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Protein interface prediction

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https://www.readbyqxmd.com/read/28228527/activation-mechanism-of-the-g-protein-coupled-sweet-receptor-heterodimer-with-sweeteners-and-allosteric-agonists
#1
Soo-Kyung Kim, Yalu Chen, Ravinder Abrol, William A Goddard, Brian Guthrie
The sweet taste in humans is mediated by the TAS1R2/TAS1R3 G protein-coupled receptor (GPCR), which belongs to the class C family that also includes the metabotropic glutamate and γ-aminobutyric acid receptors. We report here the predicted 3D structure of the full-length TAS1R2/TAS1R3 heterodimer, including the Venus Flytrap Domains (VFDs) [in the closed-open (co) active conformation], the cysteine-rich domains (CRDs), and the transmembrane domains (TMDs) at the TM56/TM56 interface. We observe that binding of agonists to VFD2 of TAS1R2 leads to major conformational changes to form a TM6/TM6 interface between TMDs of TAS1R2 and TAS1R3, which is consistent with the activation process observed biophysically on the metabotropic glutamate receptor 2 homodimer...
February 22, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28217262/the-effects-of-shared-information-on-semantic-calculations-in-the-gene%C3%A2-ontology
#2
Paul W Bible, Hong-Wei Sun, Maria I Morasso, Rasiah Loganantharaj, Lai Wei
The structured vocabulary that describes gene function, the gene ontology (GO), serves as a powerful tool in biological research. One application of GO in computational biology calculates semantic similarity between two concepts to make inferences about the functional similarity of genes. A class of term similarity algorithms explicitly calculates the shared information (SI) between concepts then substitutes this calculation into traditional term similarity measures such as Resnik, Lin, and Jiang-Conrath. Alternative SI approaches, when combined with ontology choice and term similarity type, lead to many gene-to-gene similarity measures...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/28212602/happi-2-a-comprehensive-and-high-quality-map-of-human-annotated-and-predicted-protein-interactions
#3
Jake Y Chen, Ragini Pandey, Thanh M Nguyen
BACKGROUND: Human protein-protein interaction (PPI) data is essential to network and systems biology studies. PPI data can help biochemists hypothesize how proteins form complexes by binding to each other, how extracellular signals propagate through post-translational modification of de-activated signaling molecules, and how chemical reactions are coupled by enzymes involved in a complex biological process. Our capability to develop good public database resources for human PPI data has a direct impact on the quality of future research on genome biology and medicine...
February 17, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28205569/heteroaryldihydropyrimidine-hap-and-sulfamoylbenzamide-sba-inhibit-hepatitis-b-virus-replication-by-different-molecular-mechanisms
#4
Zheng Zhou, Taishan Hu, Xue Zhou, Steffen Wildum, Fernando Garcia-Alcalde, Zhiheng Xu, Daitze Wu, Yi Mao, Xiaojun Tian, Yuan Zhou, Fang Shen, Zhisen Zhang, Guozhi Tang, Isabel Najera, Guang Yang, Hong C Shen, John A T Young, Ning Qin
Heteroaryldihydropyrimidine (HAP) and sulfamoylbenzamide (SBA) are promising non-nucleos(t)ide HBV replication inhibitors. HAPs are known to promote core protein mis-assembly, but the molecular mechanism of abnormal assembly is still elusive. Likewise, the assembly status of core protein induced by SBA remains unknown. Here we show that SBA, unlike HAP, does not promote core protein mis-assembly. Interestingly, two reference compounds HAP_R01 and SBA_R01 bind to the same pocket at the dimer-dimer interface in the crystal structures of core protein Y132A hexamer...
February 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28182405/blip-ii-employs-differential-hotspot-residues-to-bind-structurally-similar-staphylococcus-aureus-pbp2a-and-class-a-%C3%AE-lactamases
#5
Carolyn J Adamski, Timothy Palzkill
The interaction of β-lactamase inhibitory protein II (BLIP-II) with β-lactamases serves as a model system to investigate the principles underlying protein-protein interactions. Previous studies have focused on identifying the determinants of binding affinity and specificity between BLIP-II and class A β-lactamases. However, interactions between BLIP-II and other bacterial proteins have yet to be explored. Here, we provide evidence that BLIP-II binds penicillin binding protein 2a (PBP2a) from methicillin-resistant Staphylococcus aureus (MRSA) with a KD in the low micromolar range...
February 16, 2017: Biochemistry
https://www.readbyqxmd.com/read/28174738/microgeographic-proteomic-networks-of-the-human-colonic-mucosa-and-their-association-with-inflammatory-bowel-disease
#6
Xiaoxiao Li, James LeBlanc, David Elashoff, Ian McHardy, Maomeng Tong, Bennett Roth, Andrew Ippoliti, Gildardo Barron, Dermot McGovern, Keely McDonald, Rodney Newberry, Thomas Graeber, Steve Horvath, Lee Goodglick, Jonathan Braun
BACKGROUND & AIMS: Interactions between mucosal cell types, environmental stressors, and intestinal microbiota contribute to pathogenesis in inflammatory bowel disease (IBD). Here, we applied metaproteomics of the mucosal-luminal interface to study the disease-related biology of the human colonic mucosa. METHODS: We recruited a discovery cohort of 51 IBD and non-IBD subjects endoscopically sampled by mucosal lavage at 6 colonic regions, and a validation cohort of 38 no-IBD subjects...
September 2016: Cellular and Molecular Gastroenterology and Hepatology
https://www.readbyqxmd.com/read/28168669/multiscale-modelling-of-bionano-interface
#7
Hender Lopez, Erik G Brandt, Alexander Mirzoev, Dmitry Zhurkin, Alexander Lyubartsev, Vladimir Lobaskin
We present a framework for coarse-grained modelling of the interface between foreign nanoparticles (NP) and biological fluids and membranes. Our model includes united-atom presentations of membrane lipids and globular proteins in implicit solvent, which are based on all-atom structures of the corresponding molecules and parameterised using experimental data or atomistic simulation results. The NPs are modelled by homogeneous spheres that interact with the beads of biomolecules via a central force that depends on the NP size...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28166227/improving-protein-protein-interaction-prediction-using-evolutionary-information-from-low-quality-msas
#8
Csilla Várnai, Nikolas S Burkoff, David L Wild
Evolutionary information stored in multiple sequence alignments (MSAs) has been used to identify the interaction interface of protein complexes, by measuring either co-conservation or co-mutation of amino acid residues across the interface. Recently, maximum entropy related correlated mutation measures (CMMs) such as direct information, decoupling direct from indirect interactions, have been developed to identify residue pairs interacting across the protein complex interface. These studies have focussed on carefully selected protein complexes with large, good-quality MSAs...
2017: PloS One
https://www.readbyqxmd.com/read/28155660/a-novel-index-of-protein-protein-interface-propensity-improves-interface-residue-recognition
#9
Wentao Dai, Aiping Wu, Liangxiao Ma, Yi-Xue Li, Taijiao Jiang, Yuan-Yuan Li
BACKGROUND: Protein-protein interface holds important information of protein-protein interactions which play key roles in most biological processes. In the past few years, a lot of efforts have been made to improve interface residue recognition by characterizing protein-protein interfaces and extracting relevant features. However, most previous studies were carried out in a qualitative level, and there are also some inconsistencies between them. RESULTS: In the present work, to improve interface residue recognition, we built a novel quantitative residue protein-protein interface propensity index (QIPI) and gained a comprehensive picture of protein-protein interface through analyzing protein-protein interfaces on our comprehensive protein-protein interfaces dataset (Astral2...
December 23, 2016: BMC Systems Biology
https://www.readbyqxmd.com/read/28152994/transductive-learning-as-an-alternative-to-translation-initiation-site-identification
#10
Cristiano Lacerda Nunes Pinto, Cristiane Neri Nobre, Luis Enrique Zárate
BACKGROUND: The correct protein coding region identification is an important and latent problem in the molecular biology field. This problem becomes a challenge due to the lack of deep knowledge about the biological systems and unfamiliarity of conservative characteristics in the messenger RNA (mRNA). Therefore, it is fundamental to research for computational methods aiming to help the patterns discovery for identification of the Translation Initiation Sites (TIS). In the field of Bioinformatics, machine learning methods have been widely applied based on the inductive inference, as Inductive Support Vector Machine (ISVM)...
February 2, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28135076/surface-initiated-controlled-radical-polymerization-state-of-the-art-opportunities-and-challenges-in-surface-and-interface-engineering-with-polymer-brushes
#11
Justin O Zoppe, Nariye Cavusoglu Ataman, Piotr Mocny, Jian Wang, John Moraes, Harm-Anton Klok
The generation of polymer brushes by surface-initiated controlled radical polymerization (SI-CRP) techniques has become a powerful approach to tailor the chemical and physical properties of interfaces and has given rise to great advances in surface and interface engineering. Polymer brushes are defined as thin polymer films in which the individual polymer chains are tethered by one chain end to a solid interface. Significant advances have been made over the past years in the field of polymer brushes. This includes novel developments in SI-CRP, as well as the emergence of novel applications such as catalysis, electronics, nanomaterial synthesis and biosensing...
January 30, 2017: Chemical Reviews
https://www.readbyqxmd.com/read/28134831/spidermir-an-r-bioconductor-package-for-integrative-analysis-with-mirna-data
#12
Claudia Cava, Antonio Colaprico, Gloria Bertoli, Alex Graudenzi, Tiago C Silva, Catharina Olsen, Houtan Noushmehr, Gianluca Bontempi, Giancarlo Mauri, Isabella Castiglioni
Gene Regulatory Networks (GRNs) control many biological systems, but how such network coordination is shaped is still unknown. GRNs can be subdivided into basic connections that describe how the network members interact e.g., co-expression, physical interaction, co-localization, genetic influence, pathways, and shared protein domains. The important regulatory mechanisms of these networks involve miRNAs. We developed an R/Bioconductor package, namely SpidermiR, which offers an easy access to both GRNs and miRNAs to the end user, and integrates this information with differentially expressed genes obtained from The Cancer Genome Atlas...
January 27, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28130547/mitochondrial-protein-interactome-elucidated-by-chemical-cross-linking-mass-spectrometry
#13
Devin K Schweppe, Juan D Chavez, Chi Fung Lee, Arianne Caudal, Shane E Kruse, Rudy Stuppard, David J Marcinek, Gerald S Shadel, Rong Tian, James E Bruce
Mitochondrial protein interactions and complexes facilitate mitochondrial function. These complexes range from simple dimers to the respirasome supercomplex consisting of oxidative phosphorylation complexes I, III, and IV. To improve understanding of mitochondrial function, we used chemical cross-linking mass spectrometry to identify 2,427 cross-linked peptide pairs from 327 mitochondrial proteins in whole, respiring murine mitochondria. In situ interactions were observed in proteins throughout the electron transport chain membrane complexes, ATP synthase, and the mitochondrial contact site and cristae organizing system (MICOS) complex...
January 27, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28124908/structural-insights-how-pip2-imposes-preferred-binding-orientations-of-fak-at-lipid-membranes
#14
Florian A Herzog, Lukas Braun, Ingmar Schoen, Viola Vogel
Focal adhesion kinase (FAK) is a multidomain protein (FERM-kinase-FAT) with important signaling functions in the regulation of cell-substrate adhesions. Its inactive, autoinhibited form is recruited from the cytoplasm to the plasma membrane, where it becomes activated at PIP2 enriched regions. To elucidate the molecular basis of activation, we performed a systematic screening of binding orientations of FAK's autoinhibited FERM-kinase complex, as well as of the dissociated FERM and kinase domains alone, on model plasma membranes using coarse-grained scFix MARTINI simulations, partially corroborated by atomistic MD simulations...
February 10, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28122455/high-throughput-simulations-reveal-membrane-mediated-effects-of-alcohols-on-mscl-gating
#15
Manuel N Melo, Clément Arnarez, Hendrik Sikkema, Neeraj Kumar, Martin Walko, Herman J C Berendsen, Armagan Kocer, Siewert J Marrink, Helgi I Ingólfsson
The mechanosensitive channels of large conductance (MscL) are bacterial membrane proteins that serve as last resort emergency release valves in case of severe osmotic downshock. Sensing bilayer tension, MscL channels are sensitive to changes in the bilayer environment and are, therefore, an ideal test case for exploring membrane protein coupling. Here, we use high-throughput coarse-grained molecular dynamics simulations to characterize MscL gating kinetics in different bilayer environments under the influence of alcohols...
February 10, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28111366/orchidstra-2-0-a-transcriptomics-resource-for-the-orchid-family
#16
Ya-Ting Chao, Shao-Hua Yen, Jen-Hau Yeh, Wan-Chieh Chen, Ming-Che Shih
Orchidaceae, the orchid family, encompasses more than 25,000 species and five subfamilies. Due to their beautiful and exotic flowers, distinct biological and ecological features, orchids have aroused wide interest among both researchers and the general public. We constructed the Orchidstra database, a resource for orchid transcriptome assembly and gene annotations. The Orchistra database has been under active development since 2013. To accommodate the increasing amount of orchid transcriptome data and house more comprehensive information, Orchidstra 2...
January 22, 2017: Plant & Cell Physiology
https://www.readbyqxmd.com/read/28108234/interaction-of-ar-and-inos-in-lens-epithelial-cell-a-new-pathogenesis-and-potential-therapeutic-targets-of-diabetic-cataract
#17
Xue Li, Wenping Liu, Xinduo Huang, Jianping Xiong, Xiaoyong Wei
Although there is significant interest in revealing the role of aldose reductase (AR) and inducible nitric oxide synthase (iNOS) in diabetic cataract (DC), the interaction of AR and iNOS remains unknown. The aim of this study is to investigate the pathogenesis mechanisms and explore as a new potential therapeutic targets for DC. This study investigated the interaction of AR-iNOS through the methods of enzyme kinetics, molecular docking and molecular dynamics simulation, co-immunoprecipitation and fluorescence resonance energy transfer (FRET)...
January 17, 2017: Archives of Biochemistry and Biophysics
https://www.readbyqxmd.com/read/28106297/different-dynamics-and-pathway-of-disulfide-bonds-reduction-of-two-human-defensins-a-molecular-dynamics-simulation-study
#18
Liqun Zhang
Human defensins are a class of antimicrobial peptides that are crucial components of the innate immune system. Both human α defensin type 5(HD5) and human β defensin type 3 (hBD-3) have 6 cysteine residues which form 3 pairs of disulfide bonds under oxidizing condition. Disulfide bond linking is important to the protein structure stabilization, and the disulfide bond linking and breaking order has been shown to influence protein function. In this project, microsecond long molecular dynamics simulations were performed to study the structure and dynamics of HD5 and hBD-3 wildtype and analogs which have all 3 disulfide bonds released under reducing conditions...
January 20, 2017: Proteins
https://www.readbyqxmd.com/read/28077870/the-role-of-interfacial-lipids-in-stabilizing-membrane-protein-oligomers
#19
Kallol Gupta, Joseph A C Donlan, Jonathan T S Hopper, Povilas Uzdavinys, Michael Landreh, Weston B Struwe, David Drew, Andrew J Baldwin, Phillip J Stansfeld, Carol V Robinson
Oligomerization of membrane proteins in response to lipid binding has a critical role in many cell-signalling pathways but is often difficult to define or predict. Here we report the development of a mass spectrometry platform to determine simultaneously the presence of interfacial lipids and oligomeric stability and to uncover how lipids act as key regulators of membrane-protein association. Evaluation of oligomeric strength for a dataset of 125 α-helical oligomeric membrane proteins reveals an absence of interfacial lipids in the mass spectra of 12 membrane proteins with high oligomeric stability...
January 19, 2017: Nature
https://www.readbyqxmd.com/read/28077569/rain-rna-protein-association-and-interaction-networks
#20
Alexander Junge, Jan C Refsgaard, Christian Garde, Xiaoyong Pan, Alberto Santos, Ferhat Alkan, Christian Anthon, Christian von Mering, Christopher T Workman, Lars Juhl Jensen, Jan Gorodkin
Protein association networks can be inferred from a range of resources including experimental data, literature mining and computational predictions. These types of evidence are emerging for non-coding RNAs (ncRNAs) as well. However, integration of ncRNAs into protein association networks is challenging due to data heterogeneity. Here, we present a database of ncRNA-RNA and ncRNA-protein interactions and its integration with the STRING database of protein-protein interactions. These ncRNA associations cover four organisms and have been established from curated examples, experimental data, interaction predictions and automatic literature mining...
2017: Database: the Journal of Biological Databases and Curation
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