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Protein-protein docking

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https://www.readbyqxmd.com/read/28642707/tetrandrine-an-activator-of-autophagy-induces-autophagic-cell-death-via-pkc-%C3%AE-inhibition-and-mtor-dependent-mechanisms
#1
Vincent Kam Wai Wong, Wu Zeng, Juan Chen, Xiao Jun Yao, Elaine Lai Han Leung, Qian Qian Wang, Pauline Chiu, Ben C B Ko, Betty Yuen Kwan Law
Emerging evidence suggests the therapeutic role of autophagic modulators in cancer therapy. This study aims to identify novel traditional Chinese medicinal herbs as potential anti-tumor agents through autophagic induction, which finally lead to autophagy mediated-cell death in apoptosis-resistant cancer cells. Using bioactivity-guided purification, we identified tetrandrine (Tet) from herbal plant, Radix stephaniae tetrandrae, as an inducer of autophagy. Across a number of cancer cell lines, we found that breast cancer cells treated with tetrandrine show an increase autophagic flux and formation of autophagosomes...
2017: Frontiers in Pharmacology
https://www.readbyqxmd.com/read/28641564/investigation-on-the-interaction-of-pseudomonas-syringae-effector-avrpto-with-atrabe1d-gtpase
#2
Xiaomin Hou, Yi Gao
The tomato bacterial speck is a worldwide disease. It is caused by the infection of pathogenic pseudomonas syringae pv. tomato which delivers the effector AvrPto into the host cells via the type III secretion system. AvrPto interacts Rab8 subfamily protein in the GTP-bound form and participates in the response to pathogen infection, but the pathogenic mechanism involved by Rab8 subfamily remains elusive. Here, we investigated on the interrelationship of AvrPto8-159 with Arabidopsis thaliana GTP-restricted Rab8 subfamily protein AtRabE1d13-185Q74L through some biophysical and biochemical methods...
June 21, 2017: Protein and Peptide Letters
https://www.readbyqxmd.com/read/28641528/drug-design-synthesis-and-in-vitro-evaluation-of-substituted-benzofurans-as-hsp90-inhibitors
#3
Sundeep Kadasi, Thadeu E M M Costa, Neha Arukala, Mallika Toshakani, Chaitanya Duggineti, Sreekanth Thota, Sayan Dutta Gupta, Shiva Raj, Carmen Penido, Maria G Henriques, Nulgumnalli Manjunathaiah Raghavendra
BACKGROUND: Heat shock protein 90 is a molecular chaperone required for the stability and function of several client proteins that promote cancer cell growth and/or survival. Discovery of Hsp90 inhibitors has emerged as an attractive target of research in cancer therapeutics. Natural products like geldanamycin and radicicol are established Hsp90 inhibitors, but face limitations with toxicity and inactivity, by in vivo studies respectively. However, they lay the logical starting point for the design of novel synthetic or semi-synthetic congeners as Hsp90 inhibitors...
June 22, 2017: Medicinal Chemistry
https://www.readbyqxmd.com/read/28641512/molecular-docking-and-molecular-dynamics-simulation-based-approach-to-explore-the-dual-inhibitor-against-hiv-1-reverse-transcriptase-and-integrase
#4
Subhash Chander, Rajan Kumar Pandey, Ashok Penta, Bhanwar Singh Choudhary, Manish Sharma, Ruchi Malik, Vijay Kumar Prajapati, Sankaranarayanan Murugesan
HIV integrase (IN) and reverse transcriptase (RT) are key enzymes for the replication of HIV-1. DNA polymerase and ribonuclease H (RNase H) are the two catalytic domains of HIV-1 RT which are validated as drug targets because of their essence for replication. IN and RNase H domain of RT share the striking structural similarity; it contains conserved DDE triad (two aspartates and one glutamate) and a pair of divalent Mg2+/Mn2+ ions at their catalytic core domain. Therefore, the search of compounds with dual inhibition of IN and RNase H can be the viable and more efficacious approach for the drug development against both wild and drug resistance strains of HIV...
June 15, 2017: Combinatorial Chemistry & High Throughput Screening
https://www.readbyqxmd.com/read/28641070/elmo-proteins-transduce-g-protein-coupled-receptor-signal-to-control-reorganization-of-actin-cytoskeleton-in-chemotaxis-of-eukaryotic-cells
#5
Xuehua Xu, Tian Jin
Chemotaxis, which is chemoattractant-guided directional cell migration, plays major roles in recruitment of neutrophils, the metastasis of cancer cells, and the development of the model organism Dictyostelium discoideum. These cells share remarkable similarities in the signaling pathways by which they control chemotaxis. They all use a G protein-coupled receptor (GPCR)-mediated signal transduction pathway to sense the chemotactic gradient to guide cell migration. Diverse chemokines activate Rac through conserved GPCR signaling pathways...
June 22, 2017: Small GTPases
https://www.readbyqxmd.com/read/28640852/differential-roles-of-3-hydroxyflavone-and-7-hydroxyflavone-against-nicotine-induced-oxidative-stress-in-rat-renal-proximal-tubule-cells
#6
Bidisha Sengupta, Mehdi Sahihi, Monireh Dehkhodaei, Darrian Kelly, Istvan Arany
Plant flavonoids are well known as antioxidants against oxidative stress induced by exposure to external pollutants. Nicotine (NIC) is one of those agents which increases renal oxidative stress, an important factor in the pathogenesis of renal epithelial injury in smokers. Although several studies had been conducted on flavonoids and oxidative stress, the mechanism of the protective pathways are not fully understood. Here, we present studies on antioxidant properties of two mono-hydroxyflavone isomers, 3-hydroxyflanove (3HF)- and 7-hydroxyflavone (7HF), against nicotine-associated oxidative stress and injury in cultured renal proximal tubule cells and correlate their antioxidant properties with their chemical structure...
2017: PloS One
https://www.readbyqxmd.com/read/28640302/influence-of-substituents-on-dna-and-protein-binding-of-cyclometalated-ir-iii-complexes-and-anticancer-activity
#7
Sujay Mukhopadhyay, Roop Shikha Singh, Rajendra Prasad Paitandi, Gunjan Sharma, Biplob Koch, Daya Shankar Pandey
Synthesis of terpyridyl based ligands 3-([2,2':6',2''-terpyridin]-4'-yl)-7-methoxy-2-(methylthio)-quinolone, (L1); 3-([2,2':6',2''-terpyridin]-4'-yl)-6-methoxyquinolin-2(1H)-one, (L2); 3-([2,2'-:6',2''-terpyridin]-4'-yl)-6-methylquinolin-2(1H)-one (L3) and cyclometalated iridium(iii) complexes [[Ir(ppy)2L1](+)PF6(-) (1), [Ir(ppy)2L2](+)PF6(-) (2), [Ir(ppy)2L3](+)PF6(-) (3) (2-phenylpyridine = Hppy)] involving these ligands has been described. The ligands L1-L3 and complexes 1-3 have been thoroughly characterized by elemental analyses, spectral studies (IR, (1)H, (13)C NMR, UV/vis and fluorescence) ESI-MS, and the structure of 3 has been unambiguously authenticated by single crystal X-ray analyses...
June 22, 2017: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/28639732/simulated-isotope-exchange-patterns-enable-protein-structure-determination
#8
Antoni James Borysik
Understanding the myriad protein-protein interactions required for cell function requires efficient leveraging of biophysical data to drive computational docking. The detailed insight into protein interfaces provided by isotope exchange endows this experimental technique with a unique importance for docking approaches. However, progress in coupling these methods is hindered by the inability to interpret the complex exchange patterns in relation to protein structure. A method to simulate protein isotope exchange patterns from docking outputs is described and its utility to guide the selection of native assemblies demonstrated...
June 22, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28639379/the-in-vitro-and-in-vivo-biological-activities-of-the-leaf-of-cape-myrtle-myrsine-africana-l
#9
Hina Gul, Mushtaq Ahmad, Muhammad Zafar, M Shareez Ahmad, AmbreenAbid, Syeda Hira, Imam Shah, Muhammad Gulfraz
The cape myrtle, Myrsine africana L., is a widely used medicinal plant, which has not been well investigated. We assessed the in vivo hepatoprotective and in vitro antiproliferative and antioxidant effects of leaf extracts of M. africana chemically profiled using high-performance liquid chromatography. Three flavonoids were quantified, and gas chromatography-mass spectrometry analysis revealed the presence of common fatty acids. The animal study was conducted on mice treated with CCl4, using three doses each of the methanol and chloroform extract (100, 200 and 300 mg/kg b...
June 22, 2017: Phytotherapy Research: PTR
https://www.readbyqxmd.com/read/28637675/structure-functional-aspects-of-the-human-riboflavin-transporter-3-slc52a3-role-of-the-predicted-glycosylation-and-substrate-interacting-sites
#10
Veedamali S Subramanian, Subrata Subai, Trevor Teafatiller, Jennifer A Bohl, Hamid M Said
The human riboflavin (RF) transporter-3 (hRFVT-3; product of the SLC52A3 gene) plays an essential role in the intestinal RF absorption process and is expressed exclusively at the apical membrane domain of polarized enterocytes. Previous studies have characterized different physiological/biological aspects of this transporter, but nothing is known about the glycosylation status of the hRFVT-3 protein and role of this modification in its physiology/biology. Additionally, little is known about the residues in the hRFVT-3 protein that interact with the ligand, RF...
June 21, 2017: American Journal of Physiology. Cell Physiology
https://www.readbyqxmd.com/read/28637443/trichoderma-virens-%C3%AE-glucosidase-i-bgli-gene-expression-in-saccharomyces-cerevisiae-including-docking-and-molecular-dynamics-studies
#11
Gammadde Hewa Ishan Maduka Wickramasinghe, Pilimathalawe Panditharathna Attanayake Mudiyanselage Samith Indika Rathnayake, Naduviladath Vishvanath Chandrasekharan, Mahindagoda Siril Samantha Weerasinghe, Ravindra Lakshman Chundananda Wijesundera, Wijepurage Sandhya Sulochana Wijesundera
BACKGROUND: Cellulose, a linear polymer of β 1-4, linked glucose, is the most abundant renewable fraction of plant biomass (lignocellulose). It is synergistically converted to glucose by endoglucanase (EG) cellobiohydrolase (CBH) and β-glucosidase (BGL) of the cellulase complex. BGL plays a major role in the conversion of randomly cleaved cellooligosaccharides into glucose. As it is well known, Saccharomyces cerevisiae can efficiently convert glucose into ethanol under anaerobic conditions...
June 21, 2017: BMC Microbiology
https://www.readbyqxmd.com/read/28636189/discovery-of-alkyl-bis-oxy-dibenzimidamide-derivatives-as-novel-protein-arginine-methyltransferase-1-prmt1-inhibitors
#12
Wei-Yao Zhang, Wen-Chao Lu, Hao Jiang, Zheng-Bing Lv, Yi-Qian Xie, Fu-Lin Lian, Zhong-Jie Liang, Yu-Xi Jiang, Da-Jin Wang, Cheng Luo, Jia Jin, Fei Ye
Protein arginine methylation, a post-translational modification critical for a variety of biological processes, is catalyzed by protein arginine N-methyltransferases (PRMTs). In particular, PRMT1 is responsible for over 85% of the arginine methylation in mammalian cells. Dysregulation of PRMT1 is involved in diverse pathological diseases including cancers. However, most current PRMT1inhibitors are lack of specificity, efficacy, and bioavailability. Herein, a series of alkyl bis(oxy)dibenzimidamide derivatives were identified as selective PRMT1 inhibitors...
June 21, 2017: Chemical Biology & Drug Design
https://www.readbyqxmd.com/read/28634829/potential-inhibitory-effect-of-indolizine-derivatives-on-the-two-enzymes-nicotinamide-phosphoribosyltransferase-and-beta-lactamase-a-molecular-dynamics-study
#13
Beata Szefler, Przemysław Czeleń
Nicotinamide phosphoribosyl-transferases (NAMPT) are enzymes that play a role in targeting cancer metabolism, while beta lactamases are involved in bacterial resistance to beta-lactam antibiotics. Many protein inhibitors exhibit such property which is often correlated with their cellular potency. In order to understand such a phenomenon, the present article conducts an analysis of the dynamic behavior of complexes formed by the inhibitors, that is indolizine derivatives, with the studied enzymes. Both docking and molecular dynamics led to identification of their interactions and showed the mechanism of inhibition of the two studied enzymes...
July 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/28634712/site-directed-mutagenesis-under-the-direction-of-in-silico-protein-docking-modeling-reveals-the-active-site-residues-of-3-ketosteroid-%C3%AE-1-dehydrogenase-from-mycobacterium-neoaurum
#14
Ning Qin, Yanbing Shen, Xu Yang, Liqiu Su, Rui Tang, Wei Li, Min Wang
3-Ketosteroid-Δ(1)-dehydrogenases (KsdD) from Mycobacterium neoaurum could transform androst-4-ene-3,17-dione (AD) to androst-1,4-diene-3,17-dione. This reaction has a significant effect on the product of pharmaceutical steroid. The crystal structure and active site residues information of KsdD from Mycobacterium is not yet available, which result in the engineering of KsdD is tedious. In this study, by the way of protein modeling and site-directed mutagenesis, we find that, Y122, Y125, S138, E140 and Y541 from the FAD-binding domain and Y365 from the catalytic domain play a key role in this transformation...
July 2017: World Journal of Microbiology & Biotechnology
https://www.readbyqxmd.com/read/28634376/structural-basis-to-stabilize-the-domain-motion-of-bard1-ard-brct-by-cstf50
#15
Rajan Kumar Choudhary, Mohd Quadir Siddiqui, Pankaj S Thapa, Nikhil Gadewal, Senthil Kumar Nachimuthu, Ashok K Varma
BRCA1 associated ring domain protein 1(BARD1) is a tumor suppressor protein having a wide role in cellular processes like cell-cycle checkpoint, DNA damage repair and maintenance of genomic integrity. Germ-line mutation Gln 564 His discovered in linker region of BARD1 leads to loss of binding to Cleavage stimulating factor (CstF50), which in turn instigates the premature mRNA transcript formation and apoptosis. We have studied the dynamics of ARD domain present in the BARD1 wild-type and mutant protein in association with CstF50 using biophysical, biochemical and molecular dynamics simulations...
June 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28634119/an-ultrasensitive-stain-for-negative-protein-detection-in-sds-page-via-4-5-dibromofluorescein
#16
Dongdong Yu, Yang Wang, Shaoqing Zhang, Zhiwei Chen, Mei Xue, Ying Wang, Weitao Cong, Litai Jin, Zhongxin Zhu
A highly sensitive method for brief and economical staining of proteins in 1-D and 2-D sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) by 4',5'-Dibromofluorescein (DBF) was developed in this study. Down to 0.025-0.05ng protein could be detected within 10min (only 2 steps) by DBF stain, which is approximately 10-fold more sensitive than those of Eosin Y (EY) and SYPRO Ruby stains, and 20-fold more sensitive than that of imidazole-zinc (IZ) negative stain. In addition, the LC-MS/MS results indicated that the newly developed staining method is compatible with the downstream protein identification...
June 17, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28633568/the-potential-inhibitory-effect-of-%C3%AE-casein-on-the-aggregation-and-deposition-of-a%C3%AE-1-42-fibrils-in-alzheimer-s-disease-insight-from-in-vitro-and-in-silico-studies
#17
Sedighehsadat Hojati, Arezou Ghahghaei, Milad Lagzian
Aβ1-40 and Aβ1-42 have been shown to be the main components of the amyloid plaques found in the extracellular environment of neurons in Alzheimer's disease. β-Casein, a milk protein, has been shown to display a remarkable chaperone ability in preventing the aggregation of proteins. In this study, the ability of β-casein to suppress the amyloid fibril formation of Aβ1-42 has been examined through in vitro studies and molecular docking simulation. The results demonstrate the inhibitory effect of β-casein on fibril formation in Aβ1-42, in a concentration dependent manner, suggesting that the chaperone binds to the Aβ1-42 and prevents amyloid fibril formation...
June 20, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28633528/the-binding-space-concept-a-new-approach-to-enhance-the-reliability-of-docking-scores-and-its-application-to-predicting-butyrylcholinesterase-bche-hydrolytic-activity
#18
Giulio Vistoli, Angelica Mazzolari, Bernard Testa, Alessandro Pedretti
Docking simulations are very popular approaches able to assess the capacity of a given ligand to interact with a target. Docking simulations are usually focused on a single best complex even though many studies showed that ligands retain a significant mobility within a binding pocket by assuming different binding modes all of which may contribute to the monitored ligand affinity. The present study describes an innovative concept, the binding space, which allows an exploration of the ligand mobility within the binding pocket by simultaneously considering several ligand poses as generated by docking simulations...
June 20, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28633380/epigallocatechin-3-gallate-and-related-phenol-compounds-redirect-the-amyloidogenic-aggregation-pathway-of-ataxin-3-towards-non-toxic-aggregates-and-prevent-toxicity-in-neural-cells-and-caenorhabditis-elegans-animal-model
#19
Cristina Visentin, Francesca Pellistri, Antonino Natalello, Jacopo Vertemara, Marcella Bonanomi, Elena Gatta, Amanda Penco, Annalisa Relini, Luca De Gioia, Cristina Airoldi, Maria E Regonesi, Paolo Tortora
The protein ataxin-3 (ATX3) triggers an amyloid-related neurodegenerative disease when its polyglutamine stretch is expanded beyond a critical threshold. We formerly demonstrated that the polyphenol epigallocatechin-3-gallate (EGCG) could redirect amyloid aggregation of a full-length, expanded ATX3 (ATX3-Q55) towards non-toxic, soluble, SDS-resistant aggregates. Here, we have characterized other related phenol compounds, although smaller in size, i.e., (-)-epigallocatechin gallate (EGC), and gallic acid (GA)...
June 15, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28632334/functional-analysis-of-female-biased-odorant-binding-protein-6-for-volatile-and-nonvolatile-host-compounds-in-adelphocoris-lineolatus-goeze
#20
L Sun, Q Wang, S Yang, Q Wang, Z Zhang, A Khashaveh, Y-J Zhang, Y-Y Guo
The polyphagous mirid bug Adelphocoris lineolatus relies heavily on olfactory cues to track suitable host plants. Thus, a better understanding of the molecular basis of its olfactory detection could contribute to the development of effective pest management strategies. In the present study, we report the expression profile of the odorant binding protein gene A. lineolatus odorant binding protein 6 (AlinOBP6). Quantitative real-time PCR experiments suggest that AlinOBP6 is female adult antennae-biased. Cellular immunolocalization analyses show that AlinOBP6 is highly expressed in the lymph of both multiporous sensilla basiconica and uniporous sensilla chaetica...
June 20, 2017: Insect Molecular Biology
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