RSC - Mol. BioSyst. latest articles

The bis-phenanthridinium system flexibility and position of covalently bound uracil finely tunes the interaction with polynucleotides

Mol. BioSyst., 2013, Advance Article
DOI: 10.1039/C3MB25578F, Paper

Marina Grabar Branilovic, Sanja Tomic, Lidija-Marija Tumir, Ivo Piantanida
A series of structurally similar bis-phenanthridinium derivatives, some with uracil at different positions, revealed different interactions with various polynucleotides. Molecular modeling study revealed details of these interactions.
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Affinity Maturation and Fine Functional Mapping of an Antibody Fragment against a Novel Neutralizing Epitope on Human Vascular Endothelial Growth Factor

Mol. BioSyst., 2013, Accepted Manuscript
DOI: 10.1039/C3MB70136K, Paper

Humberto Lamdan, Jorge Victor Gavilondo, Yasmiana Munoz, Amaury Pupo, Vivian Huerta, Alexis Musacchio, Lincidio Perez, Marta Ayala, Gertrudis Rojas, Robert F Balint, James W Larrick
We have previously reported the isolation of a novel single-chain variable fragment (scFv) against vascular endothelial growth factor (VEGF), from a phage-displayed human antibody repertoire. This scFv, denominated 2H1, was...
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Network properties of decoys and CASP predicted models: A comparison with native protein structures.

Mol. BioSyst., 2013, Accepted Manuscript
DOI: 10.1039/C3MB70157C, Paper

Subhojyoti Chatterjee, Soma Ghosh, Saraswathi Vishveshwara
Protein structure space is believed to consist of a finite set of discrete folds, unlike the protein sequence space which is astronomically large, indicating that proteins from the available sequence...
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Metabolomic analysis of sun exposed skin

Mol. BioSyst., 2013, Advance Article
DOI: 10.1039/C3MB25537A, Paper

Manpreet Randhawa, Michael Southall, Samantha Tucker Samaras
It is very well known that exposure of skin to sun chronically accelerates the mechanism of aging as well as making it more susceptible toward skin cancer.
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Identification of microRNA and bioinformatics target gene analysis in beef cattle intramuscular fat and subcutaneous fat

Mol. BioSyst., 2013, Accepted Manuscript
DOI: 10.1039/C3MB70084D, Paper

Haiyang Wang, Yue Zheng, Genlin Wang, Huixia Li
microRNA (miRNA) are endogenous non-coding RNA that has been proposed play important roles in the formation of body fat. However, the differential expression of miRNA and the role of these...
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Mass Spectrometry-based Identification and Characterisation of Lysine and Arginine Methylation in the Human Proteome

Mol. BioSyst., 2013, Accepted Manuscript
DOI: 10.1039/C3MB00009E, Paper

Michael Bremang, Alessandro Cuomo, Anna Maria Agresta, Magdalena Stugiewicz, Valeria Spadotto, Tiziana Bonaldi
Protein methylation is a post-translational modification (PTM) by which a variable number of methyl groups is transferred to lysine and arginine residues within proteins. Despite increased interest in this modification...
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In silico metabolic engineering of Bacillus subtilis for improved production of riboflavin, Egl-237, (R,R)-2,3-butanediol and isobutanol

Mol. BioSyst., 2013, Advance Article
DOI: 10.1039/C3MB25568A, Paper

Tong Hao, Binbin Han, Hongwu Ma, Jing Fu, Hui Wang, Zhiwen Wang, Bincai Tang, Tao Chen, Xueming Zhao
A genome-scale metabolic network model of B. subtilis - iBsu1147 - is reconstructed and used for the overproduction of four important products.
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Structural comparison of biological networks based on dominant vertices

Mol. BioSyst., 2013, Accepted Manuscript
DOI: 10.1039/C3MB70077A, Paper

Beatriz Luna, Edgardo Galan-Vasquez, Edgardo Ugalde, Agustino Martinez-Antonio
It is a current practice to organize biological data in a network structure where vertices represent biological components and arrows represent their interactions. A great diversity of graph theoretical notions,...
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The intrinsically disordered C-terminal region of Arabidopsis thaliana TCP8 transcription factor acts both as a transactivation and self-assembly domain

Mol. BioSyst., 2013, Accepted Manuscript
DOI: 10.1039/C3MB70128J, Paper

Isabel Valsecchi, Emilie Guittard-Crilat, Regis Maldiney, Yvette Habricot, Sabrina Lignon, Regine Lebrun, Emile Miginiac, Eric Ruelland, Emmanuelle Jeannette, Sandrine Lebreton
TCPs are plant specific transcription factors with non-canonical basic helix-loop-helix domains. While Arabidopsis thaliana has 24 TCPs involved in cell proliferation and differentiation, their mode of action has not been...
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Multivalency Amplifies the Selection and Affinity of Bradykinin-Derived Peptide for Lipid Nanovesicles

Mol. BioSyst., 2013, Accepted Manuscript
DOI: 10.1039/C3MB70109C, Communication

Hubert Yin
The trimer of a Bradykinin derivative displayed more than five-fold increase in binding affinity for phosphatidylserine-enriched nanovesicles as compared to its monomeric precursor. The nanovesicle selection is directly correlated to...
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Genomic analysis reveals epistatic silencing of "expensive" genes in Escherichia coli K-12

Mol. BioSyst., 2013, Advance Article
DOI: 10.1039/C3MB70035F, Paper

Rajalakshmi Srinivasan, Deepti Chandraprakash, Revathy Krishnamurthi, Parul Singh, Vittore F. Scolari, Sandeep Krishna, Aswin Sai Narain Seshasayee
The DNA binding sites of H-NS and the function of StpA as a backup system might be selected for silencing highly transcribable genes.
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Development of a novel non-radioactive cell-based method for the screening of SGLT1 and SGLT2 inhibitors using 1-NBDG

Mol. BioSyst., 2013, Advance Article
DOI: 10.1039/C3MB70060G, Paper

Hung-Chi Chang, Su-Fu Yang, Ching-Chun Huang, Tzung-Sheng Lin, Pi-Hui Liang, Chun-Jung Lin, Lih-Ching Hsu
A novel non-radioactive cell-based system using 1-NBDG is a rapid and reliable method for the screening of SGLT inhibitors.
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Digital and analogical reality in proteomics investigation

Mol. BioSyst., 2013, 9,1062-1063
DOI: 10.1039/C3MB90013D, Editorial

Andrea Urbani, Massimo Castagnola, Mauro Fasano, Luca Bini, Alessandra Modesti, Anna Maria Timperio, Paola Roncada
Are protein functions continuous or discretized? Proteomics investigations are starting to address this non-trivial awesome question focusing upon determining the nature of biological molecular relationships.
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Proteomic analysis of temperature stress-responsive proteins in Arabidopsis thaliana rosette leaves

Mol. BioSyst., 2013, 9,1257-1267
DOI: 10.1039/C3MB70137A, Paper

Mariapina Rocco, Simona Arena, Giovanni Renzone, Gabriella Stefania Scippa, Tonia Lomaglio, Francesca Verrillo, Andrea Scaloni, Mauro Marra
Proteomics of Arabidopsis leaves subjected to low or high temperature stress.
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Crosstalk between salicylic acid and jasmonate in Arabidopsis investigated by an integrated proteomic and transcriptomic approach

Mol. BioSyst., 2013, 9,1169-1187
DOI: 10.1039/C3MB25569G, Paper

Silvia Proietti, Laura Bertini, Anna Maria Timperio, Lello Zolla, Carlo Caporale, Carla Caruso
Crosstalk between SA- and JA-mediated defence pathways is investigated for the first time by both proteomic and transcriptomic approaches.
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Application of proteomics technology in adipocyte biology

Mol. BioSyst., 2013, 9,1076-1091
DOI: 10.1039/C3MB25596D, Review Article

Johan Renes, Edwin Mariman
Obesity and its associated complications have reached epidemic proportions in Western-type societies.
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Proteomic and ionomic profiling reveals significant alterations of protein expression and calcium homeostasis in cystic fibrosis cells

Mol. BioSyst., 2013, 9,1117-1126
DOI: 10.1039/C3MB25594H, Paper

Domenico Ciavardelli, Melania D'Orazio, Luisa Pieroni, Ada Consalvo, Claudia Rossi, Paolo Sacchetta, Carmine Di Ilio, Andrea Battistoni, Andrea Urbani
Altered protein expression profiles and Ca²⁺ dyshomeostasis in cystic fibrosis cells using integrated proteomic and ionomic analysis.
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Identification and characterization of the actinomycin G gene cluster in Streptomyces iakyrus

Mol. BioSyst., 2013, 9,1286-1289
DOI: 10.1039/C3MB70081J, Communication

Xiaoling Wang, Jioji Tabudravu, Mostafa Ezzat Rateb, Krystal Joan Annand, Zhiwei Qin, Marcel Jaspars, Zixin Deng, Yi Yu, Hai Deng
A mutual dependency between a hydroxylase gene, acmG8, and a halogenase gene, acmG9, has been identified in the biosynthesis of actinomycin G.
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Integrative quantitation enables a comprehensive proteome comparison of two Mycoplasma pneumoniae genetic perturbations

Mol. BioSyst., 2013, 9,1249-1256
DOI: 10.1039/C3MB25581F, Paper

Eva Borras, Guadalupe Espadas, Francesco M. Mancuso, Tobias Maier, Cristina Chiva, Eduard Sabido
Combination of six different protein quantitation strategies allowed confidently detection of protein abundance changes among distinct M. pneumoniae strains.
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Salmonella modulates metabolism during growth under conditions that induce expression of virulence genes

Mol. BioSyst., 2013, 9,1522-1534
DOI: 10.1039/C3MB25598K, Paper

Young-Mo Kim, Brian J. Schmidt, Afshan S. Kidwai, Marcus B. Jones, Brooke L. Deatherage Kaiser, Heather M. Brewer, Hugh D. Mitchell, Bernhard O. Palsson, Jason E. McDermott, Fred Heffron, Richard D. Smith, Scott N. Peterson, Charles Ansong, Daniel R. Hyduke, Thomas O. Metz, Joshua N. Adkins
Metabolomics and omics-informed genome-scale modeling identified functional consequences of adaptive alterations in S. Typhimurium metabolism during growth under virulence conditions.
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Shotgun proteomics reveals specific modulated protein patterns in tears of patients with primary open angle glaucoma naive to therapy

Mol. BioSyst., 2013, 9,1108-1116
DOI: 10.1039/C3MB25463A, Paper

Damiana Pieragostino, Luca Agnifili, Vincenzo Fasanella, Simona D'Aguanno, Rodolfo Mastropasqua, Carmine Di Ilio, Paolo Sacchetta, Andrea Urbani, Piero Del Boccio
LC-MS^E proteomics revealed 27 differential tear proteins in naive POAG vs. CTRL,13 of them were modulated in medically controlled POAG indicating a probable influence of therapy on the same molecular pattern.
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Selective binding of 2[prime or minute]-F-c-di-GMP to Ct-E88 and Cb-E43, new class I riboswitches from Clostridium tetani and Clostridium botulinum respectively

Mol. BioSyst., 2013, 9,1535-1539
DOI: 10.1039/C3MB25560C, Paper

Yiling Luo, Jie Zhou, Jingxin Wang, T. Kwaku Dayie, Herman O. Sintim
Two new class I c-di-GMP riboswitch aptamers have been experimentally verified to bind to c-di-GMP with nanomolar K_d and can be differentiated using 2[prime or minute]-F-c-di-GMP.
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Genotype-phenotype relationships in light of a modular protein interaction landscape

Mol. BioSyst., 2013, 9,1064-1067
DOI: 10.1039/C3MB25583B, Opinion

Matthias Gstaiger, Ruedi Aebersold
Better approaches tackling the modular nature of proteomes will have dramatic effects on the understanding of genotype-phenotype relationships, argue Matthias Gstaiger and Ruedi Aebersold.
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Complementary biochemical approaches applied to the identification of plastidial calmodulin-binding proteins

Mol. BioSyst., 2013, 9,1234-1248
DOI: 10.1039/C3MB00004D, Paper

Elisa Dell'Aglio, Cecile Giustini, Daniel Salvi, Sabine Brugiere, Faustine Delpierre, Lucas Moyet, Mathieu Baudet, Daphne Seigneurin-Berny, Michel Matringe, Myriam Ferro, Norbert Rolland, Gilles Curien
Using a proteomic approach, we identified new plastidial CaM-binding candidates and validated a subset of them by overlay assays and fluorescence anisotropy.
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A controllable gene expression system in liposomes that includes a positive feedback loop

Mol. BioSyst., 2013, 9,1282-1285
DOI: 10.1039/C3MB70032A, Communication

Shungo Kobori, Norikazu Ichihashi, Yasuaki Kazuta, Tetsuya Yomo
A positive feedback loop was introduced into a LacI-dependent gene expression system to enhance the signal to noise ratio.
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Computationally identifying virulence factors based on KEGG pathways

Mol. BioSyst., 2013, 9,1447-1452
DOI: 10.1039/C3MB70024K, Paper

Weiren Cui, Lei Chen, Tao Huang, Qian Gao, Min Jiang, Ning Zhang, Lulu Zheng, Kaiyan Feng, Yudong Cai, Hongwei Wang
The distribution of the main KEGG pathways of virulence: CJE, ECP and PAE.
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Discovery of Rho-kinase inhibitors by docking-based virtual screening

Mol. BioSyst., 2013, 9,1511-1521
DOI: 10.1039/C3MB00016H, Paper

Mingyun Shen, Huidong Yu, Youyong Li, Pixu Li, Peichen Pan, Shunye Zhou, Liling Zhang, Shang Li, Simon Ming-Yuen Lee, Tingjun Hou
Rho kinases (ROCK1 and ROCK2) belong to serine/threonine (Ser/Thr) protein kinase family, and play the central roles in the organization of the actin cytoskeleton.
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The pleiotropic effect of WD-40 domain containing proteins on cellular differentiation and production of secondary metabolites in Streptomyces coelicolor

Mol. BioSyst., 2013, 9,1453-1469
DOI: 10.1039/C3MB25542E, Paper

Ales Ulrych, Jana Goldova, Miroslav Petricek, Oldrich Benada, Olga Kofronova, Petra Rampirova, Katerina Petrickova, Pavel Branny
The two S. coelicolor WD-40 genes studied (wdpB and wdpC) have an important effect on morphological and physiological differentiation.
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A proteomics approach to study the molecular basis of enhanced salt tolerance in barley (Hordeum vulgare L.) conferred by the root mutualistic fungus Piriformospora indica

Mol. BioSyst., 2013, 9,1498-1510
DOI: 10.1039/C3MB70069K, Paper

Mehdi Alikhani, Behnam Khatabi, Mozhgan Sepehri, Mojtaba Khayam Nekouei, Mohsen Mardi, Ghasem Hosseini Salekdeh
Piriformospora indica is a root-interacting mutualistic fungus capable of enhancing plant growth, increasing plant resistance to a wide variety of pathogens, and improving plant stress tolerance under extreme environmental conditions.
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Molecular dynamic simulations of the tubulin-human gamma synuclein complex: structural insight into the regulatory mechanism involved in inducing resistance against Taxol

Mol. BioSyst., 2013, 9,1470-1488
DOI: 10.1039/C3MB25427E, Paper

Manivel Panneerselvam, Kannan Muthu, Muthukumaran Jayaraman, Upasana Sridharan, Pranitha Jenardhanan, Krishna Ramadas
Association of human gamma synuclein with tubulin induces extensive conformational changes in both tubulin monomers and protects them from the action of Taxol.
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Gossypol induces apoptosis in ovarian cancer cells through oxidative stress

Mol. BioSyst., 2013, 9,1489-1497
DOI: 10.1039/C3MB25461E, Paper

Jia Wang, Lixu Jin, Xiaoyu Li, Haiyun Deng, Yuling Chen, Qingquan Lian, Renshan Ge, Haiteng Deng
Gossypol induces cell death by GSH depletion and changes of redox states in metabolic and stress response proteins.
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Delay-managed tradeoff in the molecular dynamics of the segmentation clock

Mol. BioSyst., 2013, 9,1436-1446
DOI: 10.1039/C3MB70046A, Paper

Henglin Song, Zhanjiang Yuan, Tianshou Zhou
In the polar coordinate, there is a delay-managed tradeoff between phase coherence and phase averaged amplitude noise.
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Differential protein profiling of renal cell carcinoma urinary exosomes

Mol. BioSyst., 2013, 9,1220-1233
DOI: 10.1039/C3MB25582D, Paper

F. Raimondo, L. Morosi, S. Corbetta, C. Chinello, P. Brambilla, P. Della Mina, A. Villa, G. Albo, C. Battaglia, S. Bosari, F. Magni, M. Pitto
The proteome of urinary exosomes from renal cell carcinoma patients is reproducibly different from healthy controls, as shown by a radar plot comparing the differential levels of selected proteins.
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Network-based drug repositioning

Mol. BioSyst., 2013, 9,1268-1281
DOI: 10.1039/C3MB25382A, Review Article

Zikai Wu, Yong Wang, Luonan Chen
We unified the single drug repositioning and drug combinations into one framework and summarized the recent progresses by the network concept.
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Large-scale investigation of oxygen response mutants in Saccharomyces cerevisiae

Mol. BioSyst., 2013, 9,1351-1359
DOI: 10.1039/C3MB25516F, Paper

Bahram Samanfar, Katayoun Omidi, Mohsen Hooshyar, Ben Laliberte, MD Alamgir, Andrew J. Seal, Eman Ahmed-Muhsin, Duber Frey Viteri, Kamaleldin Said, Firoozeh Chalabian, Ardeshir Golshani, Gabriel Wainer, Daniel Burnside, Kristina Shostak, Magdalena Bugno, William G. Willmore, Myron L. Smith, Ashkan Golshani
A genome-wide screen of a yeast non-essential gene-deletion library was used to identify sick phenotypes due to oxygen deprivation.
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Biomarkers of food intake and metabolite differences between plasma and red blood cell matrices; a human metabolomic profile approach

Mol. BioSyst., 2013, 9,1411-1422
DOI: 10.1039/C3MB25554A, Paper

Ursula Catalan, Miguel-Angel Rodriguez, Maria-Rosa Ras, Alba Macia, Roger Mallol, Maria Vinaixa, Sara Fernandez-Castillejo, Rosa-Maria Valls, Anna Pedret, Julian L Griffin, Reza Salek, Xavier Correig, M ^a Jose Motilva, Rosa Sola
Untargeted metabolomic analyses of plasma and red blood cells (RBCs) can provide complementary information on biomarkers of food consumption.
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Postnatal cardiomyocyte growth and mitochondrial reorganization cause multiple changes in the proteome of human cardiomyocytes

Mol. BioSyst., 2013, 9,1210-1219
DOI: 10.1039/C3MB25556E, Paper

Jaakko L. O. Pohjoismaki, Marcus Kruger, Natalie Al-Furoukh, Anssi Lagerstedt, Pekka J. Karhunen, Thomas Braun
Comparison of fetal and adult human heart proteomes reflects the structural and biochemical differences between the two.
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Metabolomic investigation of Arthus reaction in a rat model using proton nuclear magnetic resonance (1H NMR) spectroscopy and rapid resolution liquid chromatography (RRLC)

Mol. BioSyst., 2013, 9,1423-1435
DOI: 10.1039/C3MB25412G, Paper

Xiaoli Zhang, Jianmin Shen, Bei Cao, Luan Xu, Tong Zhao, Xiaoyan Liu, Haixia Zhang
Arthus reaction (AR), a type of unconventional immune complex-mediated inflammation, is likely accompanied by alterations in circulating metabolites.
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Some remarks on predicting multi-label attributes in molecular biosystems

Mol. BioSyst., 2013, 9,1092-1100
DOI: 10.1039/C3MB25555G, Review Article

Kuo-Chen Chou
Many molecular biosystems and biomedical systems belong to the multi-label systems in which each of their constituent molecules possesses one or more than one function or feature, and hence needs one or more than one label to indicate its attribute(s).
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Solution conformational features and interfacial properties of an intrinsically disordered peptide coupled to alkyl chains: a new class of peptide amphiphiles

Mol. BioSyst., 2013, 9,1401-1410
DOI: 10.1039/C3MB25507G, Paper

Antonella Accardo, Marilisa Leone, Diego Tesauro, Rosa Aufiero, Anais Benarouche, Jean-Francois Cavalier, Sonia Longhi, Frederic Carriere, Filomena Rossi
The first investigation of the behavior of intrinsically disordered peptide are reported as a polar head connected to alkyl chains.
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Metabolomics of developing zebrafish embryos using gas chromatography- and liquid chromatography-mass spectrometry

Mol. BioSyst., 2013, 9,1372-1380
DOI: 10.1039/C3MB25450J, Paper

Shao-Min Huang, Fengguo Xu, Siew Hong Lam, Zhiyuan Gong, Choon Nam Ong
Metabolomics using GC/MS and LC/MS revealed significant small molecule changes including amino acids, carbohydrates and lipids during zebrafish embryogenesis.
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A comprehensive analysis of the influence of drug binding kinetics on drug action at molecular and systems levels

Mol. BioSyst., 2013, 9,1381-1389
DOI: 10.1039/C3MB25471B, Paper

Ning Yin, Jianfeng Pei, Luhua Lai
A comprehensive computational analysis at molecular and network levels exemplifies the importance of binding kinetics in various drug properties.
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Topological patterns in microRNA-gene regulatory network: studies in colorectal and breast cancer

Mol. BioSyst., 2013, 9,1360-1371
DOI: 10.1039/C3MB25518B, Paper

Debarka Sengupta, Sanghamitra Bandyopadhyay
Breast and colorectal cancer specific microRNA-gene network is used to study the intrinsic topological patterns involved in disease pathogenesis.
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JAK/STAT signalling - an executable model assembled from molecule-centred modules demonstrating a module-oriented database concept for systems and synthetic biology

Mol. BioSyst., 2013, 9,1290-1307
DOI: 10.1039/C3MB25593J, Paper

Mary Ann Blatke, Anna Dittrich, Christian Rohr, Monika Heiner, Fred Schaper, Wolfgang Marwan
Modules consisting of a Petri net with associated metadata each describing the reaction mechanisms of one given protein can be automatically composed into a kinetic model of a regulatory network.
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A Boolean view separates platelet activatory and inhibitory signalling as verified by phosphorylation monitoring including threshold behaviour and integrin modulation

Mol. BioSyst., 2013, 9,1326-1339
DOI: 10.1039/C3MB25597B, Paper

Marcel Mischnik, Desislava Boyanova, Katharina Hubertus, Jorg Geiger, Nicole Philippi, Marcus Dittrich, Gaby Wangorsch, Jens Timmer, Thomas Dandekar
Platelet activation and inhibition is studied by Boolean and first dynamic models.
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Secretome analysis of Glioblastoma cell line - HNGC-2

Mol. BioSyst., 2013, 9,1390-1400
DOI: 10.1039/C3MB25383J, Paper

Manoj Kumar Gupta, Ravindra Varma Polisetty, Kalidoss Ramamoorthy, Shivani Tiwary, Navjot Kaur, Megha S. Uppin, Anjali Shiras, Ravi Sirdeshmukh
HNGC-2 cell secretome analysis revealed tumor-associated proteins and pathways useful for clinical applications.
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Homology modeling of dihydrofolate reductase from T. gondii bonded to antagonists: molecular docking and molecular dynamics simulations

Mol. BioSyst., 2013, 9,1308-1315
DOI: 10.1039/C3MB25530A, Paper

Debora Pacheco Homem, Rogerio Flores, Priscilla Tosqui, Thiago de Castro Rozada, Ernani Abicht Basso, Arquimedes Gasparotto Junior, Flavio Augusto Vicente Seixas
Deep computational approach was used to solve the tertiary structure of the DHFR enzyme as a target for discovery of new drug candidates against toxoplasmosis.
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Rapid mass spectrometric determination of disulfide connectivity in peptides and proteins

Mol. BioSyst., 2013, 9,1340-1350
DOI: 10.1039/C3MB25534D, Paper

Moitrayee Bhattacharyya, Kallol Gupta, Konkallu Hanumae Gowd, Padmanabhan Balaram
Determination of disulfide connectivity in peptides and proteins through direct mass spectrometric gas-phase fragmentation, in unison with solution-phase proteolysis.
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Prediction of human genes and diseases targeted by xenobiotics using predictive toxicogenomic-derived models (PTDMs)

Mol. BioSyst., 2013, 9,1316-1325
DOI: 10.1039/C3MB25309K, Paper

Feixiong Cheng, Weihua Li, Yadi Zhou, Jie Li, Jie Shen, Philip W. Lee, Yun Tang
A computational-systems toxicology framework of Predictive Toxicogenomics-Derived Models was built to prioritize human genes and diseases targeted by Xenobiotics.
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Red blood cell metabolism under prolonged anaerobic storage

Mol. BioSyst., 2013, 9,1196-1209
DOI: 10.1039/C3MB25575A, Paper

Angelo D'Alessandro, Federica Gevi, Lello Zolla
MS-based untargeted metabolomics confirmed oxygen dependent modulation of red blood cell metabolism.
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Essential genes in Bacillus subtilis: a re-evaluation after ten years

Mol. BioSyst., 2013, 9,1068-1075
DOI: 10.1039/C3MB25595F, Review Article

Fabian M. Commichau, Nico Pietack, Jorg Stulke
An overview of essential genes in Bacillus subtilis with emphasis on changes in the list of essential genes since 2003.
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Unravelling the bull fertility proteome

Mol. BioSyst., 2013, 9,1188-1195
DOI: 10.1039/C3MB25494A, Paper

Alessio Soggiu, Cristian Piras, Hany Ahmed Hussein, Michele De Canio, Alessandro Gaviraghi, Andrea Galli, Andrea Urbani, Luigi Bonizzi, Paola Roncada
A representative 2-DE map of a cryopreserved bull semen sample. Differentially expressed proteins are indicated in the map.
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Alteration of proteomic profiles in PBMC isolated from patients with Fabry disease: preliminary findings

Mol. BioSyst., 2013, 9,1162-1168
DOI: 10.1039/C3MB25402J, Paper

Diego Cigna, Claudia D'Anna, Carmela Zizzo, Daniele Francofonte, Iacopo Sorrentino, Paolo Colomba, Giuseppe Albeggiani, Alessandro Armini, Laura Bianchi, Luca Bini, Giovanni Duro
In Fabry patients, we found, by a proteomic approach, some down-regulated proteins (CALX, Rho GDI2, Rho GDI1, NCC27) and others upregulated (NSE, 1433T, 1433Z, Gal-1). These data could be related to pathophysiological aspects of disease.
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Effect of IR laser on myoblasts: a proteomic study

Mol. BioSyst., 2013, 9,1147-1161
DOI: 10.1039/C2MB25398D, Paper

Monica Monici, Francesca Cialdai, Francesco Ranaldi, Paolo Paoli, Francesca Boscaro, Gloriano Moneti, Anna Caselli
IR laser treatment induces a general cytoskeleton reorganization and promotes the myoblast differentiation in vitro.
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Urinary exosomes and diabetic nephropathy: a proteomic approach

Mol. BioSyst., 2013, 9,1139-1146
DOI: 10.1039/C2MB25396H, Paper

F. Raimondo, S. Corbetta, L. Morosi, C. Chinello, E. Gianazza, G. Castoldi, C. Di Gioia, C. Bombardi, A. Stella, C. Battaglia, C. Bianchi, F. Magni, M. Pitto
Label-free LC-MS/MS assessment of differential proteome in urinary exosomes from ZDF diabetic rats, and immunoblotting validation, as exemplified by proteins in the inserts (MUP1, CD10, and PEPD).
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Detection of high molecular weight proteins by MALDI imaging mass spectrometry

Mol. BioSyst., 2013, 9,1101-1107
DOI: 10.1039/C2MB25296A, Method

Veronica Mainini, Giorgio Bovo, Clizia Chinello, Erica Gianazza, Marco Grasso, Giorgio Cattoretti, Fulvio Magni
Detection of high molecular weight proteins on thin tissue sections by imaging mass spectrometry is improved by the use of ferulic acid.
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Comparative proteome profiling of breast tumor cell lines by gel electrophoresis and mass spectrometry reveals an epithelial mesenchymal transition associated protein signature

Mol. BioSyst., 2013, 9,1127-1138
DOI: 10.1039/C2MB25401H, Paper

Daniele Vergara, Pasquale Simeone, Piero del Boccio, Claudia Toto, Damiana Pieragostino, Andrea Tinelli, Raffaele Acierno, Saverio Alberti, Michel Salzet, Gianluigi Giannelli, Paolo Sacchetta, Michele Maffia
In this work, we present a comparative proteome analysis of two breast cancer cell lines providing information about a set of proteins involved in the process of epithelial mesenchymal transition.
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Comparative analyses of stress-responsive genes in Arabidopsis thaliana: insight from genomic data mining, functional enrichment, pathway analysis and phenomics

Mol. BioSyst., 2013, Advance Article
DOI: 10.1039/C3MB70072K, Paper

Mahantesha Naika, Khader Shameer, Ramanathan Sowdhamini
Novel insight into similarity and diversity of functional modules, molecular pathways and plant phenotypes associated with stress-responsive genes in Arabidopsis thaliana.
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Transport of nucleosides in vcCNT facilitated by sodium gradients from Molecular Dynamics Simulations

Mol. BioSyst., 2013, Accepted Manuscript
DOI: 10.1039/C3MB70126C, Paper

Zhiwei Feng, Tingjun Hou, Youyong Li
Nucleosides are required for DNA and RNA synthesis, and the nucleoside adenosine has a function in a variety of signaling processes. Nucleosides require a specialized class of integral membrane proteins,...
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Information content and scalability in signal transduction network reconstruction formats

Mol. BioSyst., 2013, Advance Article
DOI: 10.1039/C3MB00005B, Review Article

Magdalena Rother, Ulrike Munzner, Sebastian Thieme, Marcus Krantz
A brief discussion of the challenges in (global) signal transduction network reconstruction and the pros and cons of current formats.
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Urea in aqueous solution studied by quantum mechanical charge field-molecular dynamics (QMCF-MD)

Mol. BioSyst., 2013, Advance Article
DOI: 10.1039/C3MB25522K, Paper

Alexander K. H. Weiss, Thomas S. Hofer
This work presents a quantum mechanical charge field-molecular dynamics (QMCF-MD) simulation of urea in dilute aqueous solution.
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Human cathelicidin peptide LL37 binds telomeric G-quadruplex

Mol. BioSyst., 2013, Advance Article
DOI: 10.1039/C3MB70030E, Communication

Jagannath Jana, Rajiv Kumar Kar, Anirban Ghosh, Atanu Biswas, Surajit Ghosh, Anirban Bhunia, Subhrangsu Chatterjee
Human telomeric G-quadruplex wears a necklace.
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Influence of PNA containing 8-aza-7-deazaadenine on structure stability and binding affinity of PNA[middle dot]DNA duplex: insights from thermodynamics, counter ion, hydration and molecular dynamics analysis

Mol. BioSyst., 2013, Advance Article
DOI: 10.1039/C3MB25561A, Paper

Sharad K. Gupta, Souvik Sur, Rajendra Prasad Ojha, Vibha Tandon
The modified PNA strand provides sufficient increased binding affinity towards DNA-strand. The MD simulation confirmed that modified duplexes have three hydrogen bonds between DPP-dT base pairs and hydrogen bond distances between DPP-dT are shorter in comparison to A-dT in normal duplex.
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Exploring higher-order EGFR oligomerisation and phosphorylation-a combined experimental and theoretical approach

Mol. BioSyst., 2013, Advance Article
DOI: 10.1039/C3MB70073A, Paper

Noga Kozer, Dipak Barua, Suzanne Orchard, Eduoard C. Nice, Antony W. Burgess, William S. Hlavacek, Andrew H. A. Clayton
Biophysics, biochemistry and rule-based modelling are combined to reveal a positive correlation between higher-order EGF receptor oligomer formation and phosphorylation.
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Identification of calcium binding sites on calsequestrin 1 and their implications for polymerization

Mol. BioSyst., 2013, Advance Article
DOI: 10.1039/C3MB25588C, Paper

Amit Kumar, Harapriya Chakravarty, Naresh C. Bal, Tuniki Balaraju, Nivedita Jena, Gauri Misra, Chandralata Bal, Enrico Pieroni, Muthu Periasamy, Ashoke Sharon
Sites of Ca²⁺ binding on the CASQ1 back-to-back dimer.
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Genome-scale reconstruction and in silico analysis of Aspergillus terreus metabolism

Mol. BioSyst., 2013, Advance Article
DOI: 10.1039/C3MB70090A, Paper

Jie Liu, Qian Gao, Nan Xu, Liming Liu
The genome-scale metabolic model well characterized the metabolism of A. terreus.
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Social networks to biological networks: systems biology of Mycobacterium tuberculosis

Mol. BioSyst., 2013, Advance Article
DOI: 10.1039/C3MB25546H, Review Article

Rohit Vashisht, Anshu Bhardwaj, OSDD Consortium, Samir K. Brahmachari
Contextualizing relevant information to construct a network that represents a given biological process presents a fundamental challenge in the network science of biology.
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Biomarkers for Early Diagnosis of Type 2 Diabetic Nephropathy: a Study Based on Integrated Biomarker System

Mol. BioSyst., 2013, Accepted Manuscript
DOI: 10.1039/C3MB25543C, Paper

Min Huang, Qionglin Liang, Ping Li, Jianfei Xia, Yong Wang, Ping Hu, Zhiting Jiang, Yongxin He, Liqiong Pang, Lida Han, Yiming Wang, Guo-An Luo
Diabetic nephropathy is a devastating disease that affects more and more diabetic patients. And complete cure is very hard to achieve once the disease is diagnosed in current medical conditions....
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Oxidative status interactome map: towards novel approaches in experiment planning, data analysis, diagnostics and therapy

Mol. BioSyst., 2013, Accepted Manuscript
DOI: 10.1039/C3MB70096H, Paper

Peter Zolotukhin, Yulia Kozlova, Anastasiya Dovzhik, Konstantin Kovalenko, Kseniya Kutsyn, Anzhela Alexsandrova, Tatyana Shkurat
Experimental evidence suggests an immense variety of processes associated with and aimed at producing reactive oxygen and/or nitrogen species. Clinical studies implicate an enormous range of pathologies associated with reactive...
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Transcriptional feedback in the insulin signalling pathway modulates ageing in both Caenorhabditis elegans and Drosophila melanogaster

Mol. BioSyst., 2013, Advance Article
DOI: 10.1039/C3MB25485B, Paper

Dobril K. Ivanov, Irene Papatheodorou, Matthias Ziehm, Janet M. Thornton
Using manually curated signalling models of the IIS/TOR pathways, transcriptional feedback is shown to modulate ageing in worms and flies.
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Synthesizing oncogenic signal-processing systems that function as both "signal counters" and "signal blockers" in cancer cells

Mol. BioSyst., 2013, Advance Article
DOI: 10.1039/C3MB70093C, Paper

Yuchen Liu, Weiren Huang, Dexi Zhou, Yonghua Han, Yonggang Duan, Xiaoyue Zhang, Hu Zhang, Zhimao Jiang, Yaoting Gui, Zhiming Cai
Here, we provide two scalable translational synthetic regulatory systems that count the intensity of oncogenic signal in cancer cells and trigger apoptosis without affecting normal cells.
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The Mitochondrial Italian Human Proteome Project Initiative (mt-HPP)

Mol. BioSyst., 2013, Accepted Manuscript
DOI: 10.1039/C3MB70065H, Review Article

Andrea Urbani, Michele De Canio
Mitochondria carry maternally inherited genetic material, called the mitochondrial genome (mtDNA) which can be defined as the 25th Human Chromosome. The chromosome-centric Human Proteome Project (c-HPP) has initially focused its...
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Genomics and proteomics in solving brain complexity

Mol. BioSyst., 2013, Advance Article
DOI: 10.1039/C3MB25391K, Review Article

Beena M. Kadakkuzha, Sathyanarayanan V. Puthanveettil
The human brain is extraordinarily complex, composed of billions of neurons and trillions of synaptic connections.
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In silico investigation and targeting of amyloid [small beta] oligomers of different size.

Mol. BioSyst., 2013, Accepted Manuscript
DOI: 10.1039/C3MB70086K, Paper

Ida Autiero, Michele Saviano, Emma Langella
Aggregation of Amyloid [small beta] (A[small beta]) peptide into fibrils has been implicated in the pathogenesis of Alzheimer's disease (AD). As a result, in recent years, substantial efforts have been expended in...
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Mechanism of action-based classification of antibiotics using high-content bacterial image analysis

Mol. BioSyst., 2013, Advance Article
DOI: 10.1039/C3MB70027E, Paper

Kelly C. Peach, Walter M. Bray, Dustin Winslow, Peter F. Linington, Roger G. Linington
This bacterial image analysis platform measures dose-dependent phenotypic size and shape metrics and matches the trajectories of these metrics to fit lines to predict antibiotic modes of action.
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Understanding traditional Chinese medicine anti-inflammatory herbal formulae by simulating their regulatory functions in the human arachidonic acid metabolic network

Mol. BioSyst., 2013, Advance Article
DOI: 10.1039/C3MB25605G, Paper

Shuo Gu, Ning Yin, Jianfeng Pei, Luhua Lai
Molecular docking and network simulations were used to reveal the combinatorial effects of traditional Chinese medicines to intervene in disease networks and suggest new herbal combinations.
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