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Protein-protein docking

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https://www.readbyqxmd.com/read/28089350/rickettsia-prowazekii-methionine-aminopeptidase-as-a-promising-target-for-the-development-of-antibacterial-agents
#1
Travis R Helgren, Congling Chen, Phumvadee Wangtrakuldee, Thomas E Edwards, Bart L Staker, Jan Abendroth, Banumathi Sankaran, Nicole A Housley, Peter J Myler, Jonathon P Audia, James R Horn, Timothy J Hagen
Methionine aminopeptidase (MetAP) is a class of ubiquitous enzymes essential for the survival of numerous bacterial species. These enzymes are responsible for the cleavage of N-terminal formyl-methionine initiators from nascent proteins to initiate post-translational modifications that are often essential to proper protein function. Thus, inhibition of MetAP activity has been implicated as a novel antibacterial target. We tested this idea in the present study by targeting the MetAP enzyme in the obligate intracellular pathogen Rickettsia prowazekii...
November 10, 2016: Bioorganic & Medicinal Chemistry
https://www.readbyqxmd.com/read/28088574/time-dependence-of-the-enhancement-effect-of-chemical-enhancers-molecular-mechanisms-of-enhancing-kinetics
#2
Xiaochang Liu, Peng Quan, Shanshan Li, Chao Liu, Yuan Zhao, Yongshan Zhao, Liang Fang
Chemical enhancers are widely used for facilitating drug penetration in transdermal drug delivery system (TDDS). However, there is a lack of knowledge about how the enhancement effect changes over time. In this study, on the basis of kinetic parameters of enhancement effect, molecular details of the dynamic enhancement process was described and a new hypothesis of the recovery mechanism of the skin barrier function was proposed. Using pretreated skin and flurbiprofen patch, the effects of Azone (AZ) and menthol decanoate (MT-10) were evaluated with in vitro permeation experiment and further confirmed by confocal laser scanning microscopy (CLSM) and TEWL...
January 11, 2017: Journal of Controlled Release: Official Journal of the Controlled Release Society
https://www.readbyqxmd.com/read/28088302/the-cyp79a1-catalyzed-conversion-of-tyrosine-to-e-p-hydroxyphenylacetaldoxime-unravelled-using-an-improved-method-for-homology-modeling
#3
Dario Vazquez-Albacete, Marco Montefiori, Stefan Kol, Mohammed Saddik Motawia, Birger Lindberg Møller, Lars Olsen, Morten H H Nørholm
The vast diversity and membrane-bound nature of plant P450s makes it challenging to study the structural characteristics of this class of enzymes especially with respect to accurate intermolecular enzyme-substrate interactions. To address this problem we here apply a modified hybrid structure strategy for homology modeling of plant P450s. This allows for structural elucidation based on conserved motifs in the protein sequence and secondary structure predictions. We modeled the well-studied Sorghum bicolor cytochrome P450 CYP79A1 catalyzing the first step in the biosynthesis of the cyanogenic glucoside dhurrin...
January 11, 2017: Phytochemistry
https://www.readbyqxmd.com/read/28079879/the-cluspro-web-server-for-protein-protein-docking
#4
Dima Kozakov, David R Hall, Bing Xia, Kathryn A Porter, Dzmitry Padhorny, Christine Yueh, Dmitri Beglov, Sandor Vajda
The ClusPro server (https://cluspro.org) is a widely used tool for protein-protein docking. The server provides a simple home page for basic use, requiring only two files in Protein Data Bank (PDB) format. However, ClusPro also offers a number of advanced options to modify the search; these include the removal of unstructured protein regions, application of attraction or repulsion, accounting for pairwise distance restraints, construction of homo-multimers, consideration of small-angle X-ray scattering (SAXS) data, and location of heparin-binding sites...
February 2017: Nature Protocols
https://www.readbyqxmd.com/read/28079375/docking-of-macrocycles-comparing-rigid-and-flexible-docking-in-glide
#5
Hiba Alogheli, Gustav Olanders, Wesley Schaal, Peter Brandt, Anders Karlen
In recent years, there has been an increased interest in using macrocyclic compounds for drug discovery and development. To address docking of these commonly large and flexible compounds, a screening and a validation set were assembled from the PDB consisting of 16 and 31 macrocycle containing protein complexes, respectively. The macrocycles were docked in Glide by rigid docking of pre-generated conformational ensembles produced by the macrocycle conformational sampling method (MCS) in Schrödinger Release 2015-3 or by direct Glide Flexible Docking after performing ring-templating...
January 12, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28079198/oligomerization-of-fvflm-peptides-and-their-ability-to-inhibit-beta-amyloid-peptides-aggregation-consideration-as-a-possible-model
#6
M Kouza, A Banerji, A Kolinski, I A Buhimschi, A Kloczkowski
Preeclampsia, a pregnancy-specific disorder, shares typical pathophysiological features with protein misfolding disorders including Alzheimer's disease. Characteristic for preeclampsia is the involvement of multiple proteins of which fragments of SERPINA1 and β-amyloid co-aggregate in urine and placenta of preeclamptic women. To explore the biophysical basis of this interaction, we investigated the multidimensional efficacy of the FVFLM sequence in SERPINA1, as a model inhibitory agent of β-amyloid aggregation...
January 12, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28079053/molecular-evidence-for-the-involvement-of-a-polygalacturonase-inhibiting-protein-ghpgip1-in-enhanced-resistance-to-verticillium-and-fusarium-wilts-in-cotton
#7
Nana Liu, Xueyan Zhang, Yun Sun, Ping Wang, Xiancai Li, Yakun Pei, Fuguang Li, Yuxia Hou
Polygalacturonase-inhibiting protein (PGIP), belonging to a group of plant defence proteins, specifically inhibits endopolygalacturonases secreted by pathogens. Herein, we showed that purified GhPGIP1 is a functional inhibitor of Verticillium dahliae and Fusarium oxysporum f. sp. vasinfectum, the two fungal pathogens causing cotton wilt. Transcription of GhPGIP1 was increased in cotton upon infection, wounding, and treatment with defence hormone and H2O2. Resistance by GhPGIP1 was examined by its virus-induced gene silencing in cotton and overexpression in Arabidopsis...
January 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28078726/dissecting-the-cytochrome-p450-1a2-and-3a4-mediated-metabolism-of-aflatoxin-b1-in-ligand-and-protein-contributions
#8
Lars Olsen, Flemming S Jørgensen, Silvia Bonomo
Aflatoxin B1 (AFB1) is a chemically intriguing compound because it has several potential sites of metabolism (SOMs) while only some of them are observed experimentally. Cytochrome P450 (CYP) 3A4 and 1A2 are the major isoforms involved in its metabolism. Here, we systematically investigate reactivity and accessibility of all possible SOMs in these two CYPs to elucidate AFB1 metabolism. Density functional theory (DFT) calculations were used to determine activation energies for each possible reaction. Aliphatic hydroxylation on position 9A and 3α are energetically favored, whereas position 9 is the preferred site for epoxidation...
January 12, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28078551/the-proteolysis-adaptor-nbla-binds-to-the-n-terminus-of-%C3%AE-phycocyanin-implications-for-the-mechanism-of-phycobilisome-degradation
#9
Amelia Y Nguyen, William P Bricker, Hao Zhang, Daniel A Weisz, Michael L Gross, Himadri B Pakrasi
Phycobilisome (PBS) complexes are massive light-harvesting apparati in cyanobacteria that capture and funnel light energy to the photosystem. PBS complexes are dynamically degraded during nutrient deprivation, which causes severe chlorosis, and resynthesized during nutrient repletion. PBS degradation occurs rapidly after nutrient step down, and is specifically triggered by non-bleaching protein A (NblA), a small proteolysis adaptor that facilitates interactions between a Clp chaperone and phycobiliproteins...
January 11, 2017: Photosynthesis Research
https://www.readbyqxmd.com/read/28078411/in-vitro-and-in-silico-assessment-of-the-structure-dependent-binding-of-bisphenol-analogues-to-glucocorticoid-receptor
#10
Jie Zhang, Tiehua Zhang, Tianzhu Guan, Hansong Yu, Tiezhu Li
Widespread use of bisphenol A (BPA) and other bisphenol analogues has attracted increasing attention for their potential adverse effects. As environmental endocrine-disrupting compounds (EDCs), bisphenols (BPs) may activate a variety of nuclear receptors, including glucocorticoid receptor (GR). In this work, the binding of 11 BPs to GR was investigated by fluorescence polarization (FP) assay in combination with molecular dynamics simulations. The human glucocorticoid receptor was prepared as a soluble recombinant protein...
January 11, 2017: Analytical and Bioanalytical Chemistry
https://www.readbyqxmd.com/read/28077807/folding-of-apomyoglobin-analysis-of-transient-intermediate-structure-during-refolding-using-quick-hydrogen-deuterium-exchange-and-nmr
#11
Chiaki Nishimura
The structures of apomyoglobin folding intermediates have been widely analyzed using physical chemistry methods including fluorescence, circular dichroism, small angle X-ray scattering, NMR, mass spectrometry, and rapid mixing. So far, at least two intermediates (on sub-millisecond- and millisecond-scales) have been demonstrated for apomyoglobin folding. The combination of pH-pulse labeling and NMR is a useful tool for analyzing the kinetic intermediates at the atomic level. Its use has revealed that the latter-phase kinetic intermediate of apomyoglobin (6 ms) was composed of helices A, B, G and H, whereas the equilibrium intermediate, called the pH 4 molten-globule intermediate, was composed mainly of helices A, G and H...
2017: Proceedings of the Japan Academy. Series B, Physical and Biological Sciences
https://www.readbyqxmd.com/read/28077258/discovery-of-new-mura-inhibitors-using-induced-fit-simulation-and-docking
#12
Kaja Rožman, Samo Lešnik, Boris Brus, Martina Hrast, Matej Sova, Delphine Patin, Hélène Barreteau, Janez Konc, Dušanka Janežič, Stanislav Gobec
We report on the successful application of ProBiS-CHARMMing web server in the discovery of new inhibitors of MurA, an enzyme that catalyzes the first committed cytoplasmic step of bacterial peptidoglycan synthesis. The available crystal structures of Escherichia coli MurA in the Protein Data Bank have binding sites whose small volume does not permit the docking of drug-like molecules. To prepare the binding site for docking, the ProBiS-CHARMMing web server was used to simulate the induced-fit effect upon ligand binding to MurA, resulting in a larger, more holo-like binding site...
December 31, 2016: Bioorganic & Medicinal Chemistry Letters
https://www.readbyqxmd.com/read/28076345/structure-of-a-spliceosome-remodelled-for-exon-ligation
#13
Sebastian M Fica, Chris Oubridge, Wojciech P Galej, Max E Wilkinson, Xiao-Chen Bai, Andrew J Newman, Kiyoshi Nagai
The spliceosome excises introns from pre-mRNAs in two sequential trans-esterifications - branching and exon ligation(1) - catalysed at a single catalytic metal site in U6 snRNA(2,3). The recent structures of the spliceosomal C complex(4,5) with the cleaved 5'-exon and lariat-3'-exon bound to the catalytic centre revealed that branching-specific factors such as Cwc25 lock the branch helix into position for nucleophilic attack of the branch adenosine at the 5'-splice site. Furthermore, the ATPase Prp16 is positioned to bind and translocate the intron downstream of the branch point to destabilize branching-specific factors and release the branch helix from the active site(4)...
January 11, 2017: Nature
https://www.readbyqxmd.com/read/28074360/exploring-the-stability-of-ligand-binding-modes-to-proteins-by-molecular-dynamics-simulations
#14
Kai Liu, Etsurou Watanabe, Hironori Kokubo
The binding mode prediction is of great importance to structure-based drug design. The discrimination of various binding poses of ligand generated by docking is a great challenge not only to docking score functions but also to the relatively expensive free energy calculation methods. Here we systematically analyzed the stability of various ligand poses under molecular dynamics (MD) simulation. First, a data set of 120 complexes was built based on the typical physicochemical properties of drug-like ligands. Three potential binding poses (one correct pose and two decoys) were selected for each ligand from self-docking in addition to the experimental pose...
January 10, 2017: Journal of Computer-aided Molecular Design
https://www.readbyqxmd.com/read/28073818/transcriptional-coregulator-rip140-an-essential-regulator-of-physiology
#15
Jaya Nautiyal
Transcriptional coregulators drive gene regulatory decisions in the transcriptional space. While transcription factors including all nuclear receptors provide a docking platform for coregulators to bind, these proteins bring enzymatic capabilities to the gene regulatory sites. RIP140 is a transcriptional coregulator essential for several physiological processes and aberrations in its function may lead to diseased states. Unlike several other coregulators which are either known for their coactivating or corepressing roles, in gene regulation, RIP140 is capable of acting both as a coactivator and a corepressor...
January 10, 2017: Journal of Molecular Endocrinology
https://www.readbyqxmd.com/read/28070705/enzymatic-activation-of-double-targeted-5-o-l-valyl-decitabine-prodrug-by-biphenyl-hydrolase-like-protein-and-its-molecular-design-basis
#16
Wenhui Tao, Dongyang Zhao, Mengchi Sun, Meng Li, Xiangyu Zhang, Zhonggui He, Yinghua Sun, Jin Sun
A primary focus of this research was to explore the activation process and mechanism of decitabine (5-aza-2'-deoxycytidine, DAC) prodrug. Recently, it has been reported that biphenyl hydrolase-like protein (BPHL) can play an important role in the activation of some amino acid nucleoside prodrugs with a general preference for hydrophobic amino acids and 5'-esters. Therefore, we put forward a bold hypothesis that this novel enzyme may be primarily responsible for the activation process of DAC prodrug as well...
January 9, 2017: Drug Delivery and Translational Research
https://www.readbyqxmd.com/read/28070575/network-pharmacology-based-virtual-screening-of-natural-products-from-clerodendrum-species-for-identification-of-novel-anti-cancer-therapeutics
#17
Barbi Gogoi, Dhrubajyoti Gogoi, Yumnam Silla, Bibhuti Bhushan Kakoti, Brijmohan Singh Bhau
Plant-derived natural products (NPs) play a vital role in the discovery of new drug molecules and these are used for development of novel therapeutic drugs for a specific disease target. Literature review suggests that natural products possess strong inhibitory efficacy against various types of cancer cells. Clerodendrum indicum and Clerodendrum serratum are reported to have anticancer activity; therefore a study was carried out to identify selective anticancer agents from these plants species. In this report, we employed a docking weighted network pharmacological approach to understand the multi-therapeutics potentiality of C...
January 10, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28069132/molecular-regulation-of-the-spindle-assembly-checkpoint-by-kinases-and-phosphatases
#18
G Manic, F Corradi, A Sistigu, S Siteni, I Vitale
The spindle assembly checkpoint (SAC) is a surveillance mechanism contributing to the preservation of genomic stability by monitoring the microtubule attachment to, and/or the tension status of, each kinetochore during mitosis. The SAC halts metaphase to anaphase transition in the presence of unattached and/or untensed kinetochore(s) by releasing the mitotic checkpoint complex (MCC) from these improperly-oriented kinetochores to inhibit the anaphase-promoting complex/cyclosome (APC/C). The reversible phosphorylation of a variety of substrates at the kinetochore by antagonistic kinases and phosphatases is one major signaling mechanism for promptly turning on or turning off the SAC...
2017: International Review of Cell and Molecular Biology
https://www.readbyqxmd.com/read/28068084/molecular-modeling-evaluation-of-the-enantiomers-of-a-novel-adenylyl-cyclase-2-inhibitor
#19
Neha Rana, Jason M Conley, Monica Soto-Velasquez, Francisco Leon, Stephen J Cutler, Val J Watts, Markus A Lill
Adenylyl cyclase 2 (AC2) is one of nine membrane-bound isoforms of adenylyl cyclase that converts ATP into cyclic AMP (cAMP), an important second messenger molecule. Up-regulation of AC2 is linked to cancers like pancreatic and small intestinal neuroendocrine tumors (NETs). The structures of the various isoforms of adenylyl cyclases are highly homologous, posing a significant challenge to drug discovery efforts for an effective, isoform-selective modulator of AC2. In a previous study, a screen identified a potential isoform-selective and non-competitive inhibitor of AC2, SKF83566...
January 9, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28067274/computational-and-biochemical-characterization-of-two-partially-overlapping-interfaces-and-multiple-weak-affinity-k-ras-dimers
#20
Priyanka Prakash, Abdallah Sayyed-Ahmad, Kwang-Jin Cho, Drew M Dolino, Wei Chen, Hongyang Li, Barry J Grant, John F Hancock, Alemayehu A Gorfe
Recent studies found that membrane-bound K-Ras dimers are important for biological function. However, the structure and thermodynamic stability of these complexes remained unknown because they are hard to probe by conventional approaches. Combining data from a wide range of computational and experimental approaches, here we describe the structure, dynamics, energetics and mechanism of assembly of multiple K-Ras dimers. Utilizing a range of techniques for the detection of reactive surfaces, protein-protein docking and molecular simulations, we found that two largely polar and partially overlapping surfaces underlie the formation of multiple K-Ras dimers...
January 9, 2017: Scientific Reports
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