Literature DB >> 21987416

The Levinthal paradox of the interactome.

Peter Tompa1, George D Rose.   

Abstract

The central biological question of the 21st century is: how does a viable cell emerge from the bewildering combinatorial complexity of its molecular components? Here, we estimate the combinatorics of self-assembling the protein constituents of a yeast cell, a number so vast that the functional interactome could only have emerged by iterative hierarchic assembly of its component sub-assemblies. A protein can undergo both reversible denaturation and hierarchic self-assembly spontaneously, but a functioning interactome must expend energy to achieve viability. Consequently, it is implausible that a completely "denatured" cell could be reversibly renatured spontaneously, like a protein. Instead, new cells are generated by the division of pre-existing cells, an unbroken chain of renewal tracking back through contingent conditions and evolving responses to the origin of life on the prebiotic earth. We surmise that this non-deterministic temporal continuum could not be reconstructed de novo under present conditions.
Copyright © 2011 The Protein Society.

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Year:  2011        PMID: 21987416      PMCID: PMC3302650          DOI: 10.1002/pro.747

Source DB:  PubMed          Journal:  Protein Sci        ISSN: 0961-8368            Impact factor:   6.725


  38 in total

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Authors:  R L Baldwin; B H Zimm
Journal:  Proc Natl Acad Sci U S A       Date:  2000-11-07       Impact factor: 11.205

2.  Chaperone overload is a possible contributor to 'civilization diseases'.

Authors:  P Csermely
Journal:  Trends Genet       Date:  2001-12       Impact factor: 11.639

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Authors:  W A Held; B Ballou; S Mizushima; M Nomura
Journal:  J Biol Chem       Date:  1974-05-25       Impact factor: 5.157

4.  Reconstitution of Escherichia coli 30 S ribosomal subunits from purified molecular components.

Authors:  W A Held; S Mizushima; M Nomura
Journal:  J Biol Chem       Date:  1973-08-25       Impact factor: 5.157

5.  Principles that govern the folding of protein chains.

Authors:  C B Anfinsen
Journal:  Science       Date:  1973-07-20       Impact factor: 47.728

6.  Escherichia coli 30 S ribosomal proteins uniquely required for assembly.

Authors:  W A Held; M Nomura
Journal:  J Biol Chem       Date:  1975-04-25       Impact factor: 5.157

7.  Nucleosomes are assembled by an acidic protein which binds histones and transfers them to DNA.

Authors:  R A Laskey; B M Honda; A D Mills; J T Finch
Journal:  Nature       Date:  1978-10-05       Impact factor: 49.962

8.  Correlation between transcriptome and interactome mapping data from Saccharomyces cerevisiae.

Authors:  H Ge; Z Liu; G M Church; M Vidal
Journal:  Nat Genet       Date:  2001-12       Impact factor: 38.330

9.  Global analysis of protein expression in yeast.

Authors:  Sina Ghaemmaghami; Won-Ki Huh; Kiowa Bower; Russell W Howson; Archana Belle; Noah Dephoure; Erin K O'Shea; Jonathan S Weissman
Journal:  Nature       Date:  2003-10-16       Impact factor: 49.962

10.  Towards the prediction of protein interaction partners using physical docking.

Authors:  Mark Nicholas Wass; Gloria Fuentes; Carles Pons; Florencio Pazos; Alfonso Valencia
Journal:  Mol Syst Biol       Date:  2011-02-15       Impact factor: 11.429

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  8 in total

Review 1.  Searching for the Pareto frontier in multi-objective protein design.

Authors:  Vikas Nanda; Sandeep V Belure; Ofer M Shir
Journal:  Biophys Rev       Date:  2017-08-10

2.  Innovative scattering analysis shows that hydrophobic disordered proteins are expanded in water.

Authors:  Joshua A Riback; Micayla A Bowman; Adam M Zmyslowski; Catherine R Knoverek; John M Jumper; James R Hinshaw; Emily B Kaye; Karl F Freed; Patricia L Clark; Tobin R Sosnick
Journal:  Science       Date:  2017-10-13       Impact factor: 47.728

3.  Emergent Self-Organized Criticality in Gene Expression Dynamics: Temporal Development of Global Phase Transition Revealed in a Cancer Cell Line.

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4.  Modeling the assembly order of multimeric heteroprotein complexes.

Authors:  Lenna X Peterson; Yoichiro Togawa; Juan Esquivel-Rodriguez; Genki Terashi; Charles Christoffer; Amitava Roy; Woong-Hee Shin; Daisuke Kihara
Journal:  PLoS Comput Biol       Date:  2018-01-12       Impact factor: 4.475

5.  Cellular crowding imposes global constraints on the chemistry and evolution of proteomes.

Authors:  Emmanuel D Levy; Subhajyoti De; Sarah A Teichmann
Journal:  Proc Natl Acad Sci U S A       Date:  2012-11-26       Impact factor: 11.205

Review 6.  Misfolded proteins: from little villains to little helpers in the fight against cancer.

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Journal:  Front Oncol       Date:  2015-02-24       Impact factor: 6.244

Review 7.  Licensing and due process in the turnover of bacterial RNA.

Authors:  Katarzyna J Bandyra; Ben F Luisi
Journal:  RNA Biol       Date:  2013-04-01       Impact factor: 4.652

Review 8.  Hydrogel formation by multivalent IDPs: A reincarnation of the microtrabecular lattice?

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Journal:  Intrinsically Disord Proteins       Date:  2013-01-01
  8 in total

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