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Protein interface prediction

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https://www.readbyqxmd.com/read/29327289/study-of-adenylyl-cyclase-g%C3%AE-s-interactions-and-identification-of-novel-ac-ligands
#1
Appalaraju Jaggupilli, Premnath Dhanaraj, Alexander Pritchard, John L Sorensen, Shyamala Dakshinamurti, Prashen Chelikani
Adenylyl cyclases (ACs) are membrane bound enzymes that catalyze the production of cAMP from ATP in response to the activation by G-protein Gαs. Different isoforms of ACs are ubiquitously expressed in different tissues involved in regulatory mechanisms in response to specific stimulants. There are 9 AC isoforms present in humans, with AC5 and AC6 proposed to play a vital role in cardiac functions. The activity of AC6 is sensitive to nitric oxide, such that nitrosylation of the protein might regulate its function...
January 11, 2018: Molecular and Cellular Biochemistry
https://www.readbyqxmd.com/read/29325022/large-scale-exome-datasets-reveal-a-new-class-of-adaptor-related-protein-complex-2-sigma-subunit-ap2%C3%AF-mutations-located-at-the-interface-with-the-ap2-alpha-subunit-that-impair-calcium-sensing-receptor-signalling
#2
Caroline M Gorvin, Raghu Metpally, Victoria J Stokes, Fadil M Hannan, Sarath B Krishnamurthy, John D Overton, Jeffrey G Reid, Gerda E Breitwieser, Rajesh V Thakker
Mutations of the sigma subunit of the heterotetrameric adaptor-related protein complex 2 (AP2σ) impair signalling of the calcium-sensing receptor (CaSR), and cause familial hypocalciuric hypercalcaemia type 3 (FHH3). To date, FHH3-associated AP2σ mutations have only been identified at one residue, Arg15. We hypothesized that additional rare AP2σ variants may also be associated with altered CaSR function and hypercalcaemia, and sought for these by analysing >111,995 exomes (>60,706 from ExAc and dbSNP, and 51,289 from the Geisinger Health System-Regeneron DiscovEHR dataset which also contains clinical data)...
January 9, 2018: Human Molecular Genetics
https://www.readbyqxmd.com/read/29320928/interaction-of-caffeine-and-sulfadiazine-with-lysozyme-adsorbed-at-colloidal-metal-nanoparticle-interface-influence-on-drug-transport-ability-and-antibacterial-activity
#3
Vikash K Sonu, Imocha Rajkumar, Kaushik Bhattacharjee, S R Joshi, Sivaprasad Mitra
The modulated bioactivity of proteins immobilized on nanoparticle (NP) interfaces is of tremendous interest towards designing better therapeutic and diagnostic tools. In this work, binding behavior and the antibacterial activity of free lysozyme (LYS) as well as its non-covalent assembly with silver (Ag) and gold (Au) colloidal NPs were compared in presence of two model drugs, viz. sulfadiazine (SDZ) and caffeine (CAF). Intrinsic protein fluorescence was found to quench due to the formation drug-protein complex in case of CAF resulting a linear Stern-Volmer (SV) plot with KSV = 1...
January 11, 2018: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/29315406/snapshots-of-a-molecular-swivel-in-action
#4
Caitlin S Trejo, Ronald S Rock, W Marshall Stark, Martin R Boocock, Phoebe A Rice
Members of the serine family of site-specific recombinases exchange DNA strands via 180° rotation about a central protein-protein interface. Modeling of this process has been hampered by the lack of structures in more than one rotational state for any individual serine recombinase. Here we report crystal structures of the catalytic domains of four constitutively active mutants of the serine recombinase Sin, providing snapshots of rotational states not previously visualized for Sin, including two seen in the same crystal...
January 5, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29313735/viral-capsid-assembly-a-quantified-uncertainty-approach
#5
Nathan Clement, Muhibur Rasheed, Chandrajit Lal Bajaj
Most of the existing research in assembly pathway prediction/analysis of viral capsids makes the simplifying assumption that the configuration of the intermediate states can be extracted directly from the final configuration of the entire capsid. This assumption does not take into account the conformational changes of the constituent proteins as well as minor changes to the binding interfaces that continue throughout the assembly process until stabilization. This article presents a statistical-ensemble-based approach that samples the configurational space for each monomer with the relative local orientation between monomers, to capture the uncertainties in binding and conformations...
January 2018: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/29308882/prediction-of-ordered-water-molecules-in-protein-binding-sites-from-molecular-dynamics-simulations-the-impact-of-ligand-binding-on-hydration-networks
#6
Axel Rudling, Adolfo Orro, Jens Carlsson
Water plays a major role in ligand binding and is attracting increasing attention in structure-based drug design. Water molecules can make large contributions to binding affinity by bridging protein-ligand interactions or by being displaced upon complex formation, but these phenomena are challenging to model at the molecular level. Here, networks of ordered water molecules in protein binding sites were analyzed by clustering of molecular dynamics (MD) simulation trajectories. Locations of ordered waters (hydration sites) were first identified from simulations of high resolution crystal structures of 13 protein-ligand complexes...
January 8, 2018: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/29305922/gold-nanoparticle-should-understand-protein-corona-for-being-a-clinical-nanomaterial
#7
REVIEW
Fahimeh Charbgoo, Mojgan Nejabat, Khalil Abnous, Fatemeh Soltani, Seyed Mohammad Taghdisi, Mona Alibolandi, W Thomas Shier, Terry W J Steele, Mohammad Ramezani
Gold nanoparticles (AuNPs) have attracted great attention in biomedical fields due to their unique properties. However, there are few reports on clinical trial of these nanoparticles. In vivo, AuNPs face complex biological fluids containing abundant proteins, which challenge the prediction of their fate that is known as "bio-identity". These proteins attach onto the AuNPs surface forming protein corona that makes the first step of nano-bio interface and dictates the subsequent AuNPs fate. Protein corona formation even stealth active targeting effect of AuNPs...
January 4, 2018: Journal of Controlled Release: Official Journal of the Controlled Release Society
https://www.readbyqxmd.com/read/29296672/prediction-of-new-stabilizing-mutations-based-on-mechanistic-insights-from-markov-state-models
#8
Maxwell I Zimmerman, Kathryn M Hart, Carrie A Sibbald, Thomas E Frederick, John R Jimah, Catherine R Knoverek, Niraj H Tolia, Gregory R Bowman
Protein stabilization is fundamental to enzyme function and evolution, yet understanding the determinants of a protein's stability remains a challenge. This is largely due to a shortage of atomically detailed models for the ensemble of relevant protein conformations and their relative populations. For example, the M182T substitution in TEM β-lactamase, an enzyme that confers antibiotic resistance to bacteria, is stabilizing but the precise mechanism remains unclear. Here, we employ Markov state models (MSMs) to uncover how M182T shifts the distribution of different structures that TEM adopts...
December 27, 2017: ACS Central Science
https://www.readbyqxmd.com/read/29291594/a-non-enzymatic-two-step-catalytic-reduction-of-methylglyoxal-by-nanostructured-v2o5-modified-electrode
#9
Lakshmishri Ramachandra Bhat, Srinivasan Vedantham, Uma Maheswari Krishnan, John Bosco Balaguru Rayappan
Methylglyoxal (MG) is a predominant precursor for advanced glycation end products (AGEs) due to its protein glycation reactions, which are the major causes of diabetic complications. MG is explored as a significant biomarker towards the prediction of diabetic complications. With this background, a non-enzymatic electrochemical biosensor has been developed to detect MG in human blood plasma samples. Microwave synthesized V2O5 nanoplates were used as interface material in the fabrication of modified gold (Au) working electrode for electrochemical MG biosensor...
December 23, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/29288943/design-synthesis-and-evaluation-of-novel-phenyl-propionamide-derivatives-as-non-nucleoside-hepatitis-b-virus-inhibitors
#10
Jingying Qiu, Qineng Gong, Jian Gao, Wang Chen, Yinpeng Zhang, Xiaoke Gu, Daoquan Tang
As an ongoing search for potent non-nucleoside anti-HBV agents with novel structures, we described a series of phenyl propionamide derivatives (3a-b, 4a-e, 7a-g, 8a-h and 9a-b) by pharmacophore fusion strategy in the present work. All the compounds exhibited an anti-HBV activity to some extent. Among them, compounds 8d and 9b displayed most potent anti-HBV activity with IC50 values on HBV DNA replication of 0.46 and 0.14 μM, respectively. And the selective index values of 8d and 9b were more than 217.39 and 153...
December 16, 2017: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/29281985/deep-convolutional-neural-networks-for-pan-specific-peptide-mhc-class-i-binding-prediction
#11
Youngmahn Han, Dongsup Kim
BACKGROUND: Computational scanning of peptide candidates that bind to a specific major histocompatibility complex (MHC) can speed up the peptide-based vaccine development process and therefore various methods are being actively developed. Recently, machine-learning-based methods have generated successful results by training large amounts of experimental data. However, many machine learning-based methods are generally less sensitive in recognizing locally-clustered interactions, which can synergistically stabilize peptide binding...
December 28, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29281006/pine-sparky-2-for-automated-nmr-based-protein-structure-research
#12
Woonghee Lee, John L Markley
Summary: NMR (nuclear magnetic resonance) spectroscopy, along with X-ray crystallography and Cryo-EM, is one of the three major tools that enable the determination of atomic-level structural models of biological macromolecules. Of these, NMR has the unique ability to follow important processes in solution, including conformational changes, internal dynamics and protein-ligand interactions. As a means for facilitating the handling and analysis of spectra involved in these types of NMR studies, we have developed PINE-SPARKY...
December 21, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29281004/computational-identification-of-binding-energy-hot-spots-in-protein-rna-complexes-using-an-ensemble-approach
#13
Yuliang Pan, Zixiang Wang, Weihua Zhan, Lei Deng
Motivation: Identifying RNA-binding residues, especially energetically favored hot spots, can provide valuable clues for understanding the mechanisms and functional importance of protein-RNA interactions. Yet limited availability of experimentally recognized energy hot spots in protein-RNA crystal structures lead to difficulties in developing empirical identification approaches. Computational prediction of RNA-binding hot spot residues is still in its infant stage. Results: Here, we describe a computational method, PrabHot (Prediction of protein-RNA binding hot spots), that can effectively detect hot spot residues on protein-RNA binding interfaces using an ensemble of conceptually different machine learning classifiers...
December 21, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29244501/origins-of-enzyme-catalysis-experimental-findings-for-c-h-activation-new-models-and-their-relevance-to-prevailing-theoretical-constructs
#14
Judith P Klinman, Adam R Offenbacher, Shenshen Hu
The physical basis for enzymatic rate accelerations is a subject of great fundamental interest and of direct relevance to areas that include the de novo design of green catalysts and the pursuit of new drug regimens. Extensive investigations of C-H activating systems have provided considerable insight into the relationship between an enzyme's overall structure and the catalytic chemistry at its active site. This Perspective highlights recent experimental data for two members of distinct, yet iconic C-H activation enzyme classes, lipoxygenases and prokaryotic alcohol dehydrogenases...
December 15, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29244012/utilizing-knowledge-base-of-amino-acids-structural-neighborhoods-to-predict-protein-protein-interaction-sites
#15
Jan Jelínek, Petr Škoda, David Hoksza
BACKGROUND: Protein-protein interactions (PPI) play a key role in an investigation of various biochemical processes, and their identification is thus of great importance. Although computational prediction of which amino acids take part in a PPI has been an active field of research for some time, the quality of in-silico methods is still far from perfect. RESULTS: We have developed a novel prediction method called INSPiRE which benefits from a knowledge base built from data available in Protein Data Bank...
December 6, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29240760/novel-linear-motif-filtering-protocol-reveals-the-role-of-the-lc8-dynein-light-chain-in-the-hippo-pathway
#16
Gábor Erdős, Tamás Szaniszló, Mátyás Pajkos, Borbála Hajdu-Soltész, Bence Kiss, Gábor Pál, László Nyitray, Zsuzsanna Dosztányi
Protein-protein interactions (PPIs) formed between short linear motifs and globular domains play important roles in many regulatory and signaling processes but are highly underrepresented in current protein-protein interaction databases. These types of interactions are usually characterized by a specific binding motif that captures the key amino acids shared among the interaction partners. However, the computational proteome-level identification of interaction partners based on the known motif is hindered by the huge number of randomly occurring matches from which biologically relevant motif hits need to be extracted...
December 14, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/29238877/cryptogenic-cholestasis-in-young-and-adults-atp8b1-abcb11-abcb4-and-tjp2-gene-variants-analysis-by-high-throughput-sequencing
#17
Giovanni Vitale, Stefano Gitto, Francesco Raimondi, Alessandro Mattiaccio, Vilma Mantovani, Ranka Vukotic, Antonietta D'Errico, Marco Seri, Robert B Russell, Pietro Andreone
BACKGROUND: Mutations in ATP-transporters ATPB81, ABCB11, and ABCB4 are responsible for progressive familial intrahepatic cholestasis (PFIC) 1, 2 and 3, and recently the gene for tight junction protein-2 (TJP2) has been linked to PFIC4. AIM: As these four genes have been poorly studied in young people and adults, we investigated them in this context here. METHODS: In patients with cryptogenic cholestasis, we analyzed the presence of mutations by high-throughput sequencing...
December 13, 2017: Journal of Gastroenterology
https://www.readbyqxmd.com/read/29228953/a-simple-and-accurate-rule-based-modeling-framework-for-simulation-of-autocrine-paracrine-stimulation-of-glioblastoma-cell-motility-and-proliferation-by-l1cam-in-2-d-culture
#18
Justin Caccavale, David Fiumara, Michael Stapf, Liedeke Sweitzer, Hannah J Anderson, Jonathan Gorky, Prasad Dhurjati, Deni S Galileo
BACKGROUND: Glioblastoma multiforme (GBM) is a devastating brain cancer for which there is no known cure. Its malignancy is due to rapid cell division along with high motility and invasiveness of cells into the brain tissue. Simple 2-dimensional laboratory assays (e.g., a scratch assay) commonly are used to measure the effects of various experimental perturbations, such as treatment with chemical inhibitors. Several mathematical models have been developed to aid the understanding of the motile behavior and proliferation of GBM cells...
December 11, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/29226078/identification-and-in%C3%A2-silico-structural-analysis-of-gallus-gallus-protein-arginine-methyltransferase-4-prmt4
#19
Hannah Berberich, Felix Terwesten, Sinja Rakow, Peeyush Sahu, Caroline Bouchard, Marion Meixner, Sjaak Philipsen, Peter Kolb, Uta-Maria Bauer
Protein arginine methyltransferase 4 (PRMT4) is an essential epigenetic regulator of fundamental and conserved processes during vertebrate development, such as pluripotency and differentiation. Surprisingly, PRMT4 homologs have been identified in nearly all vertebrate classes except the avian genome. This raises the possibility that in birds PRMT4 functions are taken over by other PRMT family members. Here, we reveal the existence of a bona fide PRMT4 homolog in the chicken, Gallus gallus. Using a biochemical approach, we initially purified a putative chicken PRMT4 protein and thus provided the first evidence for the presence of an endogenous PRMT4-specific enzymatic activity toward histone H3 arginine 17 (H3R17) in avian cells...
December 2017: FEBS Open Bio
https://www.readbyqxmd.com/read/29212855/t-cell-densities-in-brain-metastases-are-associated-with-patient-survival-times-and-diffusion-tensor-mri-changes
#20
Rasheed Zakaria, Angela Platt-Higgins, Nitika Rathi, Mark Radon, Sumit Das, Kumar Das, Maneesh Bhojak, Andrew Brodbelt, Emmanuel Chavredakis, Michael D Jenkinson, Philip S Rudland
Brain metastases are common and are usually detected by magnetic resonance imaging (MRI). Diffusion tensor imaging (DTI) is a derivative MRI technique which can detect disruption of white matter tracts in the brain. We have matched preoperative DTI with image-guided sampling of the brain-tumor interface in 26 patients during resection of a brain metastasis and assessed mean diffusivity (MD) and fractional anisotropy (FA). The tissue samples were analysed for vascularity, inflammatory cell infiltration, growth pattern, and tumor expression of proteins associated with growth or local invasion such as Ki67, S100A4, and MMP2, 9, and 13...
December 6, 2017: Cancer Research
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