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Molecular BioSystems

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https://www.readbyqxmd.com/read/28737816/protein-stability-and-dynamics-influenced-by-ligands-in-extremophilic-complexes-a-molecular-dynamics-investigation
#1
Sara Khan, Umar Farooq, Maria Kurnikova
In this study, we explore the structural and dynamic adaptations of the Tryptophan synthase α-subunit in a ligand bound state in psychrophilic, mesophilic and hyperthermophilic organisms at different temperatures by MD simulations. We quantify the global and local fluctuations in the 40 ns time scale by analyzing the root mean square deviation/fluctuations. The distinct behavior of the active site and loop 6 is observed with the elevation of temperature. Protein stability relies more on electrostatic interactions, and these interactions might be responsible for the stability of varying temperature evolved proteins...
July 24, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28737788/a-multiscale-agent-based-framework-integrated-with-a-constraint-based-metabolic-network-model-of-cancer-for-simulating-avascular-tumor-growth
#2
Mehrdad Ghadiri, Mahshid Heidari, Sayed-Amir Marashi, Seyed Hasan Mousavi
In recent years, many efforts have been made in the field of computational modeling of cancerous tumors, in order to obtain a better understanding and predictions of their growth patterns. Furthermore, constraint-based modeling of metabolic networks has become increasingly popular, which is appropriate for the systems-level reconstruction of cell physiology. The goal of the current study is to integrate a multiscale agent-based modeling framework with a constraint-based metabolic network model of cancer cells in order to simulate the three dimensional early growth of avascular tumors...
July 24, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28731097/dba-induced-caspase-3-dependent-apoptosis-occurs-through-mitochondrial-translocation-of-cyt-c-in-the-rat-hippocampus
#3
Wenbo Jiang, Yingying Chen, Bai Li, Shuying Gao
Dibromoacetic acid (DBA), a by-product of disinfection, develops in drinking water during chlorination or ozonation processes. Water intake is the main source of DBA exposure in humans, which is potentially neurotoxic. The present study investigated the neurotoxic effects of DBA by assessing the behavioral and biochemical characteristics of Sprague Dawley rats intragastrically treated with DBA at concentrations of 20, 50 and 125 mg kg(-1) body weight for 28 consecutive days. The results indicated that animal weight gain and food consumption were not significantly affected by DBA...
July 21, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28726959/association-of-cultured-myotubes-and-fasting-plasma-metabolite-profiles-with-mitochondrial-dysfunction-in-type-2-diabetes-subjects
#4
Mohamad Hafizi Abu Bakar, Mohamad Roji Sarmidi
Accumulating evidence implicates mitochondrial dysfunction-induced insulin resistance in skeletal muscle as the root cause for the greatest hallmarks of type 2 diabetes (T2D). However, the identification of specific metabolite-based markers linked to mitochondrial dysfunction in T2D has not been adequately addressed. Therefore, we sought to identify the markers-based metabolomics for mitochondrial dysfunction associated with T2D. First, a cellular disease model was established using human myotubes treated with antimycin A, an oxidative phosphorylation inhibitor...
July 20, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28726924/peculiarities-of-thermal-denaturation-of-ompf-porin-from-yersinia-ruckeri
#5
Olga D Novikova, Dmitry K Chistyulin, Valentina A Khomenko, Evgeny V Sidorin, Natalya Yu Kim, Nina M Sanina, Olga Yu Portnyagina, Tamara F Solov'eva, Vladimir N Uversky, Valery L Shnyrov
Irreversible denaturation of membrane proteins in detergent solutions is similar to unfolding of water-soluble multidomain proteins and represents a complex, multistage process. Pore-forming proteins of Gram-negative bacteria are heat-modifiable proteins, i.e., proteins altering their molecular forms (trimers or monomers), and accordingly, their electrophoretic mobilities depending upon denaturation conditions. There are still some contradictory data on the peculiarities of the conformational changes in the porin structure with temperature...
July 20, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28726921/molecular-dynamics-simulations-and-in-vitro-analysis-of-the-crmp2-thiol-switch
#6
Daniel Möller, Manuela Gellert, Walter Langel, Christopher Horst Lillig
The collapsin response mediator protein CRMP2 (gene: DPYSL2) is crucial for neuronal development. The homotetrameric CRMP2 complex is regulated via two mechanisms: first by phosphorylation and second by the reduction and oxidation of the Cys504 residues of two adjacent subunits. Here, we have analysed the effects of this redox switch on the protein in vitro combined with force field molecular dynamics (MD). Earlier X-ray data reveal the structure of the rigid body of the molecule but lack the flexible C-terminus with the important sites for phosphorylation and redox regulation...
July 20, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28718849/an-efficient-method-to-transcription-factor-binding-sites-imputation-via-simultaneous-completion-of-multiple-matrices-with-positional-consistency
#7
Wei-Li Guo, De-Shuang Huang
Transcription factors (TFs) are DNA-binding proteins that have a central role in regulating gene expression. Identification of DNA-binding sites of TFs is a key task in understanding transcriptional regulation, cellular processes and disease. Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) enables genome-wide identification of in vivo TF binding sites. However, it is still difficult to map every TF in every cell line owing to cost and biological material availability, which poses an enormous obstacle for integrated analysis of gene regulation...
July 18, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28714509/a-comparative-review-of-computational-methods-for-pathway-perturbation-analysis-dynamical-and-topological-perspectives
#8
REVIEW
Q Vanhaelen, A M Aliper, A Zhavoronkov
Stem cells offer great promise within the field of regenerative medicine but despite encouraging results, the large scale use of stem cells for therapeutic applications still faces challenges when it comes to controlling signaling pathway responses with respect to environmental perturbations. This step is critical for the elaboration of stable and reproducible differentiation protocols, and computational modeling can be helpful to overcome these difficulties. This article is a comparative review of the mechanism-based methods used for hypothesis-driven approaches and data-driven methods which are two types of computational approaches commonly used for analysing the dynamics of pathways involved in stem cell regulation...
July 17, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28714505/the-antiproliferative-activity-of-di-2-pyridylketone-dithiocarbamate-is-partly-attributed-to-catalase-inhibition-detailing-the-interaction-by-spectroscopic-methods
#9
Cuiping Li, Youxun Liu, Yun Fu, Tengfei Huang, Lixia Kang, Changzheng Li
The bioactivity of drugs is attributed to their interaction with biological molecules, embodied in either their direct or indirect influence on enzyme activity and conformation. Di-2-pyridylketone hydrazine dithiocarbamate (DpdtC) exhibits significant antitumor activity in our preliminary study. We speculated that its activity may partly stem from enzyme inhibition due to strong metal chelating ability. To this end, we assessed its effect on catalase from erythrocytes and found evidence of inhibition, which was further confirmed by ROS determination in vivo...
July 17, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28714502/insights-into-the-rna-binding-mechanism-of-human-l1-orf1p-a-molecular-dynamics-study
#10
Muthukumaran Rajagopalan, Sangeetha Balasubramanian, Amutha Ramaswamy
The recognition and binding of nucleic acids by ORF1p, an L1 retrotransposon protein, have not yet been clearly understood due to the lack of structural knowledge. The present study attempts to identify the probable single-stranded RNA binding pathway of trimeric ORF1p using computational methods like ligand mapping methodology combined with molecular dynamics simulations. Using the ligand mapping methodology, the possible RNA interacting sites on the surface of the trimeric ORF1p were identified. The crystal structure of the ORF1p timer and an RNA molecule of 29 nucleotide bases in length were used to generate the structure of the ORF1p complex based on information on predicted binding sites as well as the functional states of the CTD...
July 17, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28714501/understanding-the-role-of-tyrosine-in-glycogenin
#11
Ander Camiruaga, Imanol Usabiaga, Aran Insausti, Emilio J Cocinero, Iker León, José A Fernández
We explored the molecular basis of tyrosine as the docking amino acid for the first glucose molecule during the synthesis of glycogen. The IR spectra show that the aromatic ring acts as bait to keep the position where the next glucose unit has to bind clear, by luring non-desirable molecules towards the aromatic ring. Only, α-/β-glucose shows particular affinity for the O3H and O4H moieties.
July 17, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28702665/structural-switch-from-a-multistranded-g-quadruplex-to-single-strands-as-a-consequence-of-point-mutation-in-the-promoter-of-the-human-grin1-gene
#12
Swati Chaudhary, Mahima Kaushik, Ritushree Kukreti, Shrikant Kukreti
A huge number of G-rich sequences forming quadruplexes are found in the human genome, especially in telomeric regions, UTRs, and the promoter regions of a number of genes. One such gene is GRIN1 encoding the NR1 subunit of the N-methyl-d-aspartate receptor (NMDA). Several lines of reports have implicated that attenuated function of NMDA results in schizophrenia, a genetic disorder characterized by hallucinations, delusions, and psychosis. Involvement of the GRIN1 gene in the pathogenesis of schizophrenia has been extensively analysed...
July 12, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28702647/an-enhanced-htert-promoter-driven-crispr-cas9-system-selectively-inhibits-the-progression-of-bladder-cancer-cells
#13
Xinbo Huang, Chengle Zhuang, Changshui Zhuang, Tiefu Xiong, Yawen Li, Yaoting Gui
The current therapies for treating tumors are lacking in efficacy and specificity. Synthetic biology principles may bring some new possible methods for curing cancer. Here we present a synthetic logic circuit based on the CRISPR/Cas9 system. The CRISPR/Cas9 technology has been applied in many biological fields, including cancer research. In this study, the expression of Cas9 nuclease was controlled indirectly by an enhanced hTERT promoter using the GAL4/upstream activating sequence (UAS) binding system. Cas9 was driven by 5XUAS, single guide RNA (sgRNA) was used to target mutant or wild-type HRAS, and the fusion gene GAL4-P65 was driven by the enhanced hTERT promoter...
July 12, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28702621/identification-of-perturbed-signaling-pathways-from-gene-expression-data-using-information-divergence
#14
Xinying Hu, Hang Wei, Haoran Zheng
Abnormal regulation of signaling pathways is the key causative factor in several diseases. Although many methods have been proposed to identify significantly differential pathways between two conditions via microarray gene expression datasets, most of them concentrate on differences in the pathway components-either the differential expression or the correlation of genes in a given pathway. However, as biological functional units, signaling pathways may have diverse activity patterns across different biological contexts...
July 12, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28702594/lpi-etslp-lncrna-protein-interaction-prediction-using-eigenvalue-transformation-based-semi-supervised-link-prediction
#15
Huan Hu, Chunyu Zhu, Haixin Ai, Li Zhang, Jian Zhao, Qi Zhao, Hongsheng Liu
RNA-protein interactions are essential for understanding many important cellular processes. In particular, lncRNA-protein interactions play important roles in post-transcriptional gene regulation, such as splicing, translation, signaling and even the progression of complex diseases. However, the experimental validation of lncRNA-protein interactions remains time-consuming and expensive, and only a few theoretical approaches are available for predicting potential lncRNA-protein associations. Here, we presented eigenvalue transformation-based semi-supervised link prediction (LPI-ETSLP) to uncover the relationship between lncRNAs and proteins...
July 12, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28702580/ploc-mplant-predict-subcellular-localization-of-multi-location-plant-proteins-by-incorporating-the-optimal-go-information-into-general-pseaac
#16
Xiang Cheng, Xuan Xiao, Kuo-Chen Chou
One of the fundamental goals in cellular biochemistry is to identify the functions of proteins in the context of compartments that organize them in the cellular environment. To realize this, it is indispensable to develop an automated method for fast and accurate identification of the subcellular locations of uncharacterized proteins. The current study is focused on plant protein subcellular location prediction based on the sequence information alone. Although considerable efforts have been made in this regard, the problem is far from being solved yet...
July 12, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28702565/identifying-the-common-genetic-networks-of-adr-adverse-drug-reaction-clusters-and-developing-an-adr-classification-model
#17
Youhyeon Hwang, Min Oh, Giup Jang, Taekeon Lee, Chihyun Park, Jaegyoon Ahn, Youngmi Yoon
Adverse drug reactions (ADRs) are one of the major concerns threatening public health and have resulted in failures in drug development. Thus, predicting ADRs and discovering the mechanisms underlying ADRs have become important tasks in pharmacovigilance. Identification of potential ADRs by computational approaches in the early stages would be advantageous in drug development. Here we propose a computational method that elucidates the action mechanisms of ADRs and predicts potential ADRs by utilizing ADR genes, drug features, and protein-protein interaction (PPI) networks...
July 12, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28692085/functional-roles-of-intrinsic-disorder-in-crispr-associated-protein-cas9
#18
Zhihua Du, Vladimir N Uversky
Protein intrinsic disorder is an important characteristic commonly detected in multifunctional or RNA- and DNA-binding proteins. Due to their high conformational flexibility and solvent accessibility, intrinsically disordered proteins (IDPs) and IDP regions (IDPRs) execute diverse functions including interaction with multiple partners, and are frequently subjected to various post-translational modifications. Recent studies on the components comprising the CRISPR (clustered regularly interspaced short palindromic repeats) system have elucidated the crystal structure of Cas9 proteins and the mechanism by which the Cas9-sgRNA complex recognizes and cleaves its target DNA...
July 10, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28692078/modeling-of-alcohol-oxidase-enzyme-of-candida-boidinii-and-in-silico-analysis-of-competitive-binding-of-proton-ionophores-and-fad-with-enzyme
#19
Mohammad Wahab Khan, Ayaluru Murali
Alcohol oxidase (AOX) is an important flavin adenine dinucleotide (FAD) dependent oxidoreductase, which is responsible for converting methanol into formaldehyde and hydrogen peroxide for the growth of methylotrophic yeast Candida boidinii. Although AOX plays a crucial role in methanol catabolism, the experimental structure of AOX from Candida boidinii has not been elucidated. This study reports the first complete in silico model of AOX from C. boidinii. This paper also reports the AOX structure modeled using the threading approach, followed by structure analysis and molecular dynamics simulation...
July 10, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28686281/identification-of-microrna-precursors-using-reduced-and-hybrid-features
#20
Asad Khan, Sajid Shah, Fazli Wahid, Fiaz Gul Khan, Saima Jabeen
MicroRNAs (also called miRNAs) are a group of short non-coding RNA molecules. They play a vital role in the gene expression of transcriptional and post-transcriptional processes. However, abnormality of their expression has been observed in cancer, heart diseases and nervous system disorders. Therefore for basic research and microRNA based therapy, it is imperative to separate real pre-miRNAs from false ones (hairpin sequences similar to pre-miRNA stem loops). Different conservation and machine learning methods have been applied for the identification of miRNAs...
July 7, 2017: Molecular BioSystems
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