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3D complex
Most of the proteins in a cell assemble into complexes to carry out their function. It is therefore crucial to understand the physicochemical properties as well as the evolution of interactions between proteins. The Protein Data...
Proteomic plasma membrane profiling reveals an essential role for gp96 in the cell surface expression of LDLR family members, including the LDL receptor and LRP6.
Michael P Weekes, Robin Antrobus, Suzanne Talbot, Simon Hör, Nikol Simecek, Duncan L Smith, Stuart Bloor, Felix Randow, Paul J Lehner
May 29, 2019
The endoplasmic reticulum chaperone gp96 is required for the cell surface expression of a narrow range of proteins, including toll-like receptors (TLRs) and integrins. To identify a more comprehensive repertoire of proteins...
Animals Antigens CD Cell Line Cell Membrane Chromatography High Pressure Liquid Down-Regulation Integrins Low Density Lipoprotein Receptor-Related Protein-6 Membrane Glycoproteins Membrane Proteins Mice Peptide Fragments Protein Interaction Mapping Proteomics Receptors LDL Tandem Mass Spectrometry Toll-Like Receptors
Synergistic insights into human health from aptamer- and antibody-based proteomic profiling.
Maik Pietzner, Eleanor Wheeler, Julia Carrasco-Zanini, Nicola D Kerrison, Erin Oerton, Mine Koprulu, Jian'an Luan, Aroon D Hingorani, Steve A Williams, Nicholas J Wareham, Claudia Langenberg
Jan 07, 2022
Mutation of the cytosolic ribosomal protein-encoding RPS10B gene affects shoot meristematic function in Arabidopsis.
Arabidopsis Arabidopsis Proteins Cytosol DNA Complementary F-Box Proteins Gene Expression Regulation Plant Genes Plant Indoleacetic Acids Inflorescence Meristem Mutation Naphthaleneacetic Acids Phenotype Plant Leaves Plant Shoots Promoter Regions Genetic Protein Interaction Mapping Receptors Cell Surface Ribosomal Proteins Transcription Factors
Interrogation of the protein-protein interactions between human BRCA2 BRC repeats and RAD51 reveals atomistic determinants of affinity.
Daniel J Cole, Eeson Rajendra, Meredith Roberts-Thomson, Bryn Hardwick, Grahame J McKenzie, Mike C Payne, Ashok R Venkitaraman, Chris-Kriton Skylaris
Aug 08, 2017
The breast cancer suppressor BRCA2 controls the recombinase RAD51 in the reactions that mediate homologous DNA recombination, an essential cellular process required for the error-free repair of DNA double-stranded breaks. The...
Amino Acid Motifs Amino Acid Sequence BRCA2 Protein Fluorescence Polarization Immunoassay Humans Models Molecular Molecular Sequence Data Mutation Protein Binding Protein Interaction Domains and Motifs Protein Interaction Mapping Protein Stability Rad51 Recombinase Repetitive Sequences Amino Acid Sequence Alignment Thermodynamics
Insights into bacterial lipoprotein trafficking from a structure of LolA bound to the LolC periplasmic domain.
Proteomic and Biochemical Comparison of the Cellular Interaction Partners of Human VPS33A and VPS33B.
Morag R Hunter, Geoffrey G Hesketh, Tomasz H Benedyk, Anne-Claude Gingras, Stephen C Graham
Sep 05, 2018
Sin3A recruits Tet1 to the PAH1 domain via a highly conserved Sin3-Interaction Domain.
The Sin3A complex acts as a transcriptional hub, integrating the function of diverse transcription factors with histone modifying enzymes, notably, histone deacetylases (HDAC) 1 and 2. The Sin3A protein sits at the centre of the...
Amino Acid Substitution DNA Mutational Analysis HEK293 Cells Humans Magnetic Resonance Spectroscopy Mixed Function Oxygenases Models Molecular Protein Binding Protein Conformation Protein Domains Protein Interaction Mapping Proto-Oncogene Proteins Repressor Proteins Sin3 Histone Deacetylase and Corepressor Complex
Cellular stress responses to chronic heat shock and shell damage in temperate Mya truncata.
Acclimation, via phenotypic flexibility, is a potential means for a fast response to climate change. Understanding the molecular mechanisms underpinning phenotypic flexibility can provide a fine-scale cellular understanding of...
Mapping RNA-Chromatin Interactions In Vivo with RNA-DamID.
Long-noncoding RNAs (lncRNAs) are emerging as regulators of development and disease. lncRNAs are expressed in exquisitely precise expression patterns in vivo and many interact with chromatin to regulate gene expression. However...
Promoter interactome of human embryonic stem cell-derived cardiomyocytes connects GWAS regions to cardiac gene networks.
Mun-Kit Choy, Biola M Javierre, Simon G Williams, Stephanie L Baross, Yingjuan Liu, Steven W Wingett, Artur Akbarov, Chris Wallace, Paula Freire-Pritchett, Peter J Rugg-Gunn, Mikhail Spivakov, Peter Fraser, Bernard D Keavney
Sep 08, 2018
Long-range chromosomal interactions bring distal regulatory elements and promoters together to regulate gene expression in biological processes. By performing promoter capture Hi-C (PCHi-C) on human embryonic stem cell-derived...
Actinin Calpain Cell Differentiation Cell Line Enhancer Elements Genetic Gene Regulatory Networks Genome Human Genome-Wide Association Study Heart Conduction System Heart Rate Heart Ventricles Histones Human Embryonic Stem Cells Humans Myocytes Cardiac Promoter Regions Genetic Protein Interaction Mapping Protein Isoforms Quantitative Trait Loci
In vivo analysis of proteomes and interactomes using Parallel Affinity Capture (iPAC) coupled to mass spectrometry.
Johanna S Rees, Nick Lowe, Irina M Armean, John Roote, Glynnis Johnson, Emma Drummond, Helen Spriggs, Edward Ryder, Steven Russell, Daniel St Johnston, Kathryn S Lilley
Jan 18, 2016
Network of protein interactions within the Drosophila inner kinetochore.
Magdalena M Richter, Jaroslaw Poznanski, Anna Zdziarska, Mariusz Czarnocki-Cieciura, Zoltan Lipinszki, Michal Dadlez, David M Glover, Marcin R Przewloka
Feb 03, 2016
HDX-MS Centromere CHROMOSOME kinetochore Mitosis structure Amino Acid Sequence Animals Centromere Chromosomal Proteins Non-Histone Drosophila Drosophila Proteins Kinetochores Microtubules Models Molecular Molecular Sequence Data Nuclear Proteins Protein Binding Protein Conformation Protein Interaction Domains and Motifs Protein Interaction Mapping Protein Interaction Maps Protein Multimerization Sequence Alignment Transcription Factors Vesicular Transport Proteins
Architecture of TAF11/TAF13/TBP complex suggests novel regulation properties of general transcription factor TFIID.
Kapil Gupta, Aleksandra A Watson, Tiago Baptista, Elisabeth Scheer, Anna L Chambers, Christine Koehler, Juan Zou, Ima Obong-Ebong, Eaazhisai Kandiah, Arturo Temblador, Adam Round, Eric Forest, Petr Man, Christoph Bieniossek, Ernest D Laue, Edward A Lemke, Juri Rappsilber, Carol V Robinson, Didier Devys, Làszlò Tora, Imre Berger
Jan 24, 2018
General transcription factor TFIID is a key component of RNA polymerase II transcription initiation. Human TFIID is a megadalton-sized complex comprising TATA-binding protein (TBP) and 13 TBP-associated factors (TAFs). TBP binds...
S. cerevisiae TBP associated factors TFIID Biochemistry biophysics core promoter DNA Gene regulation histone fold domain human structural biology Transcription Factors Crystallography X-Ray DNA Histone Acetyltransferases Humans Mass Spectrometry Promoter Regions Genetic Protein Binding Protein Conformation Protein Interaction Mapping TATA-Binding Protein Associated Factors TATA-Box Binding Protein Transcription Factor TFIID
Fractionation profiling
Georg HH Borner, Marco Y Hein, Jennifer Hirst, James R Edgar, Matthias Mann, Margaret S Robinson
Feb 13, 2019
We developed "fractionation profiling," a method for rapid proteomic analysis of membrane vesicles and protein particles. The approach combines quantitative proteomics with subcellular fractionation to generate signature protein...
Evolutionary programming as a platform for in silico metabolic engineering.
BACKGROUND: Through genetic engineering it is possible to introduce targeted genetic changes and hereby engineer the metabolism of microbial cells with the objective to obtain desirable phenotypes. However, owing to the...
Algorithms Benzaldehydes Computational Biology Computer Simulation Escherichia coli evolution Molecular Gene Expression Regulation Genetic Engineering Genome Fungal Glycerol Models Biological Models Genetic Phenotype Protein Engineering Protein Interaction Mapping Saccharomyces cerevisiae Software Succinic Acid
COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms.
Marek Ostaszewski, Anna Niarakis, Alexander Mazein, Inna Kuperstein, Robert Phair, Aurelio Orta-Resendiz, Vidisha Singh, Sara Sadat Aghamiri, Marcio Luis Acencio, Enrico Glaab, Andreas Ruepp, Gisela Fobo, Corinna Montrone, Barbara Brauner, Goar Frishman, Luis Cristóbal Monraz Gómez, Julia Somers, Matti Hoch, Shailendra Kumar Gupta, Julia Scheel, Hanna Borlinghaus, Tobias Czauderna, Falk Schreiber, Arnau Montagud, Miguel Ponce de Leon, Akira Funahashi, Yusuke Hiki, Noriko Hiroi, Takahiro G Yamada, Andreas Dräger, Alina Renz, Muhammad Naveez, Zsolt Bocskei, Francesco Messina, Daniela Börnigen, Liam Fergusson, Marta Conti, Marius Rameil, Vanessa Nakonecnij, Jakob Vanhoefer, Leonard Schmiester, Muying Wang, Emily E Ackerman, Jason E Shoemaker, Jeremy Zucker, Kristie Oxford, Jeremy Teuton, Ebru Kocakaya, Gökçe Yağmur Summak, Kristina Hanspers, Martina Kutmon, Susan Coort, Lars Eijssen, Friederike Ehrhart, Devasahayam Arokia Balaya Rex, Denise Slenter, Marvin Martens, Nhung Pham, Robin Haw, Bijay Jassal, Lisa Matthews, Marija Orlic-Milacic, Andrea Senff Ribeiro, Karen Rothfels, Veronica Shamovsky, Ralf Stephan, Cristoffer Sevilla, Thawfeek Varusai, Jean-Marie Ravel, Rupsha Fraser, Vera Ortseifen, Silvia Marchesi, Piotr Gawron, Ewa Smula, Laurent Heirendt, Venkata Satagopam, Guanming Wu, Anders Riutta, Martin Golebiewski, Stuart Owen, Carole Goble, Xiaoming Hu, Rupert W Overall, Dieter Maier, Angela Bauch, Benjamin M Gyori, John A Bachman, Carlos Vega, Valentin Grouès, Miguel Vazquez, Pablo Porras, Luana Licata, Marta Iannuccelli, Francesca Sacco, Anastasia Nesterova, Anton Yuryev, Anita de Waard, Denes Turei, Augustin Luna, Ozgun Babur, Sylvain Soliman, Alberto Valdeolivas, Marina Esteban-Medina, Maria Peña-Chilet, Kinza Rian, Tomáš Helikar, Bhanwar Lal Puniya, Dezso Modos, Agatha Treveil, Marton Olbei, Bertrand De Meulder, Stephane Ballereau, Aurélien Dugourd, Aurélien Naldi, Vincent Noël, Laurence Calzone, Chris Sander, Emek Demir, Tamas Korcsmaros, Tom C Freeman, Franck Augé, Jacques S Beckmann, Jan Hasenauer, Olaf Wolkenhauer, Egon L Wilighagen, Alexander R Pico, Chris T Evelo, Marc E Gillespie, Lincoln D Stein, Henning Hermjakob, Peter D'Eustachio, Julio Saez-Rodriguez, Joaquin Dopazo, Alfonso Valencia, Hiroaki Kitano, Emmanuel Barillot, Charles Auffray, Rudi Balling, Reinhard Schneider, COVID-19 Disease Map Community
Nov 22, 2021
We need to effectively combine the knowledge from surging literature with complex datasets to propose mechanistic models of SARS-CoV-2 infection, improving data interpretation and predicting key targets of intervention. Here, we...
computable knowledge repository Large-scale Biocuration omics data analysis open access community effort systems biomedicine Antiviral Agents covid-19 Computational Biology Computer Graphics Cytokines Data Mining Databases Factual Gene Expression Regulation Host Microbial Interactions Humans Immunity Cellular Immunity Humoral Immunity Innate Lymphocytes Metabolic Networks and Pathways Myeloid Cells Protein Interaction Mapping SARS-CoV-2 Signal Transduction Software Transcription Factors Viral Proteins COVID-19 Drug Treatment
Prediction by graph theoretic measures of structural effects in proteins arising from non-synonymous single nucleotide polymorphisms.
Recent analyses of human genome sequences have given rise to impressive advances in identifying non-synonymous single nucleotide polymorphisms (nsSNPs). By contrast, the annotation of nsSNPs and their links to diseases are...
Artificial Intelligence Computational Biology DNA Mutational Analysis Genetic Predisposition to Disease Humans Models Genetic Models Molecular Neural Networks Computer Polymorphism Single Nucleotide Predictive Value of Tests Protein Conformation Protein Interaction Mapping Proteins Sequence Alignment Sequence Analysis Protein Thermodynamics
Discarding functional residues from the substitution table improves predictions of active sites within three-dimensional structures.
Substitutions of individual amino acids in proteins may be under very different evolutionary restraints depending on their structural and functional roles. The Environment Specific Substitution Table (ESST) describes the pattern...
mCSM-PPI2
Benchmarking Binding Sites Crystallography X-Ray Datasets as Topic Humans Internet Machine Learning Mutation Missense Protein Binding Protein Conformation alpha-Helical Protein Conformation beta-Strand Protein Interaction Domains and Motifs Protein Interaction Mapping Proteins Software Thermodynamics
Hyperactivation of HUSH complex function by Charcot-Marie-Tooth disease mutation in MORC2
IA Tchasovnikarova, RT Timms, CH Douse, RC Roberts, G Dougan, RE Kingston, Y Modis, PJ Lehner
Jul 13, 2017
Adenosine Triphosphatases CRISPR-Cas Systems Charcot-Marie-Tooth disease Chromatin Assembly and Disassembly Epigenetic Repression Gene Silencing HeLa Cells Heterochromatin Histone Code Histone-Lysine N-Methyltransferase Histones Humans Lysine Methylation Multiprotein Complexes Mutation Missense Neurons Protein Domains Protein Interaction Mapping Protein Methyltransferases Protein Processing Post-Translational Transcription Factors Transgenes
Interaction between hormone-sensitive lipase and ChREBP in fat cells controls insulin sensitivity.
Pauline Morigny, Marianne Houssier, Aline Mairal, Claire Ghilain, Etienne Mouisel, Fadila Benhamed, Bernard Masri, Emeline Recazens, Pierre-Damien Denechaud, Geneviève Tavernier, Sylvie Caspar-Bauguil, Sam Virtue, Veronika Sramkova, Laurent Monbrun, Anne Mazars, Madjid Zanoun, Sandra Guilmeau, Valentin Barquissau, Diane Beuzelin, Sophie Bonnel, Marie Marques, Boris Monge-Roffarello, Corinne Lefort, Barbara Fielding, Thierry Sulpice, Arne Astrup, Bernard Payrastre, Justine Bertrand-Michel, Emmanuelle Meugnier, Laetitia Ligat, Frédéric Lopez, Hervé Guillou, Charlotte Ling, Cecilia Holm, Remi Rabasa-Lhoret, Wim HM Saris, Vladimir Stich, Peter Arner, Mikael Rydén, Cedric Moro, Nathalie Viguerie, Matthew Harms, Stefan Hallén, Antonio Vidal-Puig, Hubert Vidal, Catherine Postic, Dominique Langin
Nov 16, 2020
Impaired adipose tissue insulin signalling is a critical feature of insulin resistance. Here we identify a pathway linking the lipolytic enzyme hormone-sensitive lipase (HSL) to insulin action via the glucose-responsive...
ChREBP ELOVL Fatty Acid Elongase 6 ELOVL6 Expression Hormone-sensitive Lipase Insulin Signaling Adipocytes Adipose Tissue Animals Basic Helix-Loop-Helix Leucine Zipper Transcription Factors Biomarkers Fatty Acid Elongases Gene Expression Glucose Insulin Insulin Resistance Membrane Fluidity Mice Mice Transgenic Protein Interaction Mapping Protein Interaction Maps Signal Transduction Sterol Esterase
A protein domain interaction interface database
Sungsam Gong, Changbum Park, Hansol Choi, Junsu Ko, Insoo Jang, Jungsul Lee, Dan M Bolser, Donghoon Oh, Deok-Soo Kim, Jong Bhak
Apr 16, 2019
BACKGROUND: Most proteins function by interacting with other molecules. Their interaction interfaces are highly conserved throughout evolution to avoid undesirable interactions that lead to fatal disorders in cells. Rational...
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