Literature DB >> 31143927

PRECOG: PREdicting COupling probabilities of G-protein coupled receptors.

Gurdeep Singh1,2, Asuka Inoue3, J Silvio Gutkind4, Robert B Russell1,2, Francesco Raimondi1,2.   

Abstract

G-protein coupled receptors (GPCRs) control multiple physiological states by transducing a multitude of extracellular stimuli into the cell via coupling to intra-cellular heterotrimeric G-proteins. Deciphering which G-proteins couple to each of the hundreds of GPCRs present in a typical eukaryotic organism is therefore critical to understand signalling. Here, we present PRECOG (precog.russelllab.org): a web-server for predicting GPCR coupling, which allows users to: (i) predict coupling probabilities for GPCRs to individual G-proteins instead of subfamilies; (ii) visually inspect the protein sequence and structural features that are responsible for a particular coupling; (iii) suggest mutations to rationally design artificial GPCRs with new coupling properties based on predetermined coupling features.
© The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.

Entities:  

Year:  2019        PMID: 31143927      PMCID: PMC6602504          DOI: 10.1093/nar/gkz392

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN: 0305-1048            Impact factor:   16.971


  46 in total

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Authors:  F J Ehlert; M T Griffin; G W Sawyer; R Bailon
Journal:  J Pharmacol Exp Ther       Date:  1999-05       Impact factor: 4.030

2.  Analysis and prediction of functional sub-types from protein sequence alignments.

Authors:  S S Hannenhalli; R B Russell
Journal:  J Mol Biol       Date:  2000-10-13       Impact factor: 5.469

3.  Interrogating protein interaction networks through structural biology.

Authors:  Patrick Aloy; Robert B Russell
Journal:  Proc Natl Acad Sci U S A       Date:  2002-04-23       Impact factor: 11.205

4.  InterPreTS: protein interaction prediction through tertiary structure.

Authors:  Patrick Aloy; Robert B Russell
Journal:  Bioinformatics       Date:  2003-01       Impact factor: 6.937

5.  Prediction of the coupling specificity of GPCRs to four families of G-proteins using hidden Markov models and artificial neural networks.

Authors:  Nikolaos G Sgourakis; Pantelis G Bagos; Stavros J Hamodrakas
Journal:  Bioinformatics       Date:  2005-09-20       Impact factor: 6.937

6.  Proteome survey reveals modularity of the yeast cell machinery.

Authors:  Anne-Claude Gavin; Patrick Aloy; Paola Grandi; Roland Krause; Markus Boesche; Martina Marzioch; Christina Rau; Lars Juhl Jensen; Sonja Bastuck; Birgit Dümpelfeld; Angela Edelmann; Marie-Anne Heurtier; Verena Hoffman; Christian Hoefert; Karin Klein; Manuela Hudak; Anne-Marie Michon; Malgorzata Schelder; Markus Schirle; Marita Remor; Tatjana Rudi; Sean Hooper; Andreas Bauer; Tewis Bouwmeester; Georg Casari; Gerard Drewes; Gitte Neubauer; Jens M Rick; Bernhard Kuster; Peer Bork; Robert B Russell; Giulio Superti-Furga
Journal:  Nature       Date:  2006-01-22       Impact factor: 49.962

Review 7.  Mammalian G proteins and their cell type specific functions.

Authors:  Nina Wettschureck; Stefan Offermanns
Journal:  Physiol Rev       Date:  2005-10       Impact factor: 37.312

Review 8.  Impact of GPCRs in clinical medicine: monogenic diseases, genetic variants and drug targets.

Authors:  Paul A Insel; Chih-Min Tang; Ines Hahntow; Martin C Michel
Journal:  Biochim Biophys Acta       Date:  2006-10-05

9.  Jalview Version 2--a multiple sequence alignment editor and analysis workbench.

Authors:  Andrew M Waterhouse; James B Procter; David M A Martin; Michèle Clamp; Geoffrey J Barton
Journal:  Bioinformatics       Date:  2009-01-16       Impact factor: 6.937

10.  GRIFFIN: a system for predicting GPCR-G-protein coupling selectivity using a support vector machine and a hidden Markov model.

Authors:  Yukimitsu Yabuki; Takahiko Muramatsu; Takatsugu Hirokawa; Hidehito Mukai; Makiko Suwa
Journal:  Nucleic Acids Res       Date:  2005-07-01       Impact factor: 16.971

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  7 in total

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Authors:  Xintong Dong; Nathachit Limjunyawong; Elizabeth I Sypek; Gaofeng Wang; Roger V Ortines; Christine Youn; Martin P Alphonse; Dustin Dikeman; Yu Wang; Mark Lay; Ruchita Kothari; Chirag Vasavda; Priyanka Pundir; Loyal Goff; Lloyd S Miller; Wuyuan Lu; Luis A Garza; Brian S Kim; Nathan K Archer; Xinzhong Dong
Journal:  Immunity       Date:  2022-07-25       Impact factor: 43.474

2.  PRECOGx: exploring GPCR signaling mechanisms with deep protein representations.

Authors:  Marin Matic; Gurdeep Singh; Francesco Carli; Natalia De Oliveira Rosa; Pasquale Miglionico; Lorenzo Magni; J Silvio Gutkind; Robert B Russell; Asuka Inoue; Francesco Raimondi
Journal:  Nucleic Acids Res       Date:  2022-05-26       Impact factor: 19.160

3.  Agonist-Dependent Coupling of the Promiscuous Adenosine A2B Receptor to Gα Protein Subunits.

Authors:  Jan Hendrik Voss; Andhika B Mahardhika; Asuka Inoue; Christa E Müller
Journal:  ACS Pharmacol Transl Sci       Date:  2022-05-03

4.  CCR6 activation links innate immune responses to mucosa-associated lymphoid tissue lymphoma development.

Authors:  Boguslawa Korona; Dagmara Korona; Wanfeng Zhao; Andrew C Wotherspoon; Ming-Qing Du
Journal:  Haematologica       Date:  2022-06-01       Impact factor: 11.047

5.  What Makes GPCRs from Different Families Bind to the Same Ligand?

Authors:  Kwabena Owusu Dankwah; Jonathon E Mohl; Khodeza Begum; Ming-Ying Leung
Journal:  Biomolecules       Date:  2022-06-21

6.  The N-terminus of GPR37L1 is proteolytically processed by matrix metalloproteases.

Authors:  James L J Coleman; Tony Ngo; Rhyll E Smythe; Andrew J Cleave; Nicole M Jones; Robert M Graham; Nicola J Smith
Journal:  Sci Rep       Date:  2020-11-17       Impact factor: 4.379

7.  The G protein database, GproteinDb.

Authors:  Gáspár Pándy-Szekeres; Mauricio Esguerra; Alexander S Hauser; Jimmy Caroli; Christian Munk; Steven Pilger; György M Keserű; Albert J Kooistra; David E Gloriam
Journal:  Nucleic Acids Res       Date:  2022-01-07       Impact factor: 16.971

  7 in total

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