Literature DB >> 29080468

Force field development and simulations of intrinsically disordered proteins.

Jing Huang1, Alexander D MacKerell2.   

Abstract

Intrinsically disordered proteins (IDPs) play important roles in many physiological processes such as signal transduction and transcriptional regulation. Computer simulations that are based on empirical force fields have been increasingly used to understand the biophysics of disordered proteins. In this review, we focus on recent improvement of protein force fields, including polarizable force fields, concerning their accuracy in modeling intrinsically disordered proteins. Some recent benchmarks and applications of these force fields are also overviewed.
Copyright © 2017 Elsevier Ltd. All rights reserved.

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Year:  2017        PMID: 29080468      PMCID: PMC5826789          DOI: 10.1016/j.sbi.2017.10.008

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


  83 in total

1.  A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations.

Authors:  Yong Duan; Chun Wu; Shibasish Chowdhury; Mathew C Lee; Guoming Xiong; Wei Zhang; Rong Yang; Piotr Cieplak; Ray Luo; Taisung Lee; James Caldwell; Junmei Wang; Peter Kollman
Journal:  J Comput Chem       Date:  2003-12       Impact factor: 3.376

2.  Enhanced hairpin stability through loop design: the case of the protein G B1 domain hairpin.

Authors:  R Matthew Fesinmeyer; F Michael Hudson; Niels H Andersen
Journal:  J Am Chem Soc       Date:  2004-06-16       Impact factor: 15.419

3.  Comparison of multiple Amber force fields and development of improved protein backbone parameters.

Authors:  Viktor Hornak; Robert Abel; Asim Okur; Bentley Strockbine; Adrian Roitberg; Carlos Simmerling
Journal:  Proteins       Date:  2006-11-15

Review 4.  Simulations of disordered proteins and systems with conformational heterogeneity.

Authors:  Zachary A Levine; Joan-Emma Shea
Journal:  Curr Opin Struct Biol       Date:  2016-12-15       Impact factor: 6.809

Review 5.  Pathological unfoldomics of uncontrolled chaos: intrinsically disordered proteins and human diseases.

Authors:  Vladimir N Uversky; Vrushank Davé; Lilia M Iakoucheva; Prerna Malaney; Steven J Metallo; Ravi Ramesh Pathak; Andreas C Joerger
Journal:  Chem Rev       Date:  2014-05-15       Impact factor: 60.622

6.  Test and Evaluation of ff99IDPs Force Field for Intrinsically Disordered Proteins.

Authors:  Wei Ye; Dingjue Ji; Wei Wang; Ray Luo; Hai-Feng Chen
Journal:  J Chem Inf Model       Date:  2015-05-13       Impact factor: 4.956

7.  Derivation of fixed partial charges for amino acids accommodating a specific water model and implicit polarization.

Authors:  David S Cerutti; Julia E Rice; William C Swope; David A Case
Journal:  J Phys Chem B       Date:  2013-02-18       Impact factor: 2.991

8.  Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone φ, ψ and side-chain χ(1) and χ(2) dihedral angles.

Authors:  Robert B Best; Xiao Zhu; Jihyun Shim; Pedro E M Lopes; Jeetain Mittal; Michael Feig; Alexander D Mackerell
Journal:  J Chem Theory Comput       Date:  2012-07-18       Impact factor: 6.006

9.  An Analysis of Biomolecular Force Fields for Simulations of Polyglutamine in Solution.

Authors:  Aaron M Fluitt; Juan J de Pablo
Journal:  Biophys J       Date:  2015-09-01       Impact factor: 4.033

10.  The Polarizable Atomic Multipole-based AMOEBA Force Field for Proteins.

Authors:  Yue Shi; Zhen Xia; Jiajing Zhang; Robert Best; Chuanjie Wu; Jay W Ponder; Pengyu Ren
Journal:  J Chem Theory Comput       Date:  2013       Impact factor: 6.006

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  41 in total

1.  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

2.  A physically grounded damped dispersion model with particle mesh Ewald summation.

Authors:  Joshua A Rackers; Chengwen Liu; Pengyu Ren; Jay W Ponder
Journal:  J Chem Phys       Date:  2018-08-28       Impact factor: 3.488

3.  A Metastable Contact and Structural Disorder in the Estrogen Receptor Transactivation Domain.

Authors:  Yi Peng; Shufen Cao; Janna Kiselar; Xiangzhu Xiao; Zhanwen Du; An Hsieh; Soobin Ko; Yinghua Chen; Prashansa Agrawal; Wenwei Zheng; Wuxian Shi; Wei Jiang; Lin Yang; Mark R Chance; Witold K Surewicz; Matthias Buck; Sichun Yang
Journal:  Structure       Date:  2018-12-20       Impact factor: 5.006

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 Flexibility of the Protein-Protein Interfaces of the Ebola Virus VP40 Structural Matrix Filament.

Authors:  Elumalai Pavadai; Nisha Bhattarai; Prabin Baral; Robert V Stahelin; Prem P Chapagain; Bernard S Gerstman
Journal:  J Phys Chem B       Date:  2019-10-16       Impact factor: 2.991

6.  Generation of the configurational ensemble of an intrinsically disordered protein from unbiased molecular dynamics simulation.

Authors:  Utsab R Shrestha; Puneet Juneja; Qiu Zhang; Viswanathan Gurumoorthy; Jose M Borreguero; Volker Urban; Xiaolin Cheng; Sai Venkatesh Pingali; Jeremy C Smith; Hugh M O'Neill; Loukas Petridis
Journal:  Proc Natl Acad Sci U S A       Date:  2019-09-23       Impact factor: 11.205

7.  Amyloid assembly is dominated by misregistered kinetic traps on an unbiased energy landscape.

Authors:  Zhiguang Jia; Jeremy D Schmit; Jianhan Chen
Journal:  Proc Natl Acad Sci U S A       Date:  2020-04-28       Impact factor: 11.205

8.  Predicting partition coefficients of drug-like molecules in the SAMPL6 challenge with Drude polarizable force fields.

Authors:  Ye Ding; You Xu; Cheng Qian; Jinfeng Chen; Jian Zhu; Houhou Huang; Yi Shi; Jing Huang
Journal:  J Comput Aided Mol Des       Date:  2020-01-20       Impact factor: 3.686

9.  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

10.  Molecular dynamics simulations of lipid nanodiscs.

Authors:  Mohsen Pourmousa; Richard W Pastor
Journal:  Biochim Biophys Acta Biomembr       Date:  2018-05-03       Impact factor: 3.747

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