Literature DB >> 20029448

Pairing computation with experimentation: a powerful coupling for understanding T cell signalling.

Arup K Chakraborty1, Jayajit Das.   

Abstract

T cells are activated when extracellular stimuli, such as a ligand binding to the T cell receptor, are converted into functional outputs by the T cell signalling network. T cell receptor signalling is a highly complex, stochastic and dynamic process involving many interacting proteins. This complexity often confounds intuition, making it difficult to develop mechanistic principles that underly experimental observations. In this Review, we describe how computational approaches can partner successfully with biological experimentation to help address this challenge, and we illustrate this paradigm by summarizing recent work that shows new aspects of the T cell signalling network.

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Year:  2010        PMID: 20029448     DOI: 10.1038/nri2688

Source DB:  PubMed          Journal:  Nat Rev Immunol        ISSN: 1474-1733            Impact factor:   53.106


  103 in total

1.  The immunological synapse: a molecular machine controlling T cell activation.

Authors:  A Grakoui; S K Bromley; C Sumen; M M Davis; A S Shaw; P M Allen; M L Dustin
Journal:  Science       Date:  1999-07-09       Impact factor: 47.728

Review 2.  Feedback regulation of lymphocyte signalling.

Authors:  Michael Reth; Tilman Brummer
Journal:  Nat Rev Immunol       Date:  2004-04       Impact factor: 53.106

3.  Plasma membrane-associated proteins are clustered into islands attached to the cytoskeleton.

Authors:  Björn F Lillemeier; Janet R Pfeiffer; Zurab Surviladze; Bridget S Wilson; Mark M Davis
Journal:  Proc Natl Acad Sci U S A       Date:  2006-12-04       Impact factor: 11.205

4.  Isolation of cDNA clones encoding T cell-specific membrane-associated proteins.

Authors:  S M Hedrick; D I Cohen; E A Nielsen; M M Davis
Journal:  Nature       Date:  1984 Mar 8-14       Impact factor: 49.962

5.  T cell receptor signaling precedes immunological synapse formation.

Authors:  Kyeong-Hee Lee; Amy D Holdorf; Michael L Dustin; Andrew C Chan; Paul M Allen; Andrey S Shaw
Journal:  Science       Date:  2002-02-22       Impact factor: 47.728

6.  Unusual interplay of two types of Ras activators, RasGRP and SOS, establishes sensitive and robust Ras activation in lymphocytes.

Authors:  Jeroen P Roose; Marianne Mollenauer; Mary Ho; Tomohiro Kurosaki; Arthur Weiss
Journal:  Mol Cell Biol       Date:  2007-02-05       Impact factor: 4.272

7.  The lymphocyte function-associated antigen-1 receptor costimulates plasma membrane Ras via phospholipase D2.

Authors:  Adam Mor; Gabriele Campi; Guangwei Du; Yang Zheng; David A Foster; Michael L Dustin; Mark R Philips
Journal:  Nat Cell Biol       Date:  2007-05-07       Impact factor: 28.824

8.  Regulation of T cell receptor activation by dynamic membrane binding of the CD3epsilon cytoplasmic tyrosine-based motif.

Authors:  Chenqi Xu; Etienne Gagnon; Matthew E Call; Jason R Schnell; Charles D Schwieters; Christopher V Carman; James J Chou; Kai W Wucherpfennig
Journal:  Cell       Date:  2008-11-14       Impact factor: 41.582

9.  Membrane-dependent signal integration by the Ras activator Son of sevenless.

Authors:  Jodi Gureasko; William J Galush; Sean Boykevisch; Holger Sondermann; Dafna Bar-Sagi; Jay T Groves; John Kuriyan
Journal:  Nat Struct Mol Biol       Date:  2008-05-04       Impact factor: 15.369

10.  Stimulus design for model selection and validation in cell signaling.

Authors:  Joshua F Apgar; Jared E Toettcher; Drew Endy; Forest M White; Bruce Tidor
Journal:  PLoS Comput Biol       Date:  2008-02       Impact factor: 4.475

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  26 in total

1.  Dramatic reduction of dimensionality in large biochemical networks owing to strong pair correlations.

Authors:  Michael Dworkin; Sayak Mukherjee; Ciriyam Jayaprakash; Jayajit Das
Journal:  J R Soc Interface       Date:  2012-02-29       Impact factor: 4.118

Review 2.  Understanding the structure and function of the immunological synapse.

Authors:  Michael L Dustin; Arup K Chakraborty; Andrey S Shaw
Journal:  Cold Spring Harb Perspect Biol       Date:  2010-09-15       Impact factor: 10.005

3.  HIV-1 Virion Production from Single Inducible Proviruses following T-Cell Activation Ex Vivo.

Authors:  John K Bui; John W Mellors; Anthony R Cillo
Journal:  J Virol       Date:  2015-11-11       Impact factor: 5.103

Review 4.  Modeling the T cell immune response: a fascinating challenge.

Authors:  Penelope A Morel; James R Faeder; William F Hawse; Natasa Miskov-Zivanov
Journal:  J Pharmacokinet Pharmacodyn       Date:  2014-08-26       Impact factor: 2.745

5.  Design principles of cell circuits with paradoxical components.

Authors:  Yuval Hart; Yaron E Antebi; Avraham E Mayo; Nir Friedman; Uri Alon
Journal:  Proc Natl Acad Sci U S A       Date:  2012-05-04       Impact factor: 11.205

6.  Mathematical modelling and computational study of two-dimensional and three-dimensional dynamics of receptor-ligand interactions in signalling response mechanisms.

Authors:  Pilar García-Peñarrubia; Juan J Gálvez; Jesús Gálvez
Journal:  J Math Biol       Date:  2013-07-28       Impact factor: 2.259

7.  Changing face of vaccination in immunocompromised hosts.

Authors:  Daire O'Shea; Lukas A Widmer; Jörg Stelling; Adrian Egli
Journal:  Curr Infect Dis Rep       Date:  2014-09       Impact factor: 3.725

8.  The pool of preactivated Lck in the initiation of T-cell signaling: a critical re-evaluation of the Lck standby model.

Authors:  Ondřej Ballek; Jan Valečka; Jasper Manning; Dominik Filipp
Journal:  Immunol Cell Biol       Date:  2014-11-25       Impact factor: 5.126

9.  RuleMonkey: software for stochastic simulation of rule-based models.

Authors:  Joshua Colvin; Michael I Monine; Ryan N Gutenkunst; William S Hlavacek; Daniel D Von Hoff; Richard G Posner
Journal:  BMC Bioinformatics       Date:  2010-07-30       Impact factor: 3.169

10.  The duration of T cell stimulation is a critical determinant of cell fate and plasticity.

Authors:  Natasa Miskov-Zivanov; Michael S Turner; Lawrence P Kane; Penelope A Morel; James R Faeder
Journal:  Sci Signal       Date:  2013-11-05       Impact factor: 8.192

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