RSC - Mol. BioSyst. latest articles

Prediction of Chemical-Protein Interactions: Multitarget-QSAR versus Computational Chemogenomic Methods

Mol. BioSyst., 2012, Accepted Manuscript
DOI: 10.1039/C2MB25110H, Paper

Feixiong Cheng, Yadi Zhou, Jie Li, Weihua Li, Guixia Liu, Yun Tang
Elucidation of Chemical-Protein Interaction (CPI) is the basis of target identification and drug discovery. It is time-consuming and costly to determine CPI experimentally, and computational methods will facilitate the determination...
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Construction of Logic Gates with the Fluorene-Based Small Molecule/DNA Probes

Mol. BioSyst., 2012, Accepted Manuscript
DOI: 10.1039/C2MB25129A, Paper

Jing Guo, Ting Wang, Renqiang Yang
Fluorene-based small molecules (FSMs) have the optical properties and can interact with DNA. In this paper, the integrated "INH" and "AND" gates operating in parallel are developed with the fluorene-based...
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Split-superpositive GFP reassembly is a fast, efficient, and robust method for detecting protein - protein interactions in vivo

Mol. BioSyst., 2012, Accepted Manuscript
DOI: 10.1039/C2MB25130B, Method

Brian Richard McNaughton
Split-GFP reassembly is an operationally simple in vivo technique used to identify and study interactions involving proteins and/or peptides. However, the instability of split-GFP fragments, and their susceptibility to aggregation,...
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Porphyrins from a metagenomic library of the marine sponge Discodermia calyx

Mol. BioSyst., 2012, Accepted Manuscript
DOI: 10.1039/C2MB25169H, Paper

Rui He, Toshiyuki Wakimoto, Yuya Takeshige, Yoko Egami, Hiromichi Kenmoku, Takuya Ito, Bochu Wang, Yoshinori Asakawa, Ikuro Abe
Marine sponges harbouring uncultured symbiotic bacteria are important sources of biologically active compounds. Since they would be interesting resources to explore unknown functional genes by means of a metagenomic approach,...
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MOLECULAR CHAPERONES DNAK AND DNAJ SHARE PREDICTED BINDING SITES ON MOST PROTEINS IN THE E. COLI PROTEOME

Mol. BioSyst., 2012, Accepted Manuscript
DOI: 10.1039/C2MB25145K, Paper

Sharan Srinivasan, Anne Gillies, Lyra Chang, Andrea D Thompson, Jason E Gestwicki
In Escherichia coli, the molecular chaperones DnaK and DnaJ cooperate to assist the folding of newly synthesized or unfolded polypeptides. DnaK and DnaJ bind to hydrophobic motifs in these proteins...
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Impaired JAK2-induced activation of STAT3 in failing human myocytes.

Mol. BioSyst., 2012, Accepted Manuscript
DOI: 10.1039/C2MB25120E, Paper

Giulia Elisa Cambi, Gianluca Lucchese, Mah Mc Harol Djeokeng, alessandra modesti, Tania Fiaschi, Giuseppe Faggian, Guido Sani, Pietro Amedeo Modesti
Although angiotensin (Ang)II-induced Janus-activated kinase (JAK)2 phosphorylation was reported to be enhanced in failing human cardiomyocytes, the downstream balance between cardio-protective (signal transducer and activator of transcription-STAT3) and the pro-inflammatory...
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Structural and thermodynamic characterization of the self-adhesive properties of human P-cadherin

Mol. BioSyst., 2012, Accepted Manuscript
DOI: 10.1039/C2MB25161B, Communication

Shota Kudo, Jose Caaveiro, Takamitsu Miyafusa, Shuichiro Goda, Keisuke Ishii, Tadashi Matsuura, Yukio Sudou, Tatsuhiko Kodama, Takao Hamakubo, Kouhei Tsumoto
Human P-cadherin is a promising therapeutic target against cancer. However, its characterization at the molecular level is still lacking. We report that human P-cadherin associated irreversibly in a distinct dimer...
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Cell-penetrating nitroxides as molecular sensors for imaging of cancer in vivo, based on tissue redox activity

Mol. BioSyst., 2012, Accepted Manuscript
DOI: 10.1039/C2MB25128K, Paper

Zhivko Zhelev, Veselina Gadjeva, Ichio Aoki, Rumiana Bakalova, Tsuneo Saga
The present study shows that hydrophobic and cell-penetrating piperidine-type nitroxide radicals SLENU and TEMPOL, but not hydrophilic and partially penetrating or non-penetrating pyrrolidine-type nitroxides carbamoyl-PROXYL and carboxy-PROXYL, are appropriate contrast...
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Covalently trapping MutS on DNA to study DNA mismatch recognition and signaling

Mol. BioSyst., 2012, Advance Article
DOI: 10.1039/C2MB25086A, Communication

Roger J. Heinze, Svetlana Sekerina, Ines Winkler, Christian Biertumpfel, Tatiana S. Oretskaya, Elena Kubareva, Peter Friedhoff
An efficient transient protein-DNA trapping approach based on 3[prime or minute]-disulfide DNA modification.
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Chemoselective Hydroxyl Group Transformation: An Elusive Target

Mol. BioSyst., 2012, Accepted Manuscript
DOI: 10.1039/C2MB25122A, Review Article

Darci Jones Trader, Erin E. Carlson
The selective reaction of one functional group in the presence of others is not a trivial task. A noteworthy amount of research has been dedicated to the chemoselective reaction of...
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Engineering Ecosystems and Synthetic Ecologies

Mol. BioSyst., 2012, Accepted Manuscript
DOI: 10.1039/C2MB25133G, Review Article

Michael T Mee, Harris H Wang
Microbial ecosystems play an important role in nature. Engineering these systems for industrial, medical, or biotechnological purposes are important pursuits for synthetic biologists and biological engineers moving forward. Here, we...
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Metabolomics-on-a-chip and metabolic flux analysis for label-free modeling of the internal metabolism of HepG2/C3A cells

Mol. BioSyst., 2012, Advance Article
DOI: 10.1039/C2MB25049G, Paper

Djomangan Adama Ouattara, Jean-Matthieu Prot, Andrei Bunescu, Marc-Emmanuel Dumas, Benedicte Elena-Herrmann, Eric Leclerc, Celine Brochot
The metabolomics-on-a-chip approach was combined with metabolic flux analysis to infer the distribution of internal metabolic fluxes in HepG2/C3A cells.
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Multi-spectroscopic methods combined with molecular modeling dissect the interaction mechanisms of ractopamine and calf thymus DNA

Mol. BioSyst., 2012, Advance Article
DOI: 10.1039/C2MB25095K, Paper

Jun Chai, Juyuan Wang, Qifei Xu, Fang Hao, Rutao Liu
The minor groove binding was the most probable interaction mode between RAC and DNA. Hydrogen bonding force was the dominant binding force in the interaction. Electrostatic binding existed between the positive RAC and the negative phosphate groups.
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Pretubulysin derived probes as novel tools for monitoring the microtubule network via Activity-Based Protein Profiling and Fluorescence Microscopy

Mol. BioSyst., 2012, Accepted Manuscript
DOI: 10.1039/C2MB25144B, Paper

Jurgen Eirich, Jens Burkhart, Angelika Ullrich, Georg Rudolf, Angelika Vollmar, Stefan Zahler, Uli Kazmaier, Stephan Axel Sieber
Microtubules (mt) are highly dynamic polymers composed of alpha- and beta-tubulin monomers that are present in all dividing and non-dividing cells. A broad variety of natural products exists that are...
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Marked changes in red cell membrane proteins in hereditary spherocytosis: A proteomics approach

Mol. BioSyst., 2012, Accepted Manuscript
DOI: 10.1039/C2MB25009H, Paper

Chantana Polprasert, Wararat Chiangjong, Visith Thongboonkerd
Hereditary spherocytosis (HS) is the most common red cell membrane defect resulted from protein abnormalities. However, changes in red cell membrane proteins in HS remained under-investigated. We therefore evaluated red...
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Metabolomic response of human skin tissue to low dose ionizing radiation

Mol. BioSyst., 2012, Advance Article
DOI: 10.1039/C2MB25061F, Paper

Ze-Ping Hu, Young-Mo Kim, Marianne B. Sowa, R. Joe Robinson, Xiaoli Gao, Thomas O. Metz, William F. Morgan, Qibin Zhang
Effects of ionizing radiation on in vitro human skin tissue showed time and dose dependent response at metabolite level.
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The spectral networks paradigm in high throughput mass spectrometry

Mol. BioSyst., 2012, Advance Article
DOI: 10.1039/C2MB25085C, Paper

Adrian Guthals, Jeramie D. Watrous, Pieter C. Dorrestein, Nuno Bandeira
Spectral networks algorithms transform the paradigm for analysis of tandem mass spectra by finding and jointly interpreting spectra from related molecules, regardless of the structure or class of molecules.
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Alterations of protein complexes and pathways in genetic information flow and response to stimulus contribute to Escherichia coli resistance to balofloxacin

Mol. BioSyst., 2012, Accepted Manuscript
DOI: 10.1039/C2MB25090J, Paper

Xuan-xian Peng
Protein-protein interactions are pivotal in many biological processes and essential for a global understanding of cell functions. However, roles of bacterial resistance to antibiotics are largely unknown in content of...
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Influence of dietary flavonoids on the glycation of plasma p roteins

Mol. BioSyst., 2012, Accepted Manuscript
DOI: 10.1039/C2MB25038A, Paper

Liheng Liu, Yixi Xie, Zhanqian Song, Shibin Shang, xiaoqing chen
It has been suggested that the increasing glycation in diabetes can influence the ability of plasma proteins to bind to small molecules. Herein, the influence of flavonoids on the glycation...
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Metabolic regulation analysis of wild-type and arcA mutant Escherichia coli under nitrate conditions using different levels of omics data

Mol. BioSyst., 2012, Accepted Manuscript
DOI: 10.1039/C2MB25069A, Paper

Yoshihiro Toya, Kenji Nakahigashi, Masaru Tomita, Kazuyuki Shimizu
It is of practical interest to investigate the effect of nitrates on bacterial metabolic regulation of both fermentation and energy generation, as compared to aerobic and anaerobic growth without nitrates....
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Upregulated MALAT-1 contributes to bladder cancer cell migration by inducing epithelial-to-mesenchymal transition

Mol. BioSyst., 2012, Accepted Manuscript
DOI: 10.1039/C2MB25070E, Paper

Liang Ying, Qi Chen, Yawei Wang, Zhihua Zhou, Yiran Huang, feng qiu
Recent studies reveal that long non-coding RNAs (lncRNAs) have been shown to have important regulatory roles in cancer biology, and lncRNA MALAT-1 expression is upregulated in some tumors. However, the...
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Probing the binding of two sugar bearing anticancer agents aristololactam-[small beta]-D-glucoside and daunomycin to double stranded RNA polynucleotides: a combined spectroscopic and calorimetric study

Mol. BioSyst., 2012, Advance Article
DOI: 10.1039/C2MB25080B, Paper

Abhi Das, Gopinatha Suresh Kumar
Structural and thermodynamic aspects of the binding of the sugar bearing alkaloid aristololactam-[small beta]-D-glucoside in comparison with daunomycin to ds RNAs are presented. The results provide fundamental basis for design and development of new RNA targeted drugs.
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Galvestine-1, a novel chemical probe for the study of the glycerolipid homeostasis system in plant cells

Mol. BioSyst., 2012, Advance Article
DOI: 10.1039/C2MB25067E, Review Article

Laurence Boudiere, Cyrille Y. Botte, Nadia Saidani, Mathieu Lajoie, Jessica Marion, Laurent Brehelin, Yoshiki Yamaryo-Botte, Beatrice Satiat-Jeunemaitre, Christelle Breton, Agnes Girard-Egrot, Olivier Bastien, Juliette Jouhet, Denis Falconet, Maryse A. Block, Eric Marechal
Analysis of plant glycerolipid homeostasis by combining biochemistry, cell biology, genetics and chemical genetics.
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Abl kinase constructs expressed in bacteria: facilitation of structural and functional studies including segmental labeling by expressed protein ligation

Mol. BioSyst., 2012, Advance Article
DOI: 10.1039/C2MB25051A, Paper

Rong Xu, Dongsheng Liu, David Cowburn
Segmental labeling using expressed protein ligation of bacterially expressed parts of Abl kinase provides new avenues for structure-function studies.
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A gold nanoparticles based immuno-bioprobe for detection of Vi capsular polysaccharide of Salmonella enterica serovar Typhi

Mol. BioSyst., 2012, Advance Article
DOI: 10.1039/C2MB25048A, Method

Satish Kumar Pandey, C. Raman Suri, M. Chaudhry, R. P. Tiwari, Praveen Rishi
A rapid and sensitive gold-nanobioprobe based immunoassay format has been presented for the detection of capsular Vi polysaccharide of Salmonella enterica serovar Typhi (surface antigen) using anti-Vi antibodies.
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Broadening the signal specificity of prokaryotic promoters by modifying cis-regulatory elements associated with a single transcription factor

Mol. BioSyst., 2012, Advance Article
DOI: 10.1039/C2MB25030F, Paper

Rafael Silva-Rocha, Victor de Lorenzo
The responsiveness of a promoter to a given inducer can be altered by changing the affinity of the cognate transcriptional regulator for DNA, without modifying the regulator itself.
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The origins and evolution of ubiquitination sites

Mol. BioSyst., 2012, Advance Article
DOI: 10.1039/C2MB25052G, Paper

Tzachi Hagai, Agnes Toth-Petroczy, Ariel Azia, Yaakov Levy
Protein ubiquitination is central to the regulation of various pathways in eukaryotes.
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Metabolomic analysis of polar metabolites in lipoprotein fractions identifies lipoprotein-specific metabolic profiles and their association with insulin resistance

Mol. BioSyst., 2012, Accepted Manuscript
DOI: 10.1039/C2MB25115A, Paper

Tuulia Hyotylainen, Ismo Mattila, Susanne Wiedmer, Artturi Koivuniemi, Marja-Riitta Taskinen, Hannele Yki-Jarvinen, Matej Oresic
While molecular lipid composition of lipoproteins has been investigated in detail, little is known about associations of small polar metabolites with specific lipoproteins. The aim of the present study was...
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Sensing of transcription factor binding via cyanine dye pair fluorescence lifetime changes.

Mol. BioSyst., 2012, Accepted Manuscript
DOI: 10.1039/C2MB25057H, Paper

Alexei Bogdanov, Valeriy Metelev, Surong Zhang, Anand T.N. Kumar
We designed and synthesized sensors for imaging transcription factor-DNA interactions using a complementary pair of 21-base pair long oligonucleotides (ODN) carrying two internucleoside phosphate-linked cyanine fluorophores that can either engage...
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Leveraging kinase inhibitors to develop small molecule tools for imaging kinases by fluorescence microscopy

Mol. BioSyst., 2012, Accepted Manuscript
DOI: 10.1039/C2MB25099C, Communication

Zijuan Zhang, Nicholas Kwiatkowski, Hong Zeng, Sang Min Lim, Nathanael Gray, Wei Zhang, Priscilla L. Yang
As the usage of fluorescence microscopy as a tool to study biological systems continues to grow, so does the need for additional tools that permit the selective detection of proteins...
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Understanding microscopic binding of macrophage migration inhibitory factor with phenolic hydrazones by molecular docking, molecular dynamics simulations and free energy calculations

Mol. BioSyst., 2012, Accepted Manuscript
DOI: 10.1039/C2MB25146A, Paper

Lei Xu, Youyong Li, Shunye Zhou, Tingjun Hou
Macrophage migration inhibitory factor (MIF), an immunoregulatory protein, is a potential target for a number of inflammatory diseases. In the current work, the interactions between MIF and a series of...
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Activation of monocytic cells by immunostimulatory lipids conjugated to peptide antigens.

Mol. BioSyst., 2012, Accepted Manuscript
DOI: 10.1039/C2MB25064K, Paper

Stefania Galdiero, Mariateresa Vitiello, Emiliana Finamore, Rosalba Mansi, Marilena Galdiero, Giancarlo Morelli, Diego Tesauro
Bacterial derived lipoproteins constitute potent macrophage activators in vivo and are effective stimuli, enhancing the immune response especially with respect to low or non-immunogenic compounds. In the present study we...
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Large scale phosphoproteome analysis of LNCaP human prostate cancer cells

Mol. BioSyst., 2012, Accepted Manuscript
DOI: 10.1039/C2MB25151E, Paper

Jae-Kyung Myung, Marianne D Sadar
Prostate cancer is the most frequently diagnosed cancer among men in the western world. The androgen receptor, a phosphoprotein, is suspected to be involved in all stages of the prostate...
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Modelling and experimental analysis of the role of interacting cytosolic and vacuolar pools in shaping low temperature calcium signatures in plant cells

Mol. BioSyst., 2012, Accepted Manuscript
DOI: 10.1039/C2MB25072A, Paper

Junli Liu, Heather Knight, Charlotte Hurst, Marc Knight
A major challenge to understanding low temperature calcium signatures in plants is defining how these signatures emerge from the interactions of different molecular components that are stored in different subcellular...
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Multiple-strategy analyses of ZmWRKY subgroups and functional exploration of ZmWRKY genes in pathogen responses

Mol. BioSyst., 2012, Advance Article
DOI: 10.1039/C2MB05483C, Paper

Kaifa Wei, Juan Chen, Yanfeng Chen, LingJuan Wu, Daoxin Xie
In this article, multiple-strategy analyses of ZmWRKY subgroups were performed, and expression profiles of the ZmWRKY genes in response to fungal infections and their co-regulatory network were analyzed.
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A novel zebrafish human tumor xenograft model validated for anti-cancer drug screening

Mol. BioSyst., 2012, Advance Article
DOI: 10.1039/C2MB05501E, Paper

Da-Woon Jung, Eun-Sang Oh, Si-Hwan Park, Young-Tae Chang, Cheol-Hee Kim, Seok-Yong Choi, Darren R. Williams
This study reports the first rapid reproducible zebrafish human tumor xenograft model that is validated for anti-cancer drug screening.
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The lipid composition of isolated cytoplasmic lipid droplets from a human cancer cell line, BE(2)M17

Mol. BioSyst., 2012, 8,1694-1700
DOI: 10.1039/C2MB05485J, Paper

Xiaoyan Pan, Martin Wilson, Carmel McConville, Marie-Anne Brundler, Theodoros N. Arvanitis, John P. Shockcor, Julian L. Griffin, Risto A. Kauppinen, Andrew C. Peet
Density-gradient ultracentrifugation was performed on homogenised human cancer cells to isolate LDs. Liquid Chromatography mass spectroscopy (LC-MS) and high resolution NMR was performed on lipid extracts of LDs.
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Engineering a large protein by combined rational and random approaches: stabilizing the Clostridium thermocellum cellobiose phosphorylase

Mol. BioSyst., 2012, 8,1815-1823
DOI: 10.1039/C2MB05492B, Paper

Xinhao Ye, Chenming Zhang, Y.-H. Percival Zhang
Engineering a thermostability-enhanced active Clostridium thermocellum cellobiose phosphorylase by a combination of rational design and directed evolution.
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Proteolysis of beta-galactosidase following SigmaB activation in Bacillus subtilis

Mol. BioSyst., 2012, 8,1806-1814
DOI: 10.1039/C2MB25031D, Paper

Ulf W. Liebal, Praveen K. Sappa, Thomas Millat, Leif Steil, Georg Homuth, Uwe Volker, Olaf Wolkenhauer
The reporter protein beta-galactosidase is degraded following induction of the general stress response transcription factor SigmaB in Bacillus subtilis.
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Endothelial cell's biomechanical properties are regulated by invasive cancer cells

Mol. BioSyst., 2012, 8,1639-1649
DOI: 10.1039/C2MB25024A, Review Article

Claudia T. Mierke
Despite the old role as a passive barrier for (cancer) cell invasion, the endothelium fulfills a novel role as a regulator of cancer cell invasiveness.
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E. coli LoiP (YggG), a metalloprotease hydrolyzing Phe-Phe bonds

Mol. BioSyst., 2012, 8,1775-1782
DOI: 10.1039/C2MB05506F, Paper

Christiane Lutticke, Patrick Hauske, Urs Lewandrowski, Albert Sickmann, Markus Kaiser, Michael Ehrmann
LoiP, an Escherichia coli outer membrane lipoprotein, is a member of the metalloprotease family M48 with a distinct specificity for Phe-Phe sites.
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Short- and long-term dynamic responses of the metabolic network and gene expression in yeast to a transient change in the nutrient environment

Mol. BioSyst., 2012, 8,1760-1774
DOI: 10.1039/C2MB05443D, Paper

Duygu Dikicioglu, Warwick B. Dunn, Douglas B. Kell, Betul Kirdar, Stephen G. Oliver
We used an integrative approach to map short- and long-term dynamic transcriptome and metabolome data onto metabolic pathways and used these maps to reveal important molecular events that occur in particular pathways at distinct temporal phases following the transient relief of nutrient limitation.
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An orthogonal comparison of the proteome of human embryonic stem cells with that of human induced pluripotent stem cells of different genetic background

Mol. BioSyst., 2012, 8,1833-1840
DOI: 10.1039/C2MB25018G, Paper

Mojtaba Zamani Faradonbeh, Javad Gharechahi, Sepideh Mollamohammadi, Mohammad Pakzad, Adeleh Taei, Hassan Rassouli, Hossein Baharvand, Ghasem Hosseini Salekdeh
Induced pluripotent stem cells (iPSCs) provide an invaluable resource for drug or toxicology screening, medical research and patient-specific cell therapy.
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Evaluating the physiological state of maize (Zea mays L.) plants by direct-injection electrospray mass spectrometry (DIESI-MS)

Mol. BioSyst., 2012, 8,1658-1660
DOI: 10.1039/C2MB25056J, Communication

Martin Garcia-Flores, Sheila Juarez-Colunga, Josaphat Miguel Montero-Vargas, Janet Ana Isabel Lopez-Arciniega, Alicia Chagolla, Axel Tiessen, Robert Winkler
Direct-injection mass spectrometry permits the rapid and cost-efficient analysis of maize plants on metabolite level.
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Rewiring and dosing of systems modules as a design approach for synthetic mammalian signaling networks

Mol. BioSyst., 2012, 8,1824-1832
DOI: 10.1039/C2MB05509K, Paper

Michael M. Kampf, Raphael Engesser, Moritz Busacker, Maximilian Horner, Maria Karlsson, Matias D. Zurbriggen, Martin Fussenegger, Jens Timmer, Wilfried Weber
Synthetic biological information processing systems for the programmable interpretation of gradual input signals into desired gene expression patterns.
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Systematic determinations of SUMOylation activation intermediates and dynamics by a sensitive and quantitative FRET assay

Mol. BioSyst., 2012, 8,1723-1729
DOI: 10.1039/C2MB05465E, Paper

Yang Song, Jiayu Liao
Dynamics and intermediate determinations of the SUMOylation cascade are revealed by quantitative FRET technology.
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Genome-scale genetic manipulation methods for exploring bacterial molecular biology

Mol. BioSyst., 2012, 8,1626-1638
DOI: 10.1039/C2MB25040C, Review Article

Alla Gagarinova, Andrew Emili
This review highlights systematic procedures for exploring gene functions and the global organization of bacteria at gene, pathway, and genome levels.
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Positive regulatory dynamics by a small noncoding RNA: speeding up responses under temperature stress

Mol. BioSyst., 2012, 8,1707-1715
DOI: 10.1039/C2MB05479E, Paper

Raul Guantes, Bastien Cayrol, Florent Busi, Veronique Arluison
We integrate experimental and modeling approaches to dissect bacterial response to temperature stress, unveiling new regulatory mechanisms by sRNAs.
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Probing adenylation: using a fluorescently labelled ATP probe to directly label and immunoprecipitate VopS substrates

Mol. BioSyst., 2012, 8,1701-1706
DOI: 10.1039/C2MB25053E, Paper

Daniel M. Lewallen, Caitlin J. Steckler, Bryan Knuckley, Michael J. Chalmers, Paul R. Thompson
Identification of a fluorescent ATP analog that can be used to immunoprecipitate and identify novel VopS substrates.
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Proteoglycan sequence

Mol. BioSyst., 2012, 8,1613-1625
DOI: 10.1039/C2MB25021G, Review Article

Lingyun Li, Mellisa Ly, Robert J. Linhardt
The recent sequencing of the bikunin proteoglycan suggests new challenges and opportunities for the field of glycobiology.
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Revisiting the homology modeling of G-protein coupled receptors: [small beta]1-adrenoceptor as an example

Mol. BioSyst., 2012, 8,1686-1693
DOI: 10.1039/C2MB05491D, Paper

Mengyuan Zhu, Minyong Li
In this article, we deliberated how to carry out homology modelling in the presence of brand new GPCR crystal structures.
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Integrated investigation of lipidome and related signaling pathways uncovers molecular mechanisms of tetramethylpyrazine and butylidenephthalide protecting endothelial cells under oxidative stress

Mol. BioSyst., 2012, 8,1789-1797
DOI: 10.1039/C2MB05510D, Paper

Jie Yang, Song Yang, Ying-Jin Yuan
Comparative lipidomics reveals novel protective mechanisms of two bioactive ingredients extracted from traditional Chinese medicine on oxidatively stressed endothelial cells.
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Backbone conformational preferences of an intrinsically disordered protein in solution

Mol. BioSyst., 2012, 8,1798-1805
DOI: 10.1039/C2MB00004K, Paper

L. Michel Espinoza-Fonseca, Ian Ilizaliturri-Flores, Jose Correa-Basurto
We report the results from a very long MD simulation aimed at investigating the native conformational preferences of an intrinsically disordered protein in solution.
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Synthetic antibodies as tools to probe RNA-binding protein function

Mol. BioSyst., 2012, 8,1650-1657
DOI: 10.1039/C2MB00007E, Method

John D. Laver, Kristin Ancevicius, Pietro Sollazzo, J. Timothy Westwood, Sachdev S. Sidhu, Howard D. Lipshitz, Craig A. Smibert
We report that synthetic antibodies against RNA-binding proteins can be used to (i) co-immunoprecipitate target RNAs and (ii) block protein-RNA interactions.
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Insertion of T4-lysozyme (T4L) can be a useful tool for studying olfactory-related GPCRs

Mol. BioSyst., 2012, 8,1750-1759
DOI: 10.1039/C2MB05495G, Paper

Karolina Corin, Horst Pick, Philipp Baaske, Brian L. Cook, Stefan Duhr, Christoph J. Wienken, Dieter Braun, Horst Vogel, Shuguang Zhang
HEK293 cells expressing olfactory receptor OR17-4 with a T4-lysozyme insertion can initiate downstream signalling.
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Fabrication of nanostructures through molecular self-assembly of small amphiphilic glyco-dehydropeptides

Mol. BioSyst., 2012, 8,1742-1749
DOI: 10.1039/C2MB25023C, Paper

Manohar Mahato, Varun Arora, Rajiv Pathak, Hemant K. Gautam, Ashwani Kumar Sharma
Design and synthesis of an [small alpha],[small beta]-dehydrophenylalanine residue ([capital Delta]Phe) containing glyco-amphiphilic peptides, Boc-Phe-[capital Delta]Phe-[varepsilon]Ahx-GA (I) and H-Phe-[capital Delta]Phe-[varepsilon]Ahx-GA (II), has been reported, which formed stable self-assembled nanostructures.
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Metabolomic analysis of the plasma of patients with high-altitude pulmonary edema (HAPE) using 1H NMR

Mol. BioSyst., 2012, 8,1783-1788
DOI: 10.1039/C2MB25044F, Paper

Yongjun Luo, Junyu Zhu, Yuqi Gao
Metabolites in the plasma of HAPE may be effective for the diagnosis of HAPE and further understanding of HAPE pathogenesis.
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Proteomic analysis of a drosophila IBMPFD model reveals potential pathogenic mechanisms

Mol. BioSyst., 2012, 8,1730-1741
DOI: 10.1039/C2MB25037C, Paper

Hsin-Tzu Chan, Tian-Ren Lee, Shun-Hong Huang, Hsiao-Yun Lee, Tzu-kang Sang, Hong-Lin Chan, Ping-Chiang Lyu
2D-DIGE combined with MALDI-MS to study the IBMPFD disorder at the protein level in Drosophila melanogaster.
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Naive Bayes QSDR classification based on spiral-graph Shannon entropies for protein biomarkers in human colon cancer

Mol. BioSyst., 2012, 8,1716-1722
DOI: 10.1039/C2MB25039J, Paper

Vanessa Aguiar-Pulido, Cristian R. Munteanu, Jose A. Seoane, Enrique Fernandez-Blanco, Lazaro G. Perez-Montoto, Humberto Gonzalez-Diaz, Julian Dorado
An algorithm for colon cancer prediction is presented. Amino acid sequences are coded using spiral graph topological and Shannon entropy indices. These indices are then classified using a Naive Bayes model.
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Identification of novel components of NAD-utilizing metabolic pathways and prediction of their biochemical functions

Mol. BioSyst., 2012, 8,1661-1677
DOI: 10.1039/C2MB05487F, Paper

Robson Francisco de Souza, L. Aravind
Analysis of NAD utilization pathways reveals previously uncharacterized players in ADP ribosylation of proteins, RNA processing and biosynthesis of novel metabolites.
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Mapping the genome of Plasmodium falciparum on the drug-like chemical space reveals novel anti-malarial targets and potential drug leads

Mol. BioSyst., 2012, 8,1678-1685
DOI: 10.1039/C2MB00008C, Paper

Kasper Jensen, Damian Plichta, Gianni Panagiotou, Irene Kouskoumvekaki
We have mapped compounds with antimalarial activity on the genome of Plasmodium falciparum and have identified potentially druggable targets and drug leads.
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Hypothesis: butyrate is not an HDAC inhibitor, but a product inhibitor of deacetylation

Mol. BioSyst., 2012, 8,1609-1612
DOI: 10.1039/C2MB25028D, Opinion

Bernard M. Corfe
A unifying hypothesis integrating the metabolic and HDAC inhibitory properties of short-chain fatty acids is proposed.
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A taxonomy of organ-specific breast cancer metastases based on a protein-protein interaction network

Mol. BioSyst., 2012, Accepted Manuscript
DOI: 10.1039/C2MB25104C, Paper

Rebeca Sanz-Pamplona, Javier Garcia-Garcia, Sergi Franco, Xavier Messeguer, Keltouma Driouch, Baldo Oliva, Angels Sierra
We carried out a systems-level study of the mechanisms underlying organ-specific metastases of breast cancer. We followed a network-based approach using microarray expression data from human breast cancer metastases to...
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Ligand-based approach for the in silico discovery of multi-target inhibitors for proteins associated with HIV infection

Mol. BioSyst., 2012, Accepted Manuscript
DOI: 10.1039/C2MB25093D, Paper

Alejandro Speck-Planche, Valeria V. Kleandrova, F Luan, Maria Natalia Dias Soeiro Cordeiro
Acquired immunodeficiency syndrome (AIDS) is a dangerous disease, which leads to damage the immune system cells at the point that immune system can no longer fight against other infections that...
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Differential accumulation of host mRNAs on polyribosomes during obligate pathogen-plant interactions

Mol. BioSyst., 2012, Accepted Manuscript
DOI: 10.1039/C2MB25014D, Paper

Jackson R Moeller, Matthew J Moscou, Tim Bancroft, Ronald W. Skadsen, Roger P. Wise, Steven A Whitham
Plant pathogens elicit dramatic changes in the expression of host genes during both compatible and incompatible interactions. Gene expression profiling studies of plant-pathogen interactions have only considered messenger RNAs (mRNAs)...
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Elucidating the in vivo phosphorylation dynamics of the ERK MAP kinase using quantitative proteomics data and Bayesian model selection

Mol. BioSyst., 2012, Advance Article
DOI: 10.1039/C2MB05493K, Paper

Tina Toni, Yu-ichi Ozaki, Paul Kirk, Shinya Kuroda, Michael P. H. Stumpf
In this paper we study dynamics of the MEK/ERK phosphorylation. We employ a model selection algorithm based on approximate Bayesian computation to elucidate phosphorylation dynamics from quantitative time course data obtained from PC12 cells in vivo.
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A compendium of inborn errors of metabolism mapped onto the human metabolic network.

Mol. BioSyst., 2012, Accepted Manuscript
DOI: 10.1039/C2MB25075F, Paper

Swagatika Sahoo, Leifur Franzson, Jon J Jonsson, Ines Thiele
Inborn errors of metabolism (IEMs) are hereditary metabolic defects, which are encountered in almost all major metabolic pathways occurring in man. Many IEMs are screened for in neonates through metabolomic...
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Towards integrative annotating the cell-type specific gene functional and signaling map in vascular endothelial cells

Mol. BioSyst., 2012, Accepted Manuscript
DOI: 10.1039/C2MB25065A, Method

Jin Gu, Shao Li
Vascular endothelial cells (VECs), which form the inner surfaces of blood vessels, play essential roles in many physiological and pathological processes. VECs are exposed to various micro-environmental stimuli delivered by...
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More than just tails: intrinsic disorder in histone proteins

Mol. BioSyst., 2012, Advance Article
DOI: 10.1039/C2MB25102G, Paper

Zhenling Peng, Marcin J. Mizianty, Bin Xue, Lukasz Kurgan, Vladimir N. Uversky
Comprehensive computational analysis revealed that histones are highly disordered and intrinsic disorder extends far beyond the limits of protein tails.
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Metabolic effects of the iodothyronine functional analogue TRC150094 on the liver and skeletal muscle of high-fat diet fed overweight rats: an integrated proteomic study

Mol. BioSyst., 2012, Advance Article
DOI: 10.1039/C2MB25055A, Paper

Elena Silvestri, Daniela Glinni, Federica Cioffi, Maria Moreno, Assunta Lombardi, Pieter de Lange, Rosalba Senese, Michele Ceccarelli, Anna Maria Salzano, Andrea Scaloni, Antonia Lanni, Fernando Goglia
The iodothyronine functional analogue TRC150094 ameliorates the oxidative capacity of the liver and muscle of high-fat fed overweight rats.
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