Literature DB >> 33545530

Physics-based computational and theoretical approaches to intrinsically disordered proteins.

Joan-Emma Shea1, Robert B Best2, Jeetain Mittal3.   

Abstract

Intrinsically disordered proteins (IDPs) are an important class of proteins that do not fold to a well-defined three-dimensional shape but rather adopt an ensemble of inter-converting conformations. This feature makes their experimental characterization challenging and invites a theoretical and computational approach to complement experimental studies. In this review, we highlight the recent progress in developing new computational and theoretical approaches to study the structure and dynamics of monomeric and order higher assemblies of IDPs, with a particular emphasis on their phase separation into protein-rich condensates.
Copyright © 2021. Published by Elsevier Ltd.

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Year:  2021        PMID: 33545530      PMCID: PMC8150118          DOI: 10.1016/j.sbi.2020.12.012

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


  57 in total

1.  Structure formation in films of weakly charged block polyelectrolyte solutions.

Authors:  A V Kyrylyuk; J G E M Fraaije
Journal:  J Chem Phys       Date:  2004-11-08       Impact factor: 3.488

Review 2.  Advances in the Simulation of Protein Aggregation at the Atomistic Scale.

Authors:  Martín Carballo-Pacheco; Birgit Strodel
Journal:  J Phys Chem B       Date:  2016-03-21       Impact factor: 2.991

3.  Probing the Action of Chemical Denaturant on an Intrinsically Disordered Protein by Simulation and Experiment.

Authors:  Wenwei Zheng; Alessandro Borgia; Karin Buholzer; Alexander Grishaev; Benjamin Schuler; Robert B Best
Journal:  J Am Chem Soc       Date:  2016-09-01       Impact factor: 15.419

4.  Phase Separation and Single-Chain Compactness of Charged Disordered Proteins Are Strongly Correlated.

Authors:  Yi-Hsuan Lin; Hue Sun Chan
Journal:  Biophys J       Date:  2017-05-05       Impact factor: 4.033

5.  Solvent denaturation and stabilization of globular proteins.

Authors:  D O Alonso; K A Dill
Journal:  Biochemistry       Date:  1991-06-18       Impact factor: 3.162

6.  Evolution of All-Atom Protein Force Fields to Improve Local and Global Properties.

Authors:  Gül H Zerze; Wenwei Zheng; Robert B Best; Jeetain Mittal
Journal:  J Phys Chem Lett       Date:  2019-04-22       Impact factor: 6.475

7.  Hydropathy Patterning Complements Charge Patterning to Describe Conformational Preferences of Disordered Proteins.

Authors:  Wenwei Zheng; Gregory Dignon; Matthew Brown; Young C Kim; Jeetain Mittal
Journal:  J Phys Chem Lett       Date:  2020-04-17       Impact factor: 6.475

8.  Investigating the Conformational Ensembles of Intrinsically Disordered Proteins with a Simple Physics-Based Model.

Authors:  Yani Zhao; Robinson Cortes-Huerto; Kurt Kremer; Joseph F Rudzinski
Journal:  J Phys Chem B       Date:  2020-05-13       Impact factor: 2.991

9.  TDP-43 α-helical structure tunes liquid-liquid phase separation and function.

Authors:  Alexander E Conicella; Gregory L Dignon; Gül H Zerze; Hermann Broder Schmidt; Alexandra M D'Ordine; Young C Kim; Rajat Rohatgi; Yuna M Ayala; Jeetain Mittal; Nicolas L Fawzi
Journal:  Proc Natl Acad Sci U S A       Date:  2020-03-04       Impact factor: 11.205

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  15 in total

Review 1.  Conformational Dynamics of Intrinsically Disordered Proteins Regulate Biomolecular Condensate Chemistry.

Authors:  Anton Abyzov; Martin Blackledge; Markus Zweckstetter
Journal:  Chem Rev       Date:  2022-02-18       Impact factor: 60.622

2.  Molecular interactions contributing to FUS SYGQ LC-RGG phase separation and co-partitioning with RNA polymerase II heptads.

Authors:  Wai Shing Tang; Nina Jovic; Anastasia C Murthy; Abigail M Janke; Da Hee Seo; Theodora Myrto Perdikari; Jeetain Mittal; Nicolas L Fawzi
Journal:  Nat Struct Mol Biol       Date:  2021-11-10       Impact factor: 15.369

Review 3.  Intrinsically Disordered Proteins: Critical Components of the Wetware.

Authors:  Prakash Kulkarni; Supriyo Bhattacharya; Srisairam Achuthan; Amita Behal; Mohit Kumar Jolly; Sourabh Kotnala; Atish Mohanty; Govindan Rangarajan; Ravi Salgia; Vladimir Uversky
Journal:  Chem Rev       Date:  2022-02-16       Impact factor: 72.087

Review 4.  Biophysical studies of phase separation integrating experimental and computational methods.

Authors:  Nicolas L Fawzi; Sapun H Parekh; Jeetain Mittal
Journal:  Curr Opin Struct Biol       Date:  2021-06-15       Impact factor: 7.786

Review 5.  The Protein Folding Problem: The Role of Theory.

Authors:  Roy Nassar; Gregory L Dignon; Rostam M Razban; Ken A Dill
Journal:  J Mol Biol       Date:  2021-07-03       Impact factor: 6.151

6.  Improved coarse-grained model for studying sequence dependent phase separation of disordered proteins.

Authors:  Roshan Mammen Regy; Jacob Thompson; Young C Kim; Jeetain Mittal
Journal:  Protein Sci       Date:  2021-05-24       Impact factor: 6.993

7.  Biomolecular Condensates: Sequence Determinants of Phase Separation, Microstructural Organization, Enzymatic Activity, and Material Properties.

Authors:  Benjamin S Schuster; Roshan Mammen Regy; Elliott M Dolan; Aishwarya Kanchi Ranganath; Nina Jovic; Sagar D Khare; Zheng Shi; Jeetain Mittal
Journal:  J Phys Chem B       Date:  2021-03-04       Impact factor: 3.466

8.  Modeling the Structure and Interactions of Intrinsically Disordered Peptides with Multiple Replica, Metadynamics-Based Sampling Methods and Force-Field Combinations.

Authors:  Lunna Li; Tommaso Casalini; Paolo Arosio; Matteo Salvalaglio
Journal:  J Chem Theory Comput       Date:  2022-02-17       Impact factor: 6.578

Review 9.  Rules of Physical Mathematics Govern Intrinsically Disordered Proteins.

Authors:  Kingshuk Ghosh; Jonathan Huihui; Michael Phillips; Austin Haider
Journal:  Annu Rev Biophys       Date:  2022-02-04       Impact factor: 19.763

Review 10.  Advanced Sampling Methods for Multiscale Simulation of Disordered Proteins and Dynamic Interactions.

Authors:  Xiping Gong; Yumeng Zhang; Jianhan Chen
Journal:  Biomolecules       Date:  2021-09-28
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