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Molecular BioSystems

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https://www.readbyqxmd.com/read/28642958/phosphorylation-of-a-full-length-amyloid-%C3%AE-peptide-modulates-its-amyloid-aggregation-cell-binding-and-neurotoxic-properties
#1
Elaheh Jamasbi, Frances Separovic, Mohammed Akhter Hossain, Giuseppe Donato Ciccotosto
Amyloid beta peptide (Aβ) is the major protein component of the amyloid plaques that are present in the brains of Alzheimer's disease (AD) patients. Aβ42 peptide is a known neurotoxic agent that binds to neurons and, under specific aggregation conditions, triggers cell death. Aβ peptide can undergo specific amino acid posttranslational modifications, such as phosphorylation, that are important for modulating its proteolytic degradation, aggregation, binding to lipid membranes and neurotoxic functions. Peptides phosphorylated at serine 8 in full-length Aβ42 (pAβ42) were synthesised and compared to native Aβ42 peptide...
June 23, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28640309/computational-analysis-of-histidine-mutations-on-the-structural-stability-of-human-tyrosinases-leading-to-albinism-insurgence
#2
Mubashir Hassan, Qamar Abbas, Hussain Raza, Ahmed A Moustafa, Sung-Yum Seo
Misfolding and structural alteration in proteins lead to serious malfunctions and cause various diseases in humans. Mutations at the active binding site in tyrosinase impair structural stability and cause lethal albinism by abolishing copper binding. To evaluate the histidine mutational effect, all mutated structures were built using homology modelling. The protein sequence was retrieved from the UniProt database, and 3D models of original and mutated human tyrosinase sequences were predicted by changing the residual positions within the target sequence separately...
June 22, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28636047/decoding-the-regulatory-mechanism-of-glucose-and-insulin-induced-phosphatidylinositol-3-4-5-trisphosphate-dynamics-in-%C3%AE-cells
#3
Tagari Samanta, Peeyush Sharma, Dwijendra Kukri, Sandip Kar
In MIN6 pancreatic β-cells, glucose and insulin act in a synergistic manner to regulate the dynamics of Phosphatidylinositol (3,4,5)-trisphosphate (PIP3). However, the precise regulatory mechanism behind such an experimentally observed synergy is poorly understood. In this article, we propose a phenomenological mathematical model for studying the glucose and insulin driven PIP3 activation dynamics under various stimulatory conditions to unfold the mechanism responsible for the observed synergy. The modeling study reveals that the experimentally observed oscillation in PIP3 dynamics with disparate time scales for different external glucose doses is mainly orchestrated by the complex dynamic regulation of cytosolic Ca(2+) in β-cells...
June 21, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28636007/analysis-of-association-of-gene-variants-with-obesity-traits-in-new-zealand-european-children-at-6-years-of-age
#4
Mohanraj Krishnan, John M D Thompson, Edwin A Mitchell, Rinki Murphy, Lesley M E McCowan, Andrew N Shelling, G On Behalf Of The Children Of Scope Study Group
Childhood obesity is a public health problem, which is associated with a long-term increased risk of cardiovascular disease and premature mortality. Several gene variants have previously been identified that have provided novel insights into biological factors that contribute to the development of obesity. As obesity tracks through childhood into adulthood, identification of the genetic factors for obesity in early life is important. The objective of this study was to identify putative associations between genetic variants and obesity traits in children at 6 years of age...
June 21, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28632266/proteomic-analysis-reveals-xuesaitong-injection-attenuates-myocardial-ischemia-reperfusion-injury-by-elevating-pyruvate-dehydrogenase-mediated-aerobic-metabolism
#5
Xiaoping Zhao, Feng Zhang, Yi Wang
Xuesaitong injection (XST), which mainly consists of Panax notoginseng saponins, has been widely used for treating cardio-cerebral vascular diseases. However, the underlying mechanisms of XST associated with its cardioprotective effects are still unclear. To identify the potential target proteins of XST, two-dimensional gel electrophoresis (2-DE)-based proteomics was utilized to analyze the protein profile of myocardium in rats with myocardial ischemia/reperfusion (I/R) injury. The differentially expressed proteins were identified by matrix assisted laser desorption/ionization time-of-flight mass spectrometry...
June 20, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28627567/dissecting-binding-of-a-%C3%AE-barrel-membrane-protein-by-phage-display
#6
Luz M Meneghini, Sarvind Tripathi, Marcus A Woodworth, Sudipta Majumdar, Thomas L Poulos, Gregory A Weiss
Membrane proteins (MPs) constitute a third of all proteomes, and contribute to a myriad of cellular functions including intercellular communication, nutrient transport and energy generation. For example, TonB-dependent transporters (TBDTs) in the outer membrane of Gram-negative bacteria play an essential role transporting iron and other nutrients into the bacterial cell. The inherently hydrophobic surfaces of MPs complicates protein expression, purification, and characterization. Thus, dissecting the functional contributions of individual amino acids or structural features through mutagenesis can be a challenging ordeal...
June 19, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28621357/computational-investigation-of-the-human-sod1-mutant-cys146arg-that-directs-familial-amyotrophic-lateral-sclerosis
#7
E Srinivasan, R Rajasekaran
The genetic substitution mutation of Cys146Arg in the SOD1 protein is predominantly found in the Japanese population suffering from familial amyotrophic lateral sclerosis (FALS). A complete study of the biophysical aspects of this particular missense mutation through conformational analysis and producing free energy landscapes could provide an insight into the pathogenic mechanism of ALS disease. In this study, we utilized general molecular dynamics simulations along with computational predictions to assess the structural characterization of the protein as well as the conformational preferences of monomeric wild type and mutant SOD1...
June 16, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28612854/fragile-x-mental-retardation-protein-recognizes-a-g-quadruplex-structure-within-the-survival-motor-neuron-domain-containing-1-mrna-5-utr
#8
Damian S McAninch, Ashley M Heinaman, Cara N Lang, Kathryn R Moss, Gary J Bassell, Mihaela Rita Mihailescu, Timothy L Evans
G quadruplex structures have been predicted by bioinformatics to form in the 5'- and 3'-untranslated regions (UTRs) of several thousand mature mRNAs and are believed to play a role in translation regulation. Elucidation of these roles has primarily been focused on the 3'-UTR, with limited focus on characterizing the G quadruplex structures and functions in the 5'-UTR. Investigation of the affinity and specificity of RNA binding proteins for 5'-UTR G quadruplexes and the resulting regulatory effects have also been limited...
June 14, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28604872/predicting-protein-protein-interactions-from-protein-sequences-by-a-stacked-sparse-autoencoder-deep-neural-network
#9
Yan-Bin Wang, Zhu-Hong You, Xiao Li, Tong-Hai Jiang, Xing Chen, Xi Zhou, Lei Wang
Protein-protein interactions (PPIs) play an important role in most of the biological processes. How to correctly and efficiently detect protein interaction is a problem that is worth studying. Although high-throughput technologies provide the possibility to detect large-scale PPIs, these cannot be used to detect whole PPIs, and unreliable data may be generated. To solve this problem, in this study, a novel computational method was proposed to effectively predict the PPIs using the information of a protein sequence...
June 12, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28604846/identification-of-active-components-in-yixinshu-capsule-with-protective-effects-against-myocardial-dysfunction-on-human-induced-pluripotent-stem-cell-derived-cardiomyocytes-by-an-integrative-approach
#10
Minyu Zhang, Hongwei Wu, Feifei Guo, Yangyang Yu, Junying Wei, Ya Geng, Shifeng Wang, Shiyou Li, Hongjun Yang
Traditional Chinese medicine (TCM) preparations have significant effects on some refractory diseases; however, these compositions are complex and their mechanisms are unknown. Identification of the active components in these preparations is essential. The mortality rate for heart failure (HF) has been increasing in recent years, and myocardial dysfunction (MD) has been proved to be the pathological basis of HF. Yixinshu Capsule (YXSC) is a multi-component oral drug with therapeutic effects on HF. However, the key active components are still unclear...
June 12, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28590495/structure-based-design-of-novel-combinatorially-generated-nbtis-as-potential-dna-gyrase-inhibitors-against-various-staphylococcus-aureus-mutant-strains
#11
Anja Kolaric, Nikola Minovski
Although intercalating agents such as quinolones have had proven therapeutic success as antibacterial agents for more than 40 years, new forms of quinolone-based resistance in bacteria are continually emerging. To alleviate this problem, a new class of antibacterials is urgently needed; recently, novel bacterial topoisomerase inhibitors (NBTIs) have been found to be particularly important. Based on 67 experimentally evaluated NBTIs against wild-type (WT) DNA gyrase originating from Staphylococcus aureus, a predictive QSAR model was initially constructed and validated and was later used for in silico prediction of biological activities for an in house designed compound library of 548 novel drug-like NBTI combinatorial analogs...
June 7, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28581007/literature-based-prediction-of-novel-drug-indications-considering-relationships-between-entities
#12
Giup Jang, Taekeon Lee, Byung Mun Lee, Youngmi Yoon
There have been many attempts to identify and develop new uses for existing drugs, which is known as drug repositioning. Among these efforts, text mining is an effective means of discovering novel knowledge from a large amount of literature data. We identify a gene regulation by a drug and a phenotype based on the biomedical literature. Drugs or phenotypes can activate or inhibit gene regulation. We calculate the therapeutic possibility that a drug acts on a phenotype by means of these two types of regulation...
June 5, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28581003/mathematical-modeling-reveals-differential-regulation-of-mapk-activity-by-phosphatase-proteins-in-the-yeast-pheromone-response-pathway
#13
Nathan Dyjack, Cassandra Azeredo-Tseng, Necmettin Yildirim
To prevent indefinite cellular responses to external signals, cells utilize various adaptation mechanisms. The yeast mating-response pathway is a model cellular system that exhibits adaptation to persistent external signals. This pathway employs a mitogen-activated protein kinase (MAPK) cascade which is composed of two well-known negative feedback inhibitions that involve the yeast phosphatase proteins Ptp3 and Msg5. The phosphorylated form of the yeast MAPK protein Fus3 (pFus3) triggers the phosphorylation of both phosphatases, but transcriptionally upregulates only Msg5...
June 5, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28573295/what-shapes-eukaryotic-transcriptional-bursting
#14
REVIEW
Damien Nicolas, Nick E Phillips, Felix Naef
Isogenic cells in a common environment present a large degree of heterogeneity in gene expression. Part of this variability is attributed to transcriptional bursting: the stochastic activation and inactivation of promoters that leads to the discontinuous production of mRNA. The diversity in bursting patterns displayed by different genes suggests the existence of a connection between bursting and gene regulation. Experimental strategies such as single-molecule RNA FISH, MS2-GFP or short-lived protein reporters allow the quantification of transcriptional bursting and the comparison of bursting kinetics between conditions, allowing therefore the identification of molecular mechanisms modulating transcriptional bursting...
June 2, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28573283/the-effect-of-global-transcriptional-regulators-on-the-anaerobic-fermentative-metabolism-of-escherichia-coli
#15
Manika Kargeti, K V Venkatesh
Global transcription factors are known to regulate the anaerobic growth of Escherichia coli on glucose. These transcription factors help the organism to sense oxygen and accordingly regulate the synthesis of mixed acid producing enzymes. Five global transcription factors, namely ArcA, Fnr, IhfA-B, Crp and Fis, are known to play an important role in the growth phenotype of the organism in the transition from anaerobic to aerobic conditions. The effect of deletion of most of these global transcription factors on the growth phenotype has not been characterized under strict anaerobic fermentation conditions...
June 2, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28561845/dynamic-properties-of-the-growth-hormone-releasing-hormone-receptor-ghrhr-and-molecular-determinants-of-ghrh-binding
#16
M-T Matsoukas, G A Spyroulias
The growth hormone-releasing hormone receptor (GHRHR) is a member of the class B GPCR subfamily. GHRH, a 44-residue neuropeptide produced in the hypothalamus, regulates the secretion of growth hormone through its binding to GHRHR. It has recently been associated with several types of cancer such as prostate, breast, pancreatic and ovarian cancer. Family B GPCR peptides bind in a two-step model, where first the C-terminal region of the peptide interacts with the extracellular domain (ECD) of the receptor and subsequently, the N-terminal interacts with the seven transmembrane domain (TMD), resulting in activation...
May 31, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28561835/vhfrnai-a-web-platform-for-analysis-of-host-genes-involved-in-viral-infections-discovered-by-genome-wide-rnai-screens
#17
Anamika Thakur, Abid Qureshi, Manoj Kumar
Knockdown of host genes using high-throughput genome-wide RNA interference screens has identified numerous host factors that affect viral infections, which would be helpful in understanding host-virus interactions. We have developed a vhfRNAi web resource based on genome-wide RNAi experiments for viruses. It contains experimental details of 12 249 entries (host factors + restriction factors) for 18 viruses. Simultaneously, this resource encompasses analysis of overlapping genes, genome wide association studies, gene ontology (GO), pathogen interacting proteins, interaction networks and pathway enrichment...
May 31, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28548163/crystal-structure-of-aquifex-aeolicus-gene-product-aq1627-a-putative-phosphoglucosamine-mutase-reveals-a-unique-c-terminal-end-to-end-disulfide-linkage
#18
Upasana Sridharan, Seiki Kuramitsu, Shigeyuki Yokoyama, Thirumananseri Kumarevel, Karthe Ponnuraj
The Aq1627 gene from Aquifex aeolicus, a hyperthermophilic bacterium has been cloned and overexpressed in Escherichia coli. The protein was purified to homogeneity and its X-ray crystal structure was determined to 1.3 Å resolution using multiple wavelength anomalous dispersion phasing. The structural and sequence analysis of Aq1627 is suggestive of a putative phosphoglucosamine mutase. The structural features of Aq1627 further indicate that it could belong to a new subclass of the phosphoglucosamine mutase family...
May 26, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28540949/structure-based-in-silico-identification-of-potentially-non-steroidal-brassinosteroids-mimics
#19
Beilei Lei, Ningjuan Heng, Xiaoxue Dang, Jiyuan Liu, Xiaojun Yao, Cunli Zhang
Brassinosteroids (BRs) are a class of plant steroid hormones that play indispensable roles in cell elongation, division and plant development. To date, the numerous synthesis of BRs analogs and structure-activity relationship investigations have clearly revealed the key substituent groups relevant to the steroidal activity of BRs. However, due to the limited chemical space studied, the efforts for alternative non-steroidal compounds have produced no remarkable results. To identify potentially non-steroidal BR mimics in this study, vital interacting pharmacophore features were extracted starting from several complex structures of BRs that bound with the receptor Brassinosteroid-Insentive 1 (BRI1) and co-receptor BRI1-associated kinase 1 (BAK1), which were characterized and merged into one comprehensive pharmacophore model...
May 25, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28534914/covalent-inhibition-of-protein-tyrosine-phosphatases
#20
REVIEW
Kasi Viswanatharaju Ruddraraju, Zhong-Yin Zhang
Protein tyrosine phosphatases (PTPs) are a large family of 107 signaling enzymes that catalyze the hydrolytic removal of phosphate groups from tyrosine residues in a target protein. The phosphorylation status of tyrosine residues on proteins serve as a ubiquitous mechanism for cellular signal transduction. Aberrant function of PTPs can lead to many human diseases, such as diabetes, obesity, cancer, and autoimmune diseases. As the number of disease relevant PTPs increases, there is urgency in developing highly potent inhibitors that are selective towards specific PTPs...
May 23, 2017: Molecular BioSystems
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