Protein social behavior makes a stronger signal for partner identification than surface geometry

Proteins
Elodie Laine, Alessandra Carbone

Abstract

Cells are interactive living systems where proteins movements, interactions and regulation are substantially free from centralized management. How protein physico-chemical and geometrical properties determine who interact with whom remains far from fully understood. We show that characterizing how a protein behaves with many potential interactors in a complete cross-docking study leads to a sharp identification of its cellular/true/native partner(s). We define a sociability index, or S-index, reflecting whether a protein likes or not to pair with other proteins. Formally, we propose a suitable normalization function that accounts for protein sociability and we combine it with a simple interface-based (ranking) score to discriminate partners from non-interactors. We show that sociability is an important factor and that the normalization permits to reach a much higher discriminative power than shape complementarity docking scores. The social effect is also observed with more sophisticated docking algorithms. Docking conformations are evaluated using experimental binding sites. These latter approximate in the best possible way binding sites predictions, which have reached high accuracy in recent years. This makes our analysis help...Continue Reading

References

Feb 13, 2003·Journal of the American Chemical Society·Cyril DominguezAlexandre M J J Bonvin
May 23, 2003·Protein Science : a Publication of the Protein Society·Martin Zacharias
Jun 5, 2003·Proteins·Joel JaninCritical Assessment of PRedicted Interactions
Sep 23, 2003·Journal of Molecular Biology·Patrick AloyRobert B Russell
Dec 23, 2003·Journal of Molecular Biology·Juan Fernández-RecioRuben Abagyan
Mar 31, 2004·Journal of Molecular Biology·Hani NeuvirthGideon Schreiber
Jun 15, 2004·Current Opinion in Structural Biology·Robert B RussellAndrej Sali
Oct 21, 2004·Proteins·Juan Fernández-RecioRuben Abagyan
Jun 28, 2005·Proteins·Julian MintserisZhiping Weng
Dec 31, 2005·Proceedings of the National Academy of Sciences of the United States of America·Eric J DeedsEugene Shakhnovich
Feb 24, 2006·Nature Reviews. Molecular Cell Biology·Patrick Aloy, Robert B Russell
Mar 21, 2006·Current Opinion in Structural Biology·Jeffrey J Gray
Aug 9, 2006·Nucleic Acids Research·Shide LiangYaoqi Zhou
Jul 12, 2007·Proteins·Julian MintserisZhiping Weng
Sep 13, 2007·Proceedings of the National Academy of Sciences of the United States of America·Eric J DeedsEugene Shakhnovich
Dec 14, 2007·Nature·Carol V RobinsonWolfgang Baumeister
Aug 7, 2008·Molecular Systems Biology·Jingshan ZhangEugene Shakhnovich
Aug 19, 2008·Journal of Molecular Biology·Sophie Sacquin-MoraRichard Lavery
Mar 23, 2010·Molecular & Cellular Proteomics : MCP·Ezgi KaracaAlexandre M J J Bonvin
Mar 25, 2010·Journal of Proteome Research·Panagiotis L Kastritis, Alexandre M J J Bonvin
May 29, 2010·Molecular & Cellular Proteomics : MCP·Keren LaskerAndrej Sali
Sep 2, 2010·Proteins·Howook HwangZhiping Weng
Sep 15, 2010·Proteins·Marc F Lensink, Shoshana J Wodak
Dec 15, 2010·Proceedings of the National Academy of Sciences of the United States of America·Mu Gao, Jeffrey Skolnick
Feb 18, 2011·Molecular Systems Biology·Mark Nicholas WassAlfonso Valencia
Mar 4, 2011·Proceedings of the National Academy of Sciences of the United States of America·Muyoung HeoEugene Shakhnovich
Aug 25, 2011·BMC Bioinformatics·Joan SeguraNarcis Fernandez-Fuentes
Oct 18, 2011·Journal of Molecular Biology·Sarel J FleishmanDavid Baker
Nov 5, 2011·Nucleic Acids Research·Guilhem FaureRaphaël Guerois
Mar 20, 2012·BMC Bioinformatics·Rafael A JordanVasant Honavar
May 9, 2012·BMC Biophysics·Juliette Martin, Richard Lavery
Nov 19, 2013·Proteins·Fayyaz ul Amir Afsar MinhasAsa Ben-Hur
Jul 21, 2015·ELife·Anna Vangone, Alexandre M J J Bonvin

Citations

Jun 16, 2018·Nucleic Acids Research·Sébastien ReilleGuillaume Launay
Jun 15, 2019·Proteins·Chloé DequekerAlessandra Carbone

Methods Mentioned

BETA
in silico methods
GTPase
NIP

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.

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.

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.

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.

Neural Activity: Imaging

Imaging of neural activity in vivo has developed rapidly recently with the advancement of fluorescence microscopy, including new applications using miniaturized microscopes (miniscopes). This feed follows the progress in this growing field.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Related Papers

Methods in Molecular Biology
H J Wolfson, R Nussinov
Journal of Chemical Information and Modeling
Ramasamy Thilagavathi, Ricardo L Mancera
© 2021 Meta ULC. All rights reserved