Thermal proximity coaggregation for system-wide profiling of protein complex dynamics in cells

Science
Chris Soon Heng TanPär Nordlund

Abstract

Proteins differentially interact with each other across cellular states and conditions but efficient proteome-wide strategy to monitor them is lacking. We report the application of thermal proximity coaggregation (TPCA) for high throughput intracellular monitoring of protein complex dynamics. Significant TPCA signatures observed among well-validated protein-protein interactions correlate positively with interaction stoichiometry, and are statistically observable in more than 350 annotated human protein complexes. Using TPCA, we identify many complexes without detectable differential protein expression, including chromatin-associated complexes, modulated in S-phase of the cell cycle. Comparing six cell lines, TPCA reveals cell-specific interactions even in fundamental cellular processes. TPCA constitutes an approach for system-wide studies of protein complexes in non-engineered cells and tissues, and might be used to identify protein complexes that are modulated in diseases.

References

Aug 26, 1998·Molecular and Cellular Biology·H ChoD Reinberg
Oct 2, 2003·Proceedings of the National Academy of Sciences of the United States of America·Maarten Hoek, Bruce Stillman
Dec 19, 2003·Nucleic Acids Research·Henning HermjakobRolf Apweiler
Mar 14, 2007·Molecular Systems Biology·Rob M EwingDaniel Figeys
Apr 3, 2008·Genome Research·Trey Ideker, Roded Sharan
Sep 17, 2008·Journal of Molecular Biology·Hong-Wei WangEva Nogales
Oct 18, 2008·Nature Reviews. Genetics·William F MarzluffRobert J Duronio
May 14, 2009·Bioinformatics·Guimei LiuHon Nian Chua
Jun 3, 2009·BMC Bioinformatics·Min WuSee-Kiong Ng
Aug 5, 2009·Molecular and Cellular Biology·Belén Gómez-GonzálezAndrés Aguilera
Nov 4, 2009·Nucleic Acids Research·Andreas RueppH-Werner Mewes
May 31, 2011·Cell·Anna MalovannayaJun Qin
Nov 19, 2011·Nucleic Acids Research·Luana LicataGianni Cesareni
Mar 20, 2012·Nature Methods·Tamás NepuszAlberto Paccanaro
Sep 4, 2012·Cell·Pierre C HavugimanaAndrew Emili
Sep 17, 2014·Molecular & Cellular Proteomics : MCP·Jacek R WiśniewskiMatthias Mann
Oct 4, 2014·Science·Mikhail M SavitskiGerard Drewes
Nov 25, 2014·Cell·Thomas RollandMarc Vidal
Nov 28, 2014·Nucleic Acids Research·Andrew Chatr-AryamontriMike Tyers
Jul 18, 2015·Cell·Edward L HuttlinSteven P Gygi
Sep 22, 2015·Nature Methods·Kilian V M HuberGiulio Superti-Furga
Nov 3, 2015·Nature Methods·Friedrich B M ReinhardGerard Drewes
Nov 14, 2015·Annual Review of Pharmacology and Toxicology·Daniel Martinez Molina, Pär Nordlund

Citations

Nov 8, 2018·Molecular & Cellular Proteomics : MCP·Jeremy D VolkeningMichael R Sussman
Jul 8, 2018·Molecular Systems Biology·André MateusMikhail M Savitski
Oct 5, 2019·Molecular & Cellular Proteomics : MCP·Dorothee ChildsWolfgang Huber
Mar 6, 2020·Molecular Systems Biology·André MateusMikhail M Savitski
Jun 20, 2020·Expert Review of Proteomics·Joseph GillenAleksandra Nita-Lazar
Mar 5, 2020·Proceedings of the National Academy of Sciences of the United States of America·Kuan-Yi LuEmily R Derbyshire
Nov 1, 2019·SLAS Discovery·Brinton Seashore-LudlowThomas Lundbäck
Mar 13, 2019·Nature Communications·Sindhuja SridharanMikhail M Savitski
Dec 20, 2019·Scientific Reports·Anette LangebäckSara Lööf
Jan 22, 2020·Nature Biotechnology·Jessica PerrinGiovanna Bergamini
Feb 12, 2020·Nature Communications·Yutaka HashimotoIleana M Cristea
Jun 17, 2020·Genome Biology·Craig H KerrLeonard J Foster
Apr 15, 2020·Nature Methods·Anna JarzabBernhard Kuster
Jul 28, 2020·Bioinformatics·Nils KurzawaMikhail M Savitski
Mar 29, 2018·Science·Xiao-Han LiM Madan Babu
Oct 9, 2019·Proceedings of the National Academy of Sciences of the United States of America·Elizabeth M HartThomas J Silhavy
Jan 24, 2019·Science Signaling·Elise J NeedhamSean J Humphrey
Jan 4, 2019·Science Translational Medicine·Jerzy M DziekanPär Nordlund
Oct 21, 2020·Nature Reviews. Materials·Zhongmin TangWei Tao
Jan 13, 2021·Molecular Systems Biology·Alicia L RichardsNevan J Krogan
Dec 18, 2020·Life Sciences·Semim Akhtar AhmedAjaikumar B Kunnumakkara
Jan 16, 2021·Journal of Zhejiang University. Science. B·Zhen Chen, Junjie Chen
Feb 1, 2019·Molecular & Cellular Proteomics : MCP·Jeremy D VolkeningMichael R Sussman
Dec 11, 2020·Nature·André MateusMikhail M Savitski
Dec 1, 2019·Molecular & Cellular Proteomics : MCP·Dorothee ChildsWolfgang Huber
Mar 9, 2020·Current Opinion in Chemical Biology·Jun X HuangRaymond E Moellering
Mar 12, 2021·Briefings in Bioinformatics·Lun HuZhu-Hong You
Dec 17, 2019·Current Opinion in Structural Biology·Natalie de Souza, Paola Picotti
May 1, 2021·International Journal of Molecular Sciences·Isabell Bludau
May 28, 2021·Cellular and Molecular Life Sciences : CMLS·Teck Yew LowChris Soon Heng Tan
May 18, 2021·Chembiochem : a European Journal of Chemical Biology·Kuan-Yi LuEmily R Derbyshire

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Hereditary Sensory Autonomic Neuropathy

Hereditary Sensory Autonomic Neuropathies are a group of inherited neurodegenerative disorders characterized clinically by loss of sensation and autonomic dysfunction. Here is the latest research on these neuropathies.

Spatio-Temporal Regulation of DNA Repair

DNA repair is a complex process regulated by several different classes of enzymes, including ligases, endonucleases, and polymerases. This feed focuses on the spatial and temporal regulation that accompanies DNA damage signaling and repair enzymes and processes.

Glut1 Deficiency

Glut1 deficiency, an autosomal dominant, genetic metabolic disorder associated with a deficiency of GLUT1, the protein that transports glucose across the blood brain barrier, is characterized by mental and motor developmental delays and infantile seizures. Follow the latest research on Glut1 deficiency with this feed.

Separation Anxiety

Separation anxiety is a type of anxiety disorder that involves excessive distress and anxiety with separation. This may include separation from places or people to which they have a strong emotional connection with. It often affects children more than adults. Here is the latest research on separation anxiety.

KIF1A Associated Neurological Disorder

KIF1A associated neurological disorder (KAND) is a rare neurodegenerative condition caused by mutations in the KIF1A gene. KAND may present with a wide range and severity of symptoms including stiff or weak leg muscles, low muscle tone, a lack of muscle coordination and balance, and intellectual disability. Find the latest research on KAND here.

Regulation of Vocal-Motor Plasticity

Dopaminergic projections to the basal ganglia and nucleus accumbens shape the learning and plasticity of motivated behaviors across species including the regulation of vocal-motor plasticity and performance in songbirds. Discover the latest research on the regulation of vocal-motor plasticity here.