Literature DB >> 25863585

Relating sequence encoded information to form and function of intrinsically disordered proteins.

Rahul K Das1, Kiersten M Ruff1, Rohit V Pappu2.   

Abstract

Intrinsically disordered proteins (IDPs) showcase the importance of conformational plasticity and heterogeneity in protein function. We summarize recent advances that connect information encoded in IDP sequences to their conformational properties and functions. We focus on insights obtained through a combination of atomistic simulations and biophysical measurements that are synthesized into a coherent framework using polymer physics theories.
Copyright © 2015 Elsevier Ltd. All rights reserved.

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Year:  2015        PMID： 25863585      PMCID： PMC4512920          DOI： 10.1016/j.sbi.2015.03.008

Source DB:  PubMed          Journal:  Curr Opin Struct Biol        ISSN： 0959-440X            Impact factor:   6.809


  90 in total

1.  Peptide chain dynamics in light and heavy water: zooming in on internal friction.

Authors:  Julius C F Schulz; Lennart Schmidt; Robert B Best; Joachim Dzubiella; Roland R Netz
Journal:  J Am Chem Soc       Date:  2012-03-27       Impact factor: 15.419

2.  Chain collapse of an amyloidogenic intrinsically disordered protein.

Authors:  Neha Jain; Mily Bhattacharya; Samrat Mukhopadhyay
Journal:  Biophys J       Date:  2011-10-05       Impact factor: 4.033

3.  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

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

Authors:  Davit A Potoyan; Garegin A Papoian
Journal:  J Am Chem Soc       Date:  2011-04-25       Impact factor: 15.419

5.  Long-range correlated dynamics in intrinsically disordered proteins.

Authors:  Giacomo Parigi; Nasrollah Rezaei-Ghaleh; Andrea Giachetti; Stefan Becker; Claudio Fernandez; Martin Blackledge; Christian Griesinger; Markus Zweckstetter; Claudio Luchinat
Journal:  J Am Chem Soc       Date:  2014-11-04       Impact factor: 15.419

6.  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

7.  Mapping the potential energy landscape of intrinsically disordered proteins at amino acid resolution.

Authors:  Valéry Ozenne; Robert Schneider; Mingxi Yao; Jie-rong Huang; Loïc Salmon; Markus Zweckstetter; Malene Ringkjøbing Jensen; Martin Blackledge
Journal:  J Am Chem Soc       Date:  2012-08-28       Impact factor: 15.419

Review 8.  Disorder-function relationships for the cell cycle regulatory proteins p21 and p27.

Authors:  Diana M Mitrea; Mi-Kyung Yoon; Li Ou; Richard W Kriwacki
Journal:  Biol Chem       Date:  2012-04       Impact factor: 3.915

9.  Structural diversity in free and bound states of intrinsically disordered protein phosphatase 1 regulators.

Authors:  Joseph A Marsh; Barbara Dancheck; Michael J Ragusa; Marc Allaire; Julie D Forman-Kay; Wolfgang Peti
Journal:  Structure       Date:  2010-09-08       Impact factor: 5.006

Review 10.  A decade and a half of protein intrinsic disorder: biology still waits for physics.

Authors:  Vladimir N Uversky
Journal:  Protein Sci       Date:  2013-04-29       Impact factor: 6.725
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  118 in total

1.  Atomistic Glimpse of the Orderly Chaos of One Protein.

Authors:  Jianhan Chen
Journal:  Biophys J       Date:  2015-10-20       Impact factor: 4.033

2.  Protein polymers: Encoding phase transitions.

Authors:  Alex S Holehouse; Rohit V Pappu
Journal:  Nat Mater       Date:  2015-11       Impact factor: 43.841

3.  Electrophoretic Mobilities of the Charge Variants of DNA and Other Polyelectrolytes: Similarities, Differences, and Comparison with Theory.

Authors:  Nancy C Stellwagen
Journal:  J Phys Chem B       Date:  2017-02-24       Impact factor: 2.991

4.  HyRes: a coarse-grained model for multi-scale enhanced sampling of disordered protein conformations.

Authors:  Xiaorong Liu; Jianhan Chen
Journal:  Phys Chem Chem Phys       Date:  2017-12-13       Impact factor: 3.676

Review 5.  IDPs in macromolecular complexes: the roles of multivalent interactions in diverse assemblies.

Authors:  Ho Yee Joyce Fung; Melissa Birol; Elizabeth Rhoades
Journal:  Curr Opin Struct Biol       Date:  2018-01-04       Impact factor: 6.809

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.  LCD-Composer: an intuitive, composition-centric method enabling the identification and detailed functional mapping of low-complexity domains.

Authors:  Sean M Cascarina; David C King; Erin Osborne Nishimura; Eric D Ross
Journal:  NAR Genom Bioinform       Date:  2021-05-26

8.  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

9.  The Proline/Glycine-Rich Region of the Biofilm Adhesion Protein Aap Forms an Extended Stalk that Resists Compaction.

Authors:  Alexander E Yarawsky; Lance R English; Steven T Whitten; Andrew B Herr
Journal:  J Mol Biol       Date:  2016-11-25       Impact factor: 5.469

10.  Dynamical Oligomerisation of Histidine Rich Intrinsically Disordered ProteinS Is Regulated through Zinc-Histidine Interactions.

Authors:  Carolina Cragnell; Lasse Staby; Samuel Lenton; Birthe B Kragelund; Marie Skepö
Journal:  Biomolecules       Date:  2019-04-30
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