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Title: Secondary structure of rat and human amylin across force fields

Abstract

The aggregation of human amylin has been strongly implicated in the progression of Type II diabetes. This 37-residue peptide forms a variety of secondary structures, including random coils, α-helices, and β- hairpins. The balance between these structures depends on the chemical environment, making amylin an ideal candidate to examine inherent biases in force fields. Rat amylin differs from human amylin by only 6 residues; however, it does not form fibrils. Therefore it provides a useful complement to human amylin in studies of the key events along the aggregation pathway. In this work, the free energy of rat and human amylin was determined as a function of α-helix and β-hairpin content for the Gromos96 53a6, OPLS-AA/L, CHARMM22/CMAP, CHARMM22*, Amberff99sb*-ILDN, and Amberff03w force fields using advanced sampling techniques, specifically bias exchange metadynamics. This work represents a first systematic attempt to evaluate the conformations and the corresponding free energy of a large, clinically relevant disordered peptide in solution across force fields. The NMR chemical shifts of rIAPP were calculated for each of the force fields using their respective free energy maps, allowing us to quantitatively assess their predictions. We show that the predicted distribution of secondary structures is sensitive to the choice ofmore » force-field: Gromos53a6 is biased towards β-hairpins, while CHARMM22/CMAP predicts structures that are overly α-helical. OPLS-AA/L favors disordered structures. Amberff99sb*-ILDN, AmberFF03w and CHARMM22* provide the balance between secondary structures that is most consistent with available experimental data. In contrast to previous reports, our findings suggest that the equilibrium conformations of human and rat amylin are remarkably similar, but that subtle differences arise in transient alpha-helical and beta-strand containing structures that the human peptide can more readily adopt. We hypothesize that these transient states enable dynamic pathways that facilitate the formation of aggregates and, eventually, amyloid fibrils.« less

Authors:
 [1];  [1];  [2];  [3]
+ Show Author Affiliations
  1. Univ. of Chicago, Chicago, IL (United States)
  2. National Cheng Kung Univ., Tainan (Taiwan)
  3. Univ. of Chicago, Chicago, IL (United States); Argonne National Lab. (ANL), Argonne, IL (United States)
Publication Date:
Research Org.:
Argonne National Laboratory (ANL), Argonne, IL (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES)
OSTI Identifier:
1249116
Alternate Identifier(s):
OSTI ID: 1212376; OSTI ID: 1395962
Grant/Contract Number:  
AC02-06CH11357
Resource Type:
Accepted Manuscript
Journal Name:
PLoS ONE
Additional Journal Information:
Journal Volume: 10; Journal Issue: 7; Journal ID: ISSN 1932-6203
Publisher:
Public Library of Science
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; free energy; biochemical simulations; molecular dynamics; proline; amyloid proteins; intermolecular forces; protein structure prediction; diabetes mellitus; oligomers; molecular structure

Citation Formats

Hoffmann, Kyle Quynn, McGovern, Michael, Chiu, Chi -Cheng, and de Pablo, Juan J. Secondary structure of rat and human amylin across force fields. United States: N. p., 2015. Web. doi:10.1371/journal.pone.0134091.
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Hoffmann, Kyle Quynn, McGovern, Michael, Chiu, Chi -Cheng, & de Pablo, Juan J. Secondary structure of rat and human amylin across force fields. United States. https://doi.org/10.1371/journal.pone.0134091
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Hoffmann, Kyle Quynn, McGovern, Michael, Chiu, Chi -Cheng, and de Pablo, Juan J. Wed . "Secondary structure of rat and human amylin across force fields". United States. https://doi.org/10.1371/journal.pone.0134091. https://www.osti.gov/servlets/purl/1249116.
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@article{osti_1249116,
title = {Secondary structure of rat and human amylin across force fields},
author = {Hoffmann, Kyle Quynn and McGovern, Michael and Chiu, Chi -Cheng and de Pablo, Juan J.},
abstractNote = {The aggregation of human amylin has been strongly implicated in the progression of Type II diabetes. This 37-residue peptide forms a variety of secondary structures, including random coils, α-helices, and β- hairpins. The balance between these structures depends on the chemical environment, making amylin an ideal candidate to examine inherent biases in force fields. Rat amylin differs from human amylin by only 6 residues; however, it does not form fibrils. Therefore it provides a useful complement to human amylin in studies of the key events along the aggregation pathway. In this work, the free energy of rat and human amylin was determined as a function of α-helix and β-hairpin content for the Gromos96 53a6, OPLS-AA/L, CHARMM22/CMAP, CHARMM22*, Amberff99sb*-ILDN, and Amberff03w force fields using advanced sampling techniques, specifically bias exchange metadynamics. This work represents a first systematic attempt to evaluate the conformations and the corresponding free energy of a large, clinically relevant disordered peptide in solution across force fields. The NMR chemical shifts of rIAPP were calculated for each of the force fields using their respective free energy maps, allowing us to quantitatively assess their predictions. We show that the predicted distribution of secondary structures is sensitive to the choice of force-field: Gromos53a6 is biased towards β-hairpins, while CHARMM22/CMAP predicts structures that are overly α-helical. OPLS-AA/L favors disordered structures. Amberff99sb*-ILDN, AmberFF03w and CHARMM22* provide the balance between secondary structures that is most consistent with available experimental data. In contrast to previous reports, our findings suggest that the equilibrium conformations of human and rat amylin are remarkably similar, but that subtle differences arise in transient alpha-helical and beta-strand containing structures that the human peptide can more readily adopt. We hypothesize that these transient states enable dynamic pathways that facilitate the formation of aggregates and, eventually, amyloid fibrils.},
doi = {10.1371/journal.pone.0134091},
journal = {PLoS ONE},
number = 7,
volume = 10,
place = {United States},
year = {Wed Jul 29 00:00:00 EDT 2015},
month = {Wed Jul 29 00:00:00 EDT 2015}
}
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