Literature DB >> 28259050

Computational and theoretical advances in studies of intrinsically disordered proteins.

Robert B Best1.   

Abstract

Intrinsically disordered proteins (IDPs) are increasingly realized to play diverse biological roles, ranging from molecular signaling to the formation of membraneless organelles. Their high degree of disorder makes them more challenging to study using the techniques of conventional structural biology, because any observable will be averaged over a heterogeneous ensemble of structures. Molecular simulations and theory are therefore a natural complement to experiment for studying the structure, dynamics and function of IDPs. The diverse time and length scales relevant to the roles played by IDPs require flexibility in the techniques applied. Here, I summarize some of the developments in simulation and theory in recent years, which have been driven by the desire to better capture IDP properties at different time- and length-scales. I also provide an outlook for how methods can be improved in the future and emerging problems which may be addressed by theory and simulation.
Copyright © 2017. Published by Elsevier Ltd.

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Year:  2017        PMID: 28259050     DOI: 10.1016/j.sbi.2017.01.006

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


  61 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

Review 3.  The Structural and Functional Diversity of Intrinsically Disordered Regions in Transmembrane Proteins.

Authors:  Rajeswari Appadurai; Vladimir N Uversky; Anand Srivastava
Journal:  J Membr Biol       Date:  2019-05-28       Impact factor: 1.843

4.  The membrane axis of Alzheimer's nanomedicine.

Authors:  Yuhuan Li; Huayuan Tang; Nicholas Andrikopoulos; Ibrahim Javed; Luca Cecchetto; Aparna Nandakumar; Aleksandr Kakinen; Thomas P Davis; Feng Ding; Pu Chun Ke
Journal:  Adv Nanobiomed Res       Date:  2020-11-26

5.  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

6.  Analysis of Proline Substitutions Reveals the Plasticity and Sequence Sensitivity of Human IAPP Amyloidogenicity and Toxicity.

Authors:  Zachary Ridgway; Charles Eldrid; Alexander Zhyvoloup; Aisha Ben-Younis; Daeun Noh; Konstantinos Thalassinos; Daniel P Raleigh
Journal:  Biochemistry       Date:  2020-01-30       Impact factor: 3.162

7.  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

8.  HullRad: Fast Calculations of Folded and Disordered Protein and Nucleic Acid Hydrodynamic Properties.

Authors:  Patrick J Fleming; Karen G Fleming
Journal:  Biophys J       Date:  2018-02-27       Impact factor: 4.033

9.  Highly Disordered Amyloid-β Monomer Probed by Single-Molecule FRET and MD Simulation.

Authors:  Fanjie Meng; Mathias M J Bellaiche; Jae-Yeol Kim; Gül H Zerze; Robert B Best; Hoi Sung Chung
Journal:  Biophys J       Date:  2018-02-27       Impact factor: 4.033

10.  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

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