Literature DB >> 23913102

The spatial structure of cell signaling systems.

Ruth Nussinov1.   

Abstract

The spatial structure of the cell is highly organized at all levels: from small complexes and assemblies, to local nano- and microclusters, to global, micrometer scales across and between cells. We suggest that this multiscale spatial cell organization also organizes signaling and coordinates cellular behavior. We propose a new view of the spatial structure of cell signaling systems. This new view describes cell signaling in terms of dynamic allosteric interactions within and among distinct, spatially organized transient clusters. The clusters vary over time and space and are on length scales from nanometers to micrometers. When considered across these length scales, primary factors in the spatial organization are cell membrane domains and the actin cytoskeleton, both also highly dynamic. A key challenge is to understand the interplay across these multiple scales, link it to the physicochemical basis of the conformational behavior of single molecules and ultimately relate it to cellular function. Overall, our premise is that at these scales, cell signaling should be thought of not primarily as a sequence of diffusion-controlled molecular collisions, but instead transient, allostery-driven cluster re-forming interactions.

Entities:  

Year:  2013        PMID: 23913102      PMCID: PMC3870181          DOI: 10.1088/1478-3975/10/4/045004

Source DB:  PubMed          Journal:  Phys Biol        ISSN: 1478-3967            Impact factor:   2.583


  173 in total

Review 1.  Allosteric interactions and proton conducting pathways in proton pumping aa(3) oxidases: heme a as a key coupling element.

Authors:  Nazzareno Capitanio; Luigi Leonardo Palese; Giuseppe Capitanio; Pietro Luca Martino; Oliver-Matthias H Richter; Bernd Ludwig; Sergio Papa
Journal:  Biochim Biophys Acta       Date:  2011-11-10

2.  Function of hyperekplexia-causing α1R271Q/L glycine receptors is restored by shifting the affected residue out of the allosteric signalling pathway.

Authors:  Qiang Shan; Lu Han; Joseph W Lynch
Journal:  Br J Pharmacol       Date:  2012-04       Impact factor: 8.739

Review 3.  Cooperativity and complementarity: synergies in non-classical and classical glucocorticoid signaling.

Authors:  Ranmal A Samarasinghe; Selma F Witchell; Donald B DeFranco
Journal:  Cell Cycle       Date:  2012-08-01       Impact factor: 4.534

4.  Hot spots for allosteric regulation on protein surfaces.

Authors:  Kimberly A Reynolds; Richard N McLaughlin; Rama Ranganathan
Journal:  Cell       Date:  2011-12-23       Impact factor: 41.582

5.  Restriction of receptor movement alters cellular response: physical force sensing by EphA2.

Authors:  Khalid Salaita; Pradeep M Nair; Rebecca S Petit; Richard M Neve; Debopriya Das; Joe W Gray; Jay T Groves
Journal:  Science       Date:  2010-03-12       Impact factor: 47.728

Review 6.  Cell signaling by receptor tyrosine kinases.

Authors:  Mark A Lemmon; Joseph Schlessinger
Journal:  Cell       Date:  2010-06-25       Impact factor: 41.582

7.  Dimerizer-mediated regulation of gene expression.

Authors:  Victor M Rivera; Lori Berk; Tim Clackson
Journal:  Cold Spring Harb Protoc       Date:  2012-07-01

8.  The spatial architecture of protein function and adaptation.

Authors:  Richard N McLaughlin; Frank J Poelwijk; Arjun Raman; Walraj S Gosal; Rama Ranganathan
Journal:  Nature       Date:  2012-10-07       Impact factor: 49.962

9.  Allosteric communication in dihydrofolate reductase: signaling network and pathways for closed to occluded transition and back.

Authors:  Jie Chen; Ruxandra I Dima; D Thirumalai
Journal:  J Mol Biol       Date:  2007-08-25       Impact factor: 5.469

10.  Transcription factor Foxp3 and its protein partners form a complex regulatory network.

Authors:  Dipayan Rudra; Paul deRoos; Ashutosh Chaudhry; Rachel E Niec; Aaron Arvey; Robert M Samstein; Christina Leslie; Scott A Shaffer; David R Goodlett; Alexander Y Rudensky
Journal:  Nat Immunol       Date:  2012-08-26       Impact factor: 25.606

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  19 in total

Review 1.  Drugging Ras GTPase: a comprehensive mechanistic and signaling structural view.

Authors:  Shaoyong Lu; Hyunbum Jang; Shuo Gu; Jian Zhang; Ruth Nussinov
Journal:  Chem Soc Rev       Date:  2016-07-11       Impact factor: 54.564

2.  PtdIns(4,5)P2 and PtdIns(3,4,5)P3 dynamics during focal adhesions assembly and disassembly in a cancer cell line.

Authors:  Dhurgham Alfahad; Salem Alharethi; Bandar Alharbi; Khatab Mawlood; Philip Dash
Journal:  Turk J Biol       Date:  2020-12-14

Review 3.  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

4.  Packing Density of the Amyloid Precursor Protein in the Cell Membrane.

Authors:  Dennis de Coninck; Thomas H Schmidt; Jan-Gero Schloetel; Thorsten Lang
Journal:  Biophys J       Date:  2018-03-13       Impact factor: 4.033

5.  GTP-Dependent K-Ras Dimerization.

Authors:  Serena Muratcioglu; Tanmay S Chavan; Benjamin C Freed; Hyunbum Jang; Lyuba Khavrutskii; R Natasha Freed; Marzena A Dyba; Karen Stefanisko; Sergey G Tarasov; Attila Gursoy; Ozlem Keskin; Nadya I Tarasova; Vadim Gaponenko; Ruth Nussinov
Journal:  Structure       Date:  2015-06-04       Impact factor: 5.006

6.  Mechanisms of membrane binding of small GTPase K-Ras4B farnesylated hypervariable region.

Authors:  Hyunbum Jang; Sherwin J Abraham; Tanmay S Chavan; Ben Hitchinson; Lyuba Khavrutskii; Nadya I Tarasova; Ruth Nussinov; Vadim Gaponenko
Journal:  J Biol Chem       Date:  2015-02-24       Impact factor: 5.157

7.  A mechanism for the auto-inhibition of hyperpolarization-activated cyclic nucleotide-gated (HCN) channel opening and its relief by cAMP.

Authors:  Madoka Akimoto; Zaiyong Zhang; Stephen Boulton; Rajeevan Selvaratnam; Bryan VanSchouwen; Melanie Gloyd; Eric A Accili; Oliver F Lange; Giuseppe Melacini
Journal:  J Biol Chem       Date:  2014-05-30       Impact factor: 5.157

Review 8.  Oligomerization and nanocluster organization render specificity.

Authors:  Ruth Nussinov; Hyunbum Jang; Chung-Jung Tsai
Journal:  Biol Rev Camb Philos Soc       Date:  2014-06-11

9.  The efficacy of Raf kinase recruitment to the GTPase H-ras depends on H-ras membrane conformer-specific nanoclustering.

Authors:  Camilo Guzmán; Maja Šolman; Alessio Ligabue; Olga Blaževitš; Débora M Andrade; Luc Reymond; Christian Eggeling; Daniel Abankwa
Journal:  J Biol Chem       Date:  2014-02-25       Impact factor: 5.157

Review 10.  Signaling in the crowded cell.

Authors:  Ruth Nussinov; Chung-Jung Tsai; Hyunbum Jang
Journal:  Curr Opin Struct Biol       Date:  2021-07-02       Impact factor: 6.809

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