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Title: Evolution of All-Atom Protein Force Fields to Improve Local and Global Properties

Abstract

Experimental studies on intrinsically disordered and unfolded proteins have shown that in isolation they typically have low populations of secondary structure and exhibit distance scalings suggesting that they are at near-theta-solvent conditions. Until recently, however, all-atom force fields failed to reproduce these fundamental properties of intrinsically disordered proteins (IDPs). Recent improvements by refining against ensemble-averaged experimental observables for polypeptides in aqueous solution have addressed deficiencies including secondary structure bias, global conformational properties, and thermodynamic parameters of biophysical reactions such as folding and collapse. To date, studies utilizing these improved all-atom force fields have mostly been limited to a small set of unfolded or disordered proteins. Here, we present data generated for a diverse library of unfolded or disordered proteins using three progressively improved generations of Amber03 force fields, and we explore how global and local properties are affected by each successive change in the force field. We find that the most recent force field refinements significantly improve the agreement of the global properties such as radii of gyration and end-to-end distances with experimental estimates. However, these global properties are largely independent of the local secondary structure propensity. This result stresses the need to validate force fields with reference to amore » combination of experimental data providing information about both local and global structure formation.« less

Authors:
ORCiD logo [1];  [2]; ORCiD logo [3]; ORCiD logo [4]
+ Show Author Affiliations
  1. Lehigh Univ., Bethlehem, PA (United States). Dept. of Chemical and Biomolecular Engineering; Princeton Univ., NJ (United States). Chemical and Biological Engineering
  2. Arizona State Univ., Mesa, AZ (United States). College of Integrative Sciences and Arts
  3. National Inst. of Health (NIH), Bethesda, MD (United States). Lab. of Chemical Physics, National Inst. of Diabetes and Digestive and Kidney Diseases
  4. Lehigh Univ., Bethlehem, PA (United States). Dept. of Chemical and Biomolecular Engineering
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES); National Institutes of Health (NIH)
OSTI Identifier:
1527357
Grant/Contract Number:  
SC0013979; AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
Journal of Physical Chemistry Letters
Additional Journal Information:
Journal Volume: 10; Journal Issue: 9; Journal ID: ISSN 1948-7185
Publisher:
American Chemical Society
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY

Citation Formats

Zerze, Gül H., Zheng, Wenwei, Best, Robert B., and Mittal, Jeetain. Evolution of All-Atom Protein Force Fields to Improve Local and Global Properties. United States: N. p., 2019. Web. doi:10.1021/acs.jpclett.9b00850.
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Zerze, Gül H., Zheng, Wenwei, Best, Robert B., & Mittal, Jeetain. Evolution of All-Atom Protein Force Fields to Improve Local and Global Properties. United States. https://doi.org/10.1021/acs.jpclett.9b00850
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Zerze, Gül H., Zheng, Wenwei, Best, Robert B., and Mittal, Jeetain. Fri . "Evolution of All-Atom Protein Force Fields to Improve Local and Global Properties". United States. https://doi.org/10.1021/acs.jpclett.9b00850. https://www.osti.gov/servlets/purl/1527357.
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@article{osti_1527357,
title = {Evolution of All-Atom Protein Force Fields to Improve Local and Global Properties},
author = {Zerze, Gül H. and Zheng, Wenwei and Best, Robert B. and Mittal, Jeetain},
abstractNote = {Experimental studies on intrinsically disordered and unfolded proteins have shown that in isolation they typically have low populations of secondary structure and exhibit distance scalings suggesting that they are at near-theta-solvent conditions. Until recently, however, all-atom force fields failed to reproduce these fundamental properties of intrinsically disordered proteins (IDPs). Recent improvements by refining against ensemble-averaged experimental observables for polypeptides in aqueous solution have addressed deficiencies including secondary structure bias, global conformational properties, and thermodynamic parameters of biophysical reactions such as folding and collapse. To date, studies utilizing these improved all-atom force fields have mostly been limited to a small set of unfolded or disordered proteins. Here, we present data generated for a diverse library of unfolded or disordered proteins using three progressively improved generations of Amber03 force fields, and we explore how global and local properties are affected by each successive change in the force field. We find that the most recent force field refinements significantly improve the agreement of the global properties such as radii of gyration and end-to-end distances with experimental estimates. However, these global properties are largely independent of the local secondary structure propensity. This result stresses the need to validate force fields with reference to a combination of experimental data providing information about both local and global structure formation.},
doi = {10.1021/acs.jpclett.9b00850},
journal = {Journal of Physical Chemistry Letters},
number = 9,
volume = 10,
place = {United States},
year = {Fri Apr 05 00:00:00 EDT 2019},
month = {Fri Apr 05 00:00:00 EDT 2019}
}
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https://doi.org/10.1021/acs.jpclett.9b00850
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