Literature DB >> 23240611

Describing sequence-ensemble relationships for intrinsically disordered proteins.

Albert H Mao1, Nicholas Lyle, Rohit V Pappu.   

Abstract

Intrinsically disordered proteins participate in important protein-protein and protein-nucleic acid interactions and control cellular phenotypes through their prominence as dynamic organizers of transcriptional, post-transcriptional and signalling networks. These proteins challenge the tenets of the structure-function paradigm and their functional mechanisms remain a mystery given that they fail to fold autonomously into specific structures. Solving this mystery requires a first principles understanding of the quantitative relationships between information encoded in the sequences of disordered proteins and the ensemble of conformations they sample. Advances in quantifying sequence-ensemble relationships have been facilitated through a four-way synergy between bioinformatics, biophysical experiments, computer simulations and polymer physics theories. In the present review we evaluate these advances and the resultant insights that allow us to develop a concise quantitative framework for describing the sequence-ensemble relationships of intrinsically disordered proteins.

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Year:  2013        PMID: 23240611      PMCID: PMC4074364          DOI: 10.1042/BJ20121346

Source DB:  PubMed          Journal:  Biochem J        ISSN: 0264-6021            Impact factor:   3.857


  147 in total

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Authors:  H Jane Dyson; Peter E Wright
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3.  Self-assembly of peptides into a beta-barrel motif.

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Journal:  J Chem Phys       Date:  2004-03-22       Impact factor: 3.488

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Journal:  Proc Natl Acad Sci U S A       Date:  2004-08-16       Impact factor: 11.205

5.  N-terminal segments modulate the α-helical propensities of the intrinsically disordered basic regions of bZIP proteins.

Authors:  Rahul K Das; Scott L Crick; Rohit V Pappu
Journal:  J Mol Biol       Date:  2011-12-28       Impact factor: 5.469

6.  Scaling behavior and structure of denatured proteins.

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7.  Energy landscape analyses of disordered histone tails reveal special organization of their conformational dynamics.

Authors:  Davit A Potoyan; Garegin A Papoian
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8.  Hydrophilicity of polar amino acid side-chains is markedly reduced by flanking peptide bonds.

Authors:  M A Roseman
Journal:  J Mol Biol       Date:  1988-04-05       Impact factor: 5.469

9.  Evidence for conformational flexibility in the Tat-TAR recognition motif of cyclin T1.

Authors:  Chandreyee Das; Stephen P Edgcomb; Ralph Peteranderl; Lily Chen; Alan D Frankel
Journal:  Virology       Date:  2004-01-05       Impact factor: 3.616

10.  Determination of Conformational Equilibria in Proteins Using Residual Dipolar Couplings.

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Journal:  J Chem Theory Comput       Date:  2011-10-10       Impact factor: 6.006

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  48 in total

1.  Quantitative assessments of the distinct contributions of polypeptide backbone amides versus side chain groups to chain expansion via chemical denaturation.

Authors:  Alex S Holehouse; Kanchan Garai; Nicholas Lyle; Andreas Vitalis; Rohit V Pappu
Journal:  J Am Chem Soc       Date:  2015-02-23       Impact factor: 15.419

2.  Conformations of intrinsically disordered proteins are influenced by linear sequence distributions of oppositely charged residues.

Authors:  Rahul K Das; Rohit V Pappu
Journal:  Proc Natl Acad Sci U S A       Date:  2013-07-30       Impact factor: 11.205

3.  A quantitative measure for protein conformational heterogeneity.

Authors:  Nicholas Lyle; Rahul K Das; Rohit V Pappu
Journal:  J Chem Phys       Date:  2013-09-28       Impact factor: 3.488

4.  From sequence and forces to structure, function, and evolution of intrinsically disordered proteins.

Authors:  Julie D Forman-Kay; Tanja Mittag
Journal:  Structure       Date:  2013-09-03       Impact factor: 5.006

5.  Side chain electrostatic interactions and pH-dependent expansion of the intrinsically disordered, highly acidic carboxyl-terminus of γ-tubulin.

Authors:  Brandon J Payliss; Jackie Vogel; Anthony K Mittermaier
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6.  Commonly used FRET fluorophores promote collapse of an otherwise disordered protein.

Authors:  Joshua A Riback; Micayla A Bowman; Adam M Zmyslowski; Kevin W Plaxco; Patricia L Clark; Tobin R Sosnick
Journal:  Proc Natl Acad Sci U S A       Date:  2019-04-16       Impact factor: 11.205

7.  Decoupling of size and shape fluctuations in heteropolymeric sequences reconciles discrepancies in SAXS vs. FRET measurements.

Authors:  Gustavo Fuertes; Niccolò Banterle; Kiersten M Ruff; Aritra Chowdhury; Davide Mercadante; Christine Koehler; Michael Kachala; Gemma Estrada Girona; Sigrid Milles; Ankur Mishra; Patrick R Onck; Frauke Gräter; Santiago Esteban-Martín; Rohit V Pappu; Dmitri I Svergun; Edward A Lemke
Journal:  Proc Natl Acad Sci U S A       Date:  2017-07-17       Impact factor: 11.205

8.  Intrinsically disordered C-terminal tails of E. coli single-stranded DNA binding protein regulate cooperative binding to single-stranded DNA.

Authors:  Alexander G Kozlov; Elizabeth Weiland; Anuradha Mittal; Vince Waldman; Edwin Antony; Nicole Fazio; Rohit V Pappu; Timothy M Lohman
Journal:  J Mol Biol       Date:  2015-01-03       Impact factor: 5.469

9.  Temperature-dependent solvation modulates the dimensions of disordered proteins.

Authors:  René Wuttke; Hagen Hofmann; Daniel Nettels; Madeleine B Borgia; Jeetain Mittal; Robert B Best; Benjamin Schuler
Journal:  Proc Natl Acad Sci U S A       Date:  2014-03-21       Impact factor: 11.205

10.  Single-molecule spectroscopy reveals polymer effects of disordered proteins in crowded environments.

Authors:  Andrea Soranno; Iwo Koenig; Madeleine B Borgia; Hagen Hofmann; Franziska Zosel; Daniel Nettels; Benjamin Schuler
Journal:  Proc Natl Acad Sci U S A       Date:  2014-03-17       Impact factor: 11.205

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