Literature DB >> 21766126

How do dynamic cellular signals travel long distances?

Ruth Nussinov1.   

Abstract

Communication is essential. It is vital between cells in multi-cellular organisms, and within cells. A signaling molecule binds to a receptor protein, and initiates a cascade of dynamic events. Signaling is a multistep pathway, which allows signal amplification: if some of the molecules in a pathway transmit the signal to multiple molecules, the result can be a large number of activated molecules across the cell and multiple reactions. That is how a small number of extracellular signaling molecules can produce a major cellular response. The pathway can relay signals from the extracellular space to the nucleus. How do signals travel efficiently over long-distances across the cell? Here we argue that evolution has utilized three properties: a modular functional organization of the cellular network; sequences in some key regions of proteins, such as linkers or loops, which were pre-encoded by evolution to facilitate signaling among domains; and compact interactions between proteins which is achieved via conformational disorder.

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Year:  2011        PMID: 21766126      PMCID: PMC7449263          DOI: 10.1039/c1mb05205e

Source DB:  PubMed          Journal:  Mol Biosyst        ISSN: 1742-2051


  83 in total

Review 1.  Folding funnels and binding mechanisms.

Authors:  B Ma; S Kumar; C J Tsai; R Nussinov
Journal:  Protein Eng       Date:  1999-09

Review 2.  Conformational ensembles, signal transduction and residue hot spots: application to drug discovery.

Authors:  Saliha Ece Acuner Ozbabacan; Attila Gursoy; Ozlem Keskin; Ruth Nussinov
Journal:  Curr Opin Drug Discov Devel       Date:  2010-09

Review 3.  Charting histone modifications and the functional organization of mammalian genomes.

Authors:  Vicky W Zhou; Alon Goren; Bradley E Bernstein
Journal:  Nat Rev Genet       Date:  2010-11-30       Impact factor: 53.242

4.  Analysis of the bacterial luciferase mobile loop by replica-exchange molecular dynamics.

Authors:  Zachary T Campbell; Thomas O Baldwin; Osamu Miyashita
Journal:  Biophys J       Date:  2010-12-15       Impact factor: 4.033

5.  Conformational selection and induced fit mechanism underlie specificity in noncovalent interactions with ubiquitin.

Authors:  Tomasz Wlodarski; Bojan Zagrovic
Journal:  Proc Natl Acad Sci U S A       Date:  2009-11-03       Impact factor: 11.205

6.  Compaction properties of an intrinsically disordered protein: Sic1 and its kinase-inhibitor domain.

Authors:  Stefania Brocca; Lorenzo Testa; Frank Sobott; Maria Samalikova; Antonino Natalello; Elena Papaleo; Marina Lotti; Luca De Gioia; Silvia Maria Doglia; Lilia Alberghina; Rita Grandori
Journal:  Biophys J       Date:  2011-05-04       Impact factor: 4.033

Review 7.  Hedgehog morphogen: from secretion to reception.

Authors:  Armel Gallet
Journal:  Trends Cell Biol       Date:  2011-01-21       Impact factor: 20.808

Review 8.  Allostery and population shift in drug discovery.

Authors:  Gozde Kar; Ozlem Keskin; Attila Gursoy; Ruth Nussinov
Journal:  Curr Opin Pharmacol       Date:  2010-09-29       Impact factor: 5.547

Review 9.  The role of dynamic conformational ensembles in biomolecular recognition.

Authors:  David D Boehr; Ruth Nussinov; Peter E Wright
Journal:  Nat Chem Biol       Date:  2009-11       Impact factor: 15.040

Review 10.  Linking folding and binding.

Authors:  Peter E Wright; H Jane Dyson
Journal:  Curr Opin Struct Biol       Date:  2009-01-20       Impact factor: 6.809

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  13 in total

1.  Nanoscale protein dynamics: a new frontier for neutron spin echo spectroscopy.

Authors:  David J E Callaway; Bela Farago; Zimei Bu
Journal:  Eur Phys J E Soft Matter       Date:  2013-07-17       Impact factor: 1.890

2.  Nanoscale protein domain motion and long-range allostery in signaling proteins- a view from neutron spin echo sprectroscopy.

Authors:  David J E Callaway; Zimei Bu
Journal:  Biophys Rev       Date:  2015-06

Review 3.  Dynamic Protein Interaction Networks and New Structural Paradigms in Signaling.

Authors:  Veronika Csizmok; Ariele Viacava Follis; Richard W Kriwacki; Julie D Forman-Kay
Journal:  Chem Rev       Date:  2016-02-29       Impact factor: 60.622

4.  The free energy landscape in translational science: how can somatic mutations result in constitutive oncogenic activation?

Authors:  Chung-Jung Tsai; Ruth Nussinov
Journal:  Phys Chem Chem Phys       Date:  2014-01-21       Impact factor: 3.676

Review 5.  Dynamic multiprotein assemblies shape the spatial structure of cell signaling.

Authors:  Ruth Nussinov; Hyunbum Jang
Journal:  Prog Biophys Mol Biol       Date:  2014-07-18       Impact factor: 3.667

6.  Intrinsic disorder: signaling via highly specific but short-lived association.

Authors:  Huan-Xiang Zhou
Journal:  Trends Biochem Sci       Date:  2011-12-07       Impact factor: 13.807

7.  Dancing through Life: Molecular Dynamics Simulations and Network-Centric Modeling of Allosteric Mechanisms in Hsp70 and Hsp110 Chaperone Proteins.

Authors:  Gabrielle Stetz; Gennady M Verkhivker
Journal:  PLoS One       Date:  2015-11-30       Impact factor: 3.240

8.  The spatial structure of cell signaling systems.

Authors:  Ruth Nussinov
Journal:  Phys Biol       Date:  2013-08-02       Impact factor: 2.583

Review 9.  How do disordered regions achieve comparable functions to structured domains?

Authors:  Natasha S Latysheva; Tilman Flock; Robert J Weatheritt; Sreenivas Chavali; M Madan Babu
Journal:  Protein Sci       Date:  2015-05-15       Impact factor: 6.725

10.  Protein dynamics and conformational selection in bidirectional signal transduction.

Authors:  Ruth Nussinov; Buyong Ma
Journal:  BMC Biol       Date:  2012-01-25       Impact factor: 7.431

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