RSC - Mol. BioSyst. latest articles

Recombinant production of rhesus [small theta]-defensin-1 (RTD-1) using a bacterial expression system

Mol. BioSyst., 2012, Advance Article
DOI: 10.1039/C2MB05451E, Paper

Andrew Gould, Yilong Li, Subhabrata Majumder, Angie E. Garcia, Patrick Carlsson, Alexander Shekhtman, Julio A. Camarero
We report for the first time the recombinant expression of the rhesus [small theta]-defensin-1 (RTD-1) using a bacterial expression system.
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Identification and reconstitution of genetic regulatory networks for improved microbial tolerance to isooctane

Mol. BioSyst., 2012, Advance Article
DOI: 10.1039/C2MB05441H, Paper

Aram Kang, Matthew Wook Chang
This paper presents an engineering framework that harnesses systems biology-derived regulatory information to improve microbial phenotypes.
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PageRank-based identification of signaling crosstalk from transcriptomics data: the case of Arabidopsis thaliana

Mol. BioSyst., 2012, Advance Article
DOI: 10.1039/C2MB05365A, Method

Nooshin Omranian, Bernd Mueller-Roeber, Zoran Nikoloski
The study presents a network-based method for detection of genes involved in signaling crosstalk based on transcriptomics data.
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A meta-analysis of caloric restriction gene expression profiles to infer common signatures and regulatory mechanisms

Mol. BioSyst., 2012, Advance Article
DOI: 10.1039/C2MB05255E, Paper

Michael Plank, Daniel Wuttke, Sipko van Dam, Susan A. Clarke, Joao Pedro de Magalhaes
A conserved signature of caloric restriction in mammals was integrated with additional types of data to identify candidate transcriptional modules and regulators.
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A systematic modeling study on the pathogenic role of p38 MAPK activation in myelodysplastic syndromes

Mol. BioSyst., 2012, Advance Article
DOI: 10.1039/C2MB05184B, Paper

Huiming Peng, Jianguo Wen, Lixin Zhang, Hongwei Li, Chung-Che Chang, Youli Zu, Xiaobo Zhou
A novel computational modeling approach combining RPPA data to determine the specific signal transduction of p38 MAPK activation reveals the major differences between MDS and normal, validated by immunohistochemistry.
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Heat shock proteins as key biological targets of the marine natural cyclopeptide perthamide C

Mol. BioSyst., 2012, Advance Article
DOI: 10.1039/C2MB05507D, Paper

Luigi Margarucci, Maria Chiara Monti, Andrea Mencarelli, Chiara Cassiano, Stefano Fiorucci, Raffaele Riccio, Angela Zampella, Agostino Casapullo
HSP-90 and GRP-94 were identified as key targets of perthamide C by chemical proteomics revealing the ability of the marine metabolite to influence HSP-mediated cell apoptosis.
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A Highly Efficient Tree Structure for the Biosynthesis of Heparan Sulfate Accounts for the Commonly Observed Disaccharides and Suggests a Mechanism for Domain Synthesis

Mol. BioSyst., 2012, Accepted Manuscript
DOI: 10.1039/C2MB25019E, Paper

Edwin Yates, Timothy R Rudd
The form of the biosynthetic pathway of the biologically and medically important polysaccharides heparan sulfate and the closely related heparin remain obscure despite significant progress characterising the biosynthetic machinery. Considering...
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Exploring salivary proteomes in edentulous patients with type 2 diabetes

Mol. BioSyst., 2012, Advance Article
DOI: 10.1039/C2MB05079J, Paper

Michael B. Border, Sarah Schwartz, Jim Carlson, Christopher F. Dibble, Heidi Kohltfarber, Steven Offenbacher, John B. Buse, Sompop Bencharit
The salivary proteomic analysis of edentulous subjects using label-free quantitative mass spectrometry proteomics reveals differential expression of salivary proteins between subjects with and without type 2 diabetes.
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Proteomic analysis in clear cell renal cell carcinoma: identification of differentially expressed protein by 2-D DIGE

Mol. BioSyst., 2012, Advance Article
DOI: 10.1039/C2MB05390J, Paper

Francesca Raimondo, Claudia Salemi, Clizia Chinello, Daniela Fumagalli, Lavinia Morosi, Francesco Rocco, Stefano Ferrero, Roberto Perego, Cristina Bianchi, Cecilia Sarto, Marina Pitto, Paolo Brambilla, Fulvio Magni
2-D DIGE representation of 23 up- and 77 down-regulated proteins in RCC.
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Mathematical modeling of the low and high affinity arabinose transport systems in Escherichia coli

Mol. BioSyst., 2012, Advance Article
DOI: 10.1039/C2MB05352G, Paper

Necmettin Yildirim
In E.coli, arabinose transport from extracellular media is mediated by two genetically distinct transport systems. The model we developed predicts that the two transport systems complement each other and there is a range of extracellular arabinose concentrations at which this system is capable of showing bistability.
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Analysis of crucial factors resulting in microarray hybridization failure

Mol. BioSyst., 2012, Advance Article
DOI: 10.1039/C2MB05300D, Paper

Ting Wei, Mike N. Pearson, Karen Armstrong, Dietmar Blohm, Jue Liu
Target structure was concluded the most crucial factor resulting in microarray failure by a process of elimination in comparison to other multiple factors simultaneously.
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Shotgun proteomics and network analysis of neuroblastoma cell lines treated with curcumin

Mol. BioSyst., 2012, Advance Article
DOI: 10.1039/C2MB05498A, Paper

Simona D'Aguanno, Igea D'Agnano, Michele De Canio, Claudia Rossi, Sergio Bernardini, Giorgio Federici, Andrea Urbani
Unsupervised molecular investigation of proteome changes highlighted cell cycle arrest in the G2/M phase and accumulation of polyubiquitinated proteins in a neuroblastoma cell line sensitive to cisplatin and its resistant counterpart after curcumin treatment.
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Bioinformatic and experimental fishing for artemisinin-interacting proteins from human nasopharyngeal cancer cells

Mol. BioSyst., 2012, Advance Article
DOI: 10.1039/C2MB05437J, Paper

T. Eichhorn, S. Schloissnig, B. Hahn, A. Wendler, Rolf Mertens, W. D. Lehmann, R. L. Krauth-Siegel, T. Efferth
The anti-malarial artemisinin also exerts profound anti-cancer activity, but the mechanisms of action are incompletely understood. In the present investigation, we present a novel approach to identify artemisinin-interacting target proteins.
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NF-[small kappa]B as a potential therapeutic target in microbial diseases

Mol. BioSyst., 2012, Advance Article
DOI: 10.1039/C2MB05335G, Review

Mariateresa Vitiello, Marilena Galdiero, Emiliana Finamore, Stefania Galdiero, Massimiliano Galdiero
Modulation of NF-[small kappa]B activation and its signaling pathway during microbial infections offer novel targets for antimicrobial therapies.
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Identification of DNA-protein complexes using an improved, combined Western Blotting- Electrophoretic Mobility Shift Assay (EMSA) with a fluorescence imaging system

Mol. BioSyst., 2012, Accepted Manuscript
DOI: 10.1039/C2MB05500G, Method

Klaus Deckmann, Florian Rorsch, Gerd Geisslinger, Sabine Grosch
Electrophoretic Mobility Shift Assays (EMSAs) are used to detect DNA-protein interactions. With this type of assay it is difficult to distinguish between specific and non-specific DNA-protein complexes or to define...
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Parallel Tracking of cAMP and PKA signaling dynamics in Living Cells with FRET-based Fluorescent Biosensors

Mol. BioSyst., 2012, Accepted Manuscript
DOI: 10.1039/C2MB05514G, Paper

Nwe-Nwe Aye-Han, Michael D. Allen, Qiang Ni, Jin Zhang
Proper regulation of cellular functions relies upon a network of intricately interwoven signaling cascades in which multiple components must be tightly coordinated both spatially and temporally. To better understand how...
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Genetic screens for the control of influenza virus replication: from meta-analysis to drug discovery

Mol. BioSyst., 2012, Advance Article
DOI: 10.1039/C2MB05416G, Paper

Benoit de Chassey, Laurene Meyniel-Schicklin, Anne Aublin-Gex, Patrice Andre, Vincent Lotteau
Integration of genetic screens and protein interaction data provides a rationale to identify drug candidates against influenza virus.
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Optimized TAL effector nucleases (TALENs) for use in treatment of sickle cell disease

Mol. BioSyst., 2012, Advance Article
DOI: 10.1039/C2MB05461B, Paper

Ning Sun, Jing Liang, Zhanar Abil, Huimin Zhao
The first pair of TAL effector nucleases was created and optimized for efficient cleavage of human [small beta]-globin gene locus, which may be used in treatment of sickle cell disease.
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GENOCOP algorithm and hierarchical grid transformation for image warping of two dimensional gel eletrophoretic maps

Mol. BioSyst., 2012, Advance Article
DOI: 10.1039/C2MB05396A, Paper

Emilio Marengo, Marina Cocchi, Marco Demartini, Elisa Robotti, Daniela Cecconi, Giorgio Calabrese
Hierarchical grid transformation is a powerful approach to SDS 2DPAGE maps warping. The numerical optimization of the warping procedure is a multivariate task that can be solved efficiently using Genetic algorithms for Numerical Optimization in COnstrained Problems (GENOCOP).
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Development of diacyltetrol lipids as activators for the C1 domain of protein kinase C

Mol. BioSyst., 2012, Advance Article
DOI: 10.1039/C2MB05452C, Paper

Narsimha Mamidi, Sukhamoy Gorai, Rakesh Mukherjee, Debasis Manna
Experimental and computational studies were carried out to provide insights into the PKC C1b domain binding by the novel diacyltetrol lipids.
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Forced homodimerization of the c-Fos leucine zipper in designed bHLHZ-like hybrid proteins MaxbHLH-Fos and ArntbHLH-Fos

Mol. BioSyst., 2012, Advance Article
DOI: 10.1039/C2MB05354C, Paper

Gang Chen, Antonia T. De Jong, Jumi A. Shin
The c-Fos leucine zipper does not homodimerize in its native bZIP. However, when fused to the bHLH motif to form a non-native hybrid, this zipper dimerizes, leading to DNA-binding function.
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Analysis of cell adhesion during early stages of colon cancer based on an extended multi-valued logic approach

Mol. BioSyst., 2012, Advance Article
DOI: 10.1039/C2MB05277F, Paper

Daniel V. Guebel, Ulf Schmitz, Olaf Wolkenhauer, Julio Vera
Here we present the first large scale multi-valued logic model investigating the signalling pathways that regulate cell adhesion during colorectal cancer initiation.
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Dense surface functionalization using peptides that recognize differences in organized structures of self-assembling nanomaterials

Mol. BioSyst., 2012, Advance Article
DOI: 10.1039/C2MB05435C, Paper

Toshiki Sawada, Hisakazu Mihara
Cell adhesion to the fine-structured peptide nanofiber was highly up-regulated by modification with the plural RGDS conjugated nanofiber specific peptides.
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UPLC-MS metabolic profiling of second trimester amniotic fluid and maternal urine and comparison with NMR spectral profiling for the identification of pregnancy disorder biomarkers

Mol. BioSyst., 2012, Advance Article
DOI: 10.1039/C2MB05424H, Paper

Goncalo Graca, Brian J. Goodfellow, Antonio S. Barros, Silvia Diaz, Iola F. Duarte, Konstantina Spagou, Kirill Veselkov, Elizabeth J. Want, John C. Lindon, Isabel M. Carreira, Eulalia Galhano, Cristina Pita, Ana M. Gil
A UPLC-MS study of 2nd trimester maternal urine and amniotic fluid to investigate metabolic effects of pregnancy disorders.
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Wide-range protein photo-crosslinking achieved by a genetically encoded N[varepsilon]-(benzyloxycarbonyl)lysine derivative with a diazirinyl moiety

Mol. BioSyst., 2012, Advance Article
DOI: 10.1039/C2MB05321G, Communication

Tatsuo Yanagisawa, Nobumasa Hino, Fumie Iraha, Takahito Mukai, Kensaku Sakamoto, Shigeyuki Yokoyama
A method for wide-range in vivo protein photo-crosslinking has been developed by the site-specific incorporation of a large, photo-crosslinkable, non-natural amino acid into proteins.
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RimJ-mediated context-dependent N-terminal acetylation of the recombinant Z-domain protein in Escherichia coli

Mol. BioSyst., 2012, Advance Article
DOI: 10.1039/C2MB05499J, Communication

Lina F. Bernal-Perez, Fatima Sahyouni, Laszlo Prokai, Youngha Ryu
N-terminal acetylation of the Z-domain depends on E. coli strains and expression vectors, and is enhanced by RimJ.
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A proteomic profile of washing fluid from the colorectal tract to search for potential biomarkers of colon cancer

Mol. BioSyst., 2012, Advance Article
DOI: 10.1039/C2MB05394B, Paper

Laura Giusti, Pietro Iacconi, Ylenia Da Valle, Federica Ciregia, Tiziana Ventroni, Elena Donadio, Gino Giannaccini, Massimo Chiarugi, Liborio Torregrossa, Agnese Proietti, Fulvio Basolo, Antonio Lucacchini
Washing fluid (WF) from the colorectal tract might be a source of cellular and secreted proteins of tumours, as found for tissue samples, moreover, WF samples have allowed us to find new potential proteins involved in colorectal cancer.
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Probing the binding of two fluoroquinolones to lysozyme: a combined spectroscopic and docking study

Mol. BioSyst., 2012, Advance Article
DOI: 10.1039/C2MB05423J, Paper

Pengfei Qin, Baoling Su, Rutao Liu
Ciprofloxacin and enrofloxacin exhibited different binding properties to lysozyme, but they both resulted in the conformational and microenvironmental changes of the enzyme.
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Impaired dynamics of the late endosome/lysosome compartment in human Niemann-Pick type C skin fibroblasts carrying mutation in NPC1 gene

Mol. BioSyst., 2012, Advance Article
DOI: 10.1039/C2MB05447G, Paper

Malgorzata E. Sztolsztener, Agnieszka Dobrzyn, Slawomir Pikula, Anna Tylki-Szymanska, Joanna Bandorowicz-Pikula
Membranes of the late endosome/lysosome compartment isolated from NPC L1 cells (filled circles) are characterized by a significantly lower membrane fluidity than those from control cells (open circles).
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A reversible DNA-silver nanoclusters-based molecular fluorescence switch and its use for logic gate operation

Mol. BioSyst., 2012, 8,921-926
DOI: 10.1039/C2MB05438H, Paper

Zhenzhen Huang, Jinsong Ren, Xiaogang Qu
A reversible molecular fluorescence switch is developed based on the pH-triggered fluorescence response of transfer-based DNA-stabilized silver nanoclusters.
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Ingenuity pathways analysis of urine metabolomics phenotypes toxicity of Chuanwu in Wistar rats by UPLC-Q-TOF-HDMS coupled with pattern recognition methods

Mol. BioSyst., 2012, Advance Article
DOI: 10.1039/C1MB05366C, Paper

Hui Dong, Aihua Zhang, Hui Sun, Huiyu Wang, Xin Lu, Mo Wang, Bei Ni, Xijun Wang
A comprehensive metabolomics with pattern recognition analyses was designed to characterize long-term toxicity following treatment with Chuanwu, providing support for sensitive, non-invasive biomarkers of toxicity.
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Inter-domain movements in polyketide synthases: a molecular dynamics study

Mol. BioSyst., 2012, Advance Article
DOI: 10.1039/C2MB05425F, Paper

Swadha Anand, Debasisa Mohanty
MD simulations on multi-domain polyketide synthases reveal inter- and intra-domain flexibility which can potentially facilitate channeling of substrates during polyketide biosynthesis.
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Physical fitness level is reflected by alterations in the human plasma metabolome

Mol. BioSyst., 2012, Advance Article
DOI: 10.1039/C2MB05428K, Paper

Elin Chorell, Michael B. Svensson, Thomas Moritz, Henrik Antti
Metabolomics analysis of human blood plasma revealed robust metabolite profiles associated with moderate changes in cardiorespiratory fitness status (VO₂max).
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Robust, quantitative tools for modelling ex-vivo expansion of haematopoietic stem cells and progenitors

Mol. BioSyst., 2012, 8,913-920
DOI: 10.1039/C2MB05439F, Paper

David A. Winkler, Frank R. Burden
Modern computational modelling tools offer rapid, robust analysis of factors controlling expansion of haematopoietic stem cells and progenitors in bioreactors.
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An OR logic gate based on two molecular beacons

Mol. BioSyst., 2012, 8,927-930
DOI: 10.1039/C2MB05477A, Paper

Jing Guo, Renqiang Yang
Molecular beacons were used as inputs to activate the OR logic function by employing the mechanism of sequence recognition.
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Metabolic network analysis revealed distinct routes of deletion effects between essential and non-essential genes

Mol. BioSyst., 2012, Advance Article
DOI: 10.1039/C2MB05376D, Paper

Jing Ma, Xun Zhang, Choong Yong Ung, Yu Zong Chen, Baowen Li
This work revealed the cooperative nature of essential genes and the distinct routes of deletion effects between essential and non-essential genes.
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Molecular basis for fungicidal action of neothyonidioside, a triterpene glycoside from the sea cucumber, Australostichopus mollis

Mol. BioSyst., 2012, 8,902-912
DOI: 10.1039/C2MB05426D, Paper

Ploi Yibmantasiri, Dora C. Leahy, Bede P. Busby, Stephan Andreas Angermayr, Alice G. Sorgo, Kristina Boeger, Rosemary Heathcott, Jacqueline M. Barber, Greta Moraes, James H. Matthews, Peter T. Northcote, Paul H. Atkinson, David S. Bellows
Mechanism of antifungal natural saponin determined by functional genomics and genetics implicates membrane rigidity in multivesicular body formation.
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Lens proteomics: analysis of rat crystallins when lenses are exposed to dexamethasone

Mol. BioSyst., 2012, 8,888-901
DOI: 10.1039/C2MB05463A, Paper

Lin Wang, Wen Cheng Zhao, Xiu Li Yin, Jin Ying Ge, Zhi Gao Bu, Hong Yan Ge, Qing Feng Meng, Ping Liu
Proteomics analysis of rat crystallins and related changes in lenses exposed to dexamethasone which provide a mechanism for steroid cataracts.
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Nucleosome positioning and nucleosome stacking: two faces of the same coin

Mol. BioSyst., 2012, Advance Article
DOI: 10.1039/C2MB05407H, Paper

Julien Riposo, Julien Mozziconacci
We propose here that the regular spacing observed in eukaryotic genomes can be explained by the fact that nucleosomes are stacked in regular chromatin fibers.
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Simultaneous analysis of cardiolipin and lipid A from Helicobacter pylori by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

Mol. BioSyst., 2012, 8,720-725
DOI: 10.1039/C2MB05475B, Method

Ping Zhou, Rui Hu, Vandana Chandan, Rhonda KuoLee, Xin Liu, Wangxue Chen, Bifeng Liu, Eleonora Altman, Jianjun Li
This is the first report of simultaneous analysis of cardiolipin and lipid A from single bacterial colony with optimized MALDI matrix and extraction conditions.
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Protein conducting channels-mechanisms, structures and applications

Mol. BioSyst., 2012, 8,709-719
DOI: 10.1039/C2MB05433G, Review

Francesco Bonardi, Nico Nouwen, Ben L. Feringa, Arnold J. M. Driessen
Channels that mediate the passage of proteins across the cytoplasmic membrane function according to various mechanisms that differ in complexity.
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A C-di-GMP-proflavine-hemin supramolecular complex has peroxidase activity-implication for a simple colorimetric detection

Mol. BioSyst., 2012, 8,726-729
DOI: 10.1039/C2MB05430B, Communication

Shizuka Nakayama, Kevin Roelofs, Vincent T. Lee, Herman O. Sintim
The bacterial biofilm regulator, c-di-GMP, aggregates with proflavine and hemin to form a supramolecular peroxidase complex.
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Proteomic analysis of protein adsorption capacity of different haemodialysis membranes

Mol. BioSyst., 2012, Advance Article
DOI: 10.1039/C2MB05393D, Paper

Andrea Urbani, Santina Lupisella, Vittorio Sirolli, Sonia Bucci, Luigi Amoroso, Barbara Pavone, Luisa Pieroni, Paolo Sacchetta, Mario Bonomini
Proteomics is a useful approach to investigate the protein adsorptive properties of biomaterials used for haemodialysis membranes.
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