hypothalamic dysfunction is a key factor in depression; increasing evidence highlights neuroinflammation abnormalities as well as imbalances in neurotransmitters and the purinergic system in the pathophysiology of depression. However, little is known about the metabolomic changes in the hypothalamus of depressed patients with neuroinflammation. Herein, taking advantage of the well-established lipopolysaccharide (LPS)-induced depression mouse model, we measured metabolic changes in the hypothalamus using gas chromatography-mass spectrometry (GC-MS). Sucrose preference test (SPT), open field test (OFT), forced swimming test (FST), and tail suspension test (TST) were conducted to assess our depressive model. To better understand the metabolic disturbances occurring in the hypothalamus of depressed mice, multivariate statistics were applied to analyse the clinical significance of differentially expressed metabolites in the hypothalamus of mice with LPS-induced depression. Bioinformatic analysis was conducted to detect potential relationships among the changed metabolites. The data confirmed that mice with LPS-induced depression were good mimics of depression patients in some characteristic symptoms such as decreased sucrose intake and increased immobility. In our study, 27 differentially expressed metabolites were identified in the hypothalamus of mice with LPS-induced depression. Herein, seventeen of these metabolites decreased, whereas 10 metabolites increased. These molecular changes were closely related to perturbations in the amino acid and purine metabolisms. Our data indicate that dysfunction of amino acid and purine metabolisms is one of main characteristics of inflammation-mediated depression. These results provide new insights into the mechanisms underlying depression, which may shed some light on the role of the hypothalamus in the pathogenesis of inflammation-mediated depression.</p>","PeriodicalId":90,"journal":{"name":"Molecular BioSystems","volume":" 12","pages":" 2715-2728"},"PeriodicalIF":3.743,"publicationDate":"2017-10-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1039/C7MB00494J","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"3868196","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Host immune evasion strategies of malaria blood stage parasite","authors":"Xue Yan Yam and Peter R. Preiser","doi":"10.1039/C7MB00502D","DOIUrl":"https://doi.org/10.1039/C7MB00502D","url":null,"abstract":"<p >Host immune evasion is a key strategy for the continual survival of many microbial pathogens including Apicomplexan protozoan: <em>Plasmodium</em> spp., the causative agent of Malaria. The malaria parasite has evolved a variety of mechanisms to evade the host immune responses within its two hosts: the female <em>Anopheles</em> mosquito vector and vertebrate host. In this review, we will focus on the molecular mechanisms of the immune evasion strategies used by the <em>Plasmodium</em> parasite at the blood stage which is responsible for the clinical manifestations of human malaria. We also aim to provide some insights on the potential targets for malaria interventions through the recent advancement in understanding the molecular biology of the parasite.</p>","PeriodicalId":90,"journal":{"name":"Molecular BioSystems","volume":" 12","pages":" 2498-2508"},"PeriodicalIF":3.743,"publicationDate":"2017-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1039/C7MB00502D","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"3784100","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"An interaction network approach to study the correlation between endocrine disrupting chemicals and breast cancer†","authors":"Andrea Polo, Chiara Nittoli, Anna Crispo, Teresa Langastro, Stefania Cocco, Lorella Severino, Michelino De Laurentiis, Gennaro Ciliberto, Maurizio Montella, Alfredo Budillon and Susan Costantini","doi":"10.1039/C7MB00489C","DOIUrl":"https://doi.org/10.1039/C7MB00489C","url":null,"abstract":"<p >Endocrine disrupting chemicals (EDCs) are natural or synthetic exogenous substances affecting human health. Although present at low concentrations in the environment, they can cause a broad range of negative effects on the endocrine functions by mimicking the action of steroid hormones due to their structural similarity. Hormonal unbalance can play an important role in carcinogenesis at any stage of disease. In the case of the breast cancer, EDCs directly affect the transformation of normal breast cells into cancer cells by interfering with hormonal regulation and by inducing the alteration of factors that regulate gene expression. The principal aims of this work were to study the interaction networks of proteins modulated in breast cancer by either environmental EDCs or mycotoxins, and to identify the proteins with the strongest coordination role defined as hub nodes. Our studies evidenced the presence of seven and six hub proteins in two EDCs and mycotoxins networks, respectively. Then, by merging the two networks, we identified that three hub nodes (BCL2, ESR2 and CTNNB1) in the environmental EDCs network show direct interactions with three hub nodes (CASP8, RELA and MKI67) in the mycotoxins network. These data highlighted that two networks are linked through proteins involved in the apoptosis regulation and in processes related to cell proliferation and survival, and, thus, in breast cancer progression.</p>","PeriodicalId":90,"journal":{"name":"Molecular BioSystems","volume":" 12","pages":" 2687-2696"},"PeriodicalIF":3.743,"publicationDate":"2017-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1039/C7MB00489C","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"3868193","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Model system based proteomics to understand the host response during bacterial infections","authors":"Arumugam Kamaladevi, Shanmugam Marudhupandiyan and Krishnaswamy Balamurugan","doi":"10.1039/C7MB00372B","DOIUrl":"https://doi.org/10.1039/C7MB00372B","url":null,"abstract":"<p >Infectious diseases caused by bacterial pathogens pose a major concern to public health and, thus, greater attention must be given to providing insightful knowledge on host–pathogen interactions. There are several theories addressing the dynamics of complex mechanisms of host–pathogen interactions. The availability of an ample number of universally accepted model systems, including vertebrates, invertebrates, and mammalian cells, provides in-depth transcriptomics data to evaluate these complex mechanisms during host–pathogen interactions. Recent model system based proteomic studies have addressed the issues related to human diseases by establishing the protein profile of model animals that closely resemble the environment. As a result, model system based proteomics has been widely accepted as a powerful and effective approach to understand the highly complex host–pathogen interfaces at their protein levels. This review offers a snapshot of the contributions of selective model systems on host–bacterial pathogen interactions through proteomic approaches.</p>","PeriodicalId":90,"journal":{"name":"Molecular BioSystems","volume":" 12","pages":" 2489-2497"},"PeriodicalIF":3.743,"publicationDate":"2017-10-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1039/C7MB00372B","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"3784099","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}