Literature DB >> 27988422

Simulations of disordered proteins and systems with conformational heterogeneity.

Zachary A Levine1, Joan-Emma Shea2.   

Abstract

Intrinsically disordered proteins (IDPs) and protein regions can facilitate a wide variety of complex physiological processes such as binding, signaling, and formation of membraneless organelles. They can however also play pathological roles by aggregating into cytotoxic oligomers and fibrils. Characterizing the structure and function of disordered proteins is an onerous task, primarily because these proteins adopt transient structures, which are difficult to capture in experiments. Simulations have emerged as a powerful tool for interpreting and augmenting experimental measurements of IDPs. In this review we focus on computer simulations of disordered protein structures, functions, assemblies, and emerging questions that, taken together, give an overview of the field as it exists today.
Copyright © 2016. Published by Elsevier Ltd.

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Year:  2016        PMID: 27988422     DOI: 10.1016/j.sbi.2016.11.006

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


  24 in total

Review 1.  Force field development and simulations of intrinsically disordered proteins.

Authors:  Jing Huang; Alexander D MacKerell
Journal:  Curr Opin Struct Biol       Date:  2017-11-05       Impact factor: 6.809

Review 2.  Features of molecular recognition of intrinsically disordered proteins via coupled folding and binding.

Authors:  Jing Yang; Meng Gao; Junwen Xiong; Zhengding Su; Yongqi Huang
Journal:  Protein Sci       Date:  2019-09-04       Impact factor: 6.725

3.  Recent Force Field Strategies for Intrinsically Disordered Proteins.

Authors:  Junxi Mu; Hao Liu; Jian Zhang; Ray Luo; Hai-Feng Chen
Journal:  J Chem Inf Model       Date:  2021-02-16       Impact factor: 4.956

4.  Refining All-Atom Protein Force Fields for Polar-Rich, Prion-like, Low-Complexity Intrinsically Disordered Proteins.

Authors:  Wai Shing Tang; Nicolas L Fawzi; Jeetain Mittal
Journal:  J Phys Chem B       Date:  2020-10-20       Impact factor: 2.991

5.  Conformational Heterogeneity and FRET Data Interpretation for Dimensions of Unfolded Proteins.

Authors:  Jianhui Song; Gregory-Neal Gomes; Tongfei Shi; Claudiu C Gradinaru; Hue Sun Chan
Journal:  Biophys J       Date:  2017-09-05       Impact factor: 4.033

6.  Refinement of Peptide Conformational Ensembles by 2D IR Spectroscopy: Application to Ala‒Ala‒Ala.

Authors:  Chi-Jui Feng; Balamurugan Dhayalan; Andrei Tokmakoff
Journal:  Biophys J       Date:  2018-06-19       Impact factor: 4.033

7.  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

8.  Sequence Effects on Size, Shape, and Structural Heterogeneity in Intrinsically Disordered Proteins.

Authors:  Upayan Baul; Debayan Chakraborty; Mauro L Mugnai; John E Straub; D Thirumalai
Journal:  J Phys Chem B       Date:  2019-04-15       Impact factor: 2.991

9.  Computer Simulations Aimed at Exploring Protein Aggregation and Dissociation.

Authors:  Phuong H Nguyen; Philippe Derreumaux
Journal:  Methods Mol Biol       Date:  2022

Review 10.  Physics-based computational and theoretical approaches to intrinsically disordered proteins.

Authors:  Joan-Emma Shea; Robert B Best; Jeetain Mittal
Journal:  Curr Opin Struct Biol       Date:  2021-02-02       Impact factor: 6.809

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