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Force Field Effects in Simulations of Flexible Peptides with Varying Polyproline II Propensity

Jephthah, Stephanie LU ; Pesce, Francesco ; Lindorff-Larsen, Kresten and Skepö, Marie LU (2021) In Journal of Chemical Theory and Computation 17(10). p.6634-6646
Abstract
Five peptides previously suggested to possess polyproline II (PPII) structure have here been investigated by using atomistic molecular dynamics simulations to compare how well four different force fields known for simulating intrinsically disordered proteins relatively well (Amber ff99SB-disp, Amber ff99SB-ILDN, CHARM36IDPSFF, and CHARMM36m) can capture this secondary structure element. The results revealed that all force fields sample PPII structures but to different extents and with different propensities toward other secondary structure elements, in particular, the β-sheet and “random coils”. A cluster analysis of the simulations of histatin 5 also revealed that the conformational ensembles of the force fields are quite different. We... (More)
Five peptides previously suggested to possess polyproline II (PPII) structure have here been investigated by using atomistic molecular dynamics simulations to compare how well four different force fields known for simulating intrinsically disordered proteins relatively well (Amber ff99SB-disp, Amber ff99SB-ILDN, CHARM36IDPSFF, and CHARMM36m) can capture this secondary structure element. The results revealed that all force fields sample PPII structures but to different extents and with different propensities toward other secondary structure elements, in particular, the β-sheet and “random coils”. A cluster analysis of the simulations of histatin 5 also revealed that the conformational ensembles of the force fields are quite different. We compared the simulations to circular dichroism and nuclear magnetic resonance spectroscopy experiments and conclude that further experiments and methods for interpreting them are needed to assess the accuracy of force fields in determining PPII structure. (Less)
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; ; and
organization
publishing date
type
Contribution to journal
publication status
published
subject
in
Journal of Chemical Theory and Computation
volume
17
issue
10
pages
13 pages
publisher
The American Chemical Society (ACS)
external identifiers
  • pmid:34524800
  • scopus:85115937402
ISSN
1549-9618
DOI
10.1021/acs.jctc.1c00408
language
English
LU publication?
yes
id
76042a60-9e80-4613-aef4-89d1922db43a
date added to LUP
2021-10-09 16:44:22
date last changed
2023-04-02 18:10:58
@article{76042a60-9e80-4613-aef4-89d1922db43a,
  abstract     = {{Five peptides previously suggested to possess polyproline II (PPII) structure have here been investigated by using atomistic molecular dynamics simulations to compare how well four different force fields known for simulating intrinsically disordered proteins relatively well (Amber ff99SB-disp, Amber ff99SB-ILDN, CHARM36IDPSFF, and CHARMM36m) can capture this secondary structure element. The results revealed that all force fields sample PPII structures but to different extents and with different propensities toward other secondary structure elements, in particular, the β-sheet and “random coils”. A cluster analysis of the simulations of histatin 5 also revealed that the conformational ensembles of the force fields are quite different. We compared the simulations to circular dichroism and nuclear magnetic resonance spectroscopy experiments and conclude that further experiments and methods for interpreting them are needed to assess the accuracy of force fields in determining PPII structure.}},
  author       = {{Jephthah, Stephanie and Pesce, Francesco and Lindorff-Larsen, Kresten and Skepö, Marie}},
  issn         = {{1549-9618}},
  language     = {{eng}},
  month        = {{10}},
  number       = {{10}},
  pages        = {{6634--6646}},
  publisher    = {{The American Chemical Society (ACS)}},
  series       = {{Journal of Chemical Theory and Computation}},
  title        = {{Force Field Effects in Simulations of Flexible Peptides with Varying Polyproline II Propensity}},
  url          = {{http://dx.doi.org/10.1021/acs.jctc.1c00408}},
  doi          = {{10.1021/acs.jctc.1c00408}},
  volume       = {{17}},
  year         = {{2021}},
}