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Molecular BioSystems

Nidhi Singh, Priyanka Shah, Hemlata Dwivedi, Shikha Mishra, Renu Tripathi, Amogh A Sahasrabuddhe, Mohammad Imran Siddiqi
N-Myristoyltransferase (NMT) catalyzes the transfer of myristate to the amino-terminal glycine of a subset of proteins, a co-translational modification involved in trafficking substrate proteins to membrane locations, stabilization and protein-protein interactions. It is a studied and validated pre-clinical drug target for fungal and parasitic infections. In the present study, a machine learning approach, docking studies and CoMFA analysis have been integrated with the objective of translation of knowledge into a pipelined workflow towards the identification of putative hits through the screening of large compound libraries...
October 21, 2016: Molecular BioSystems
Ji-Yong An, Zhu-Hong You, Xing Chen, De-Shuang Huang, Guiying Yan, Da-Fu Wang
Self-interacting proteins (SIPs) play an essential role in cellular functions and the evolution of protein interaction networks (PINs). Due to the limitations of experimental self-interaction proteins detection technology, it is a very important task to develop a robust and accurate computational approach for SIPs prediction. In this study, we propose a novel computational method for predicting SIPs from protein amino acids sequence. Firstly, a novel feature representation scheme based on Local Binary Pattern (LBP) is developed, in which the evolutionary information, in the form of multiple sequence alignments, is taken into account...
October 19, 2016: Molecular BioSystems
Amanda L Mansouri, Laura N Grese, Erica L Rowe, James C Pino, S Chakra Chennubhotla, Arvind Ramanathan, Hugh M O'Neill, Valerie Berthelier, Christopher B Stanley
Proteins imparted with intrinsic disorder conduct a range of essential cellular functions. To better understand the folding and hydration properties of intrinsically disordered proteins (IDPs), we used osmotic stress to induce conformational changes in nuclear co-activator binding domain (NCBD) and activator for thyroid hormone and retinoid receptor (ACTR) separate from their mutual binding. Osmotic stress was applied by the addition of small and polymeric osmolytes, where we discovered that water contributions to NCBD folding always exceeded those for ACTR...
October 18, 2016: Molecular BioSystems
Jeganathan Manivannan, Manjunath Prashanth, Venkatesan Saravana Kumar, Manickaraj Shairam, Jayachandran Subburaj
Since there is no precise therapy for treating vascular calcification by directly targeting the vascular wall, we aim to unveil novel drug targets through mining the molecular effect of a high phosphate environment on vascular cells through computational methods. Here, we hypothesize that manipulation of the vascular pathogenic network by small molecule therapeutics predicted from prior knowledge might offer great promise. With this, we intend to understand the publicly available transcriptomic data of vascular smooth muscle cells and endothelial cells exposed to the high phosphate induced vascular calcification milieu and to re-examine the above published experiments for reasons different from those examined in the previous studies through multilevel systems biological understanding...
October 18, 2016: Molecular BioSystems
Ronald Zielman, Rudmer Postma, Aswin Verhoeven, Floor Bakels, Willebrordus P J van Oosterhout, Axel Meissner, Arn M J M van den Maagdenberg, Gisela M Terwindt, Oleg A Mayboroda, Michel D Ferrari
BACKGROUND: Migraine is a common episodic brain disorder. Treatment options and diagnosis are hampered by an incomplete understanding of disease pathophysiology and the lack of objective diagnostic markers. The aim of this study was to identify biochemical differences characteristic for different subtypes of migraine in cerebrospinal fluid (CSF) of migraine patients using an exploratory (1)H-NMR-based metabolomics approach. METHODS: CSF was obtained, in between migraine attacks, via lumbar puncture from patients with hemiplegic migraine, migraine with aura, migraine without aura, and healthy controls...
October 13, 2016: Molecular BioSystems
Arthitaya Meeprasert, Supot Hannongbua, Nawee Kungwan, Thanyada Rungrotmongkol
Hepatitis C virus (HCV) is a serious cause of liver inflammation, cirrhosis and the development of hepatocellular carcinoma. Its NS3/4A serine protease functions to cleave a specific peptide bond, which is an important step in HCV replication. Thus the NS3/4A protease has become one of the main drug-targets in the design and development of anti-HCV agents. Unfortunately, high mutation rates in HCV have been reported due to the lack of RNA proofreading activity resulting in drug resistance. Herein, all-atom molecular dynamics simulations were employed to understand and illustrate the effects of the NS3/4A D168V mutation on faldaprevir (FDV) and danoprevir (DNV) binding efficiency...
October 12, 2016: Molecular BioSystems
Oveis Jamialahmadi, Ehsan Motamedian, Sameereh Hashemi-Najafabadi
Correction for 'BiKEGG: a COBRA toolbox extension for bridging the BiGG and KEGG databases' by Oveis Jamialahmadi et al., Mol. BioSyst., 2016, DOI: .
October 12, 2016: Molecular BioSystems
Daniel Ian McSkimming, Shima Dastgheib, Timothy R Baffi, Dominic P Byrne, Samantha Ferries, Steven Thomas Scott, Alexandra C Newton, Claire E Eyers, Krzysztof J Kochut, Patrick A Eyers, Natarajan Kannan
Multiple sequence alignments (MSAs) are a fundamental analysis tool used throughout biology to investigate relationships between protein sequence, structure, function, evolutionary history, and patterns of disease-associated variants. However, their widespread application in systems biology research is currently hindered by the lack of user-friendly tools to simultaneously visualize, manipulate and query the information conceptualized in large sequence alignments, and the challenges in integrating MSAs with multiple orthogonal data such as cancer variants and post-translational modifications, which are often stored in heterogeneous data sources and formats...
October 12, 2016: Molecular BioSystems
Kamalika Sen, Arijita Sarkar, Ranjan Kumar Maji, Zhumur Ghosh, Sanjib Gupta, Tapash Chandra Ghosh
Chronic myelogenous leukemia (CML) is a myeloproliferative disorder characterized by increased proliferation or abnormal accumulation of granulocytic cell line without the depletion of their capacity to differentiate. A reciprocal chromosomal translocation proceeding to the 'Philadelphia chromosome', involving the ABL proto-oncogene and BCR gene residing on Chromosome 9 and 22 respectively, is observed to be attributed to CML pathogenesis. Recent studies have been unraveling the crucial role of genomic 'dark matter' or the non-coding repertoire in cancer initiation and progression...
October 12, 2016: Molecular BioSystems
H Chai, J Zhang, G Yang, Z Ma
DNA-binding proteins play a pivotal role in various biological activities. Identification of DNA-binding residues (DBRs) is of great importance for understanding the mechanism of gene regulations and chromatin remodeling. Most traditional computational methods usually construct their predictors on static non-redundant datasets. They excluded many homologous DNA-binding proteins so as to guarantee the generalization capability of their models. However, those ignored samples may potentially provide useful clues when studying protein-DNA interactions, which have not obtained enough attention...
October 12, 2016: Molecular BioSystems
Soujanya D Yelamanchi, Manish Kumar, Anil K Madugundu, Lathika Gopalakrishnan, Gourav Dey, Sandip Chavan, Gajanan Sathe, Premendu P Mathur, Harsha Gowda, Anita Mahadevan, Susarla K Shankar, T S Keshava Prasad
The pineal gland is a neuroendocrine gland located at the center of the brain. It is known to regulate various physiological functions in the body through secretion of the neurohormone melatonin. Comprehensive characterization of the human pineal gland proteome has not been undertaken to date. We employed a high-resolution mass spectrometry-based approach to characterize the proteome of the human pineal gland. A total of 5874 proteins were identified from the human pineal gland in this study. Of these, 5820 proteins were identified from the human pineal gland for the first time...
October 7, 2016: Molecular BioSystems
Sung Hyeon Lee, Seunghyup Jeong, Jua Lee, In Seok Yeo, Myung Jin Oh, Unyong Kim, Sumin Kim, Su Hee Kim, Seung-Yeol Park, Jae-Han Kim, Se Hoon Park, Jung Hoe Kim, Hyun Joo An
Gastric cancer has one of the highest cancer mortality rates worldwide, largely because of difficulties in early-stage detection. Aberrant glycosylation in serum proteins is associated with many human diseases including inflammation and various types of cancer. Serum-based global glycan profiling using mass spectrometry has been explored and has already led to several potential glycan markers for several disease states. However, localization of the aberrant glycosylation is desirable in order to improve the specificity and sensitivity for clinical use...
October 5, 2016: Molecular BioSystems
Rui Hu, Hong-Kin Yap, Yik-Hong Fung, Yong Wang, Wing-Lam Cheong, Lok-Yan So, Chui-Shan Tsang, Lawrence Yoon Suk Lee, Warrick Ken Cheung Lo, Jian Yuan, Ning Sun, Yun-Chung Leung, Guoqiang Yang, Kwok-Yin Wong
Fluorescent labeling of biomacromolecules to 'light up' biological events through non-invasive methods is of great importance, but is still challenging in terms of fluorophore properties and the labeling methods used. Herein, we designed and synthesized a biocompatible and conformation sensitive tetraphenylethene derivative EPB with aggregation induced emission (AIE) properties. By introducing EPB into TEM-1 β-lactamase (TEM-1 Bla) through a two-step approach, a conformation-dependent fluorescent sensor EPB104-Bla was genetically engineered, which was applied to monitor the protein-protein interaction (PPI) with β-lactamase inhibitor protein (BLIP)...
October 4, 2016: Molecular BioSystems
Matthias G Beuerle, Neil P Dufton, Anna M Randi, Ian R Gould
The ETS family of transcription factors regulate gene targets by binding to a core GGAA DNA-sequence. The ETS factor ERG is required for homeostasis and lineage-specific functions in endothelial cells, some subset of haemopoietic cells and chondrocytes; its ectopic expression is linked to oncogenesis in multiple tissues. To date details of the DNA-binding process of ERG including DNA-sequence recognition outside the core GGAA-sequence are largely unknown. We combined available structural and experimental data to perform molecular dynamics simulations to study the DNA-binding process of ERG...
October 3, 2016: Molecular BioSystems
Kourosh Honarmand Ebrahimi, Eckhard Bill, Peter-Leon Hagedoorn, Wilfred R Hagen
Ferritin is a nanocage protein made of 24 subunits. Its major role is to manage intracellular concentrations of free Fe(ii) and Fe(iii) ions, which is pivotal for iron homeostasis across all domains of life. This function of the protein is regulated by a conserved di-iron catalytic center and has been the subject of extensive studies over the past 50 years. Yet, it has not been fully understood how Fe(ii) is oxidized in the di-iron catalytic center and it is not known why eukaryotic and microbial ferritins oxidize Fe(ii) with different kinetics...
September 29, 2016: Molecular BioSystems
Sonali Lokhande, Biranchi N Patra, Animesh Ray
Huntington's disease is a rare neurodegenerative disorder whose complex pathophysiology exhibits system-wide changes in the body, with striking and debilitating clinical features targeting the central nervous system. Among the various molecular functions affected in this disease, mitochondrial dysfunction and transcriptional dysregulation are some of the most studied aspects of this disease. However, there is evidence of the involvement of a mutant Huntingtin protein in the processes of DNA damage, chromosome condensation and DNA repair...
September 29, 2016: Molecular BioSystems
Bartosz Różycki, Marek Cieplak
Cellulosomes are complex multi-enzyme machineries which efficiently degrade plant cell-wall polysaccharides. The multiple domains of the cellulosome proteins are often tethered together by intrinsically disordered regions. The properties and functions of these disordered linkers are not well understood. In this work, we study endoglucanase Cel8A, which is a relevant enzymatic component of the cellulosomes of Clostridium thermocellum. We use both all-atom and coarse-grained simulations to investigate how the conformations of the catalytic domain of Cel8A are affected by the disordered linker at its C terminus...
September 29, 2016: Molecular BioSystems
Luisa A Ferreira, Vladimir N Uversky, Boris Y Zaslavsky
Partition coefficients of non-ionic essentially nonpolar compounds between air and rat biological tissues and between blood and other tissues were examined and found to be linearly interrelated according to the previously established equation for partition coefficients of solutes in aqueous two-phase systems: log Kblood-tissue-1 = k0 + k1 log Kblood-tissue-2 + k2 log Kblood-tissue-3, where k0, k1, and k2 are constants. Analysis of partition coefficients of amphiphilic and ionizable drugs between blood and different tissues in rats in vivo showed that the above relationship holds for the blood-tissue partition coefficients of these compounds as well...
September 28, 2016: Molecular BioSystems
Jyoti Singh Tomar, Manju Narwal, Pravindra Kumar, Rama Krishna Peddinti
The rise of multiple-drug resistance in bacterial pathogens imposes a serious public health concern and has led to increased interest in studying various pathways as well as enzymes. Different DNA glycosylases collaborate during bacterial infection and disease by overcoming the effects of ROS- and RNS-mediated host innate immunity response. 3-Methyladenine DNA glycosylase I, an essential DNA repair enzyme, was chosen for the present study from the MDR species of A. baumannii. The enzyme was especially chosen because of its functional significance in A...
September 26, 2016: Molecular BioSystems
Sudipta Acharya, Sriparna Saha
Distance plays an important role in the clustering process for allocating data points to different clusters. Several distance or proximity measures have been developed and reported in the literature to determine dissimilarities between two given points. The choice of distance measure depends on a particular domain as well as different data sets of the same domain. It is important to automatically determine the appropriate distance measure which acts best for a particular data set. In this study we have developed an automatic clustering technique using the search capability of multiobjective optimization which can automatically determine the relevant distance measure and the corresponding partitioning from a given data set...
September 26, 2016: Molecular BioSystems
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