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

Research output: Contribution to journal › Journal article › Research › peer-review

Standard

Force Field Effects in Simulations of Flexible Peptides with Varying Polyproline II Propensity. / Jephthah, Stéphanie; Pesce, Francesco; Lindorff-Larsen, Kresten; Skepö, Marie.

In: Journal of Chemical Theory and Computation, Vol. 17, No. 10, 2021, p. 6634-6646.

Research output: Contribution to journal › Journal article › Research › peer-review

Harvard

Jephthah, S, Pesce, F, Lindorff-Larsen, K & Skepö, M 2021, 'Force Field Effects in Simulations of Flexible Peptides with Varying Polyproline II Propensity', Journal of Chemical Theory and Computation, vol. 17, no. 10, pp. 6634-6646. https://doi.org/10.1021/acs.jctc.1c00408

APA

Jephthah, S., Pesce, F., Lindorff-Larsen, K., & Skepö, M. (2021). Force Field Effects in Simulations of Flexible Peptides with Varying Polyproline II Propensity. Journal of Chemical Theory and Computation, 17(10), 6634-6646. https://doi.org/10.1021/acs.jctc.1c00408

Vancouver

Jephthah S, Pesce F, Lindorff-Larsen K, Skepö M. Force Field Effects in Simulations of Flexible Peptides with Varying Polyproline II Propensity. Journal of Chemical Theory and Computation. 2021;17(10):6634-6646. https://doi.org/10.1021/acs.jctc.1c00408

Author

Jephthah, Stéphanie ; Pesce, Francesco ; Lindorff-Larsen, Kresten ; Skepö, Marie. / Force Field Effects in Simulations of Flexible Peptides with Varying Polyproline II Propensity. In: Journal of Chemical Theory and Computation. 2021 ; Vol. 17, No. 10. pp. 6634-6646.

Bibtex

@article{c324f3809d4247309b797b3f340dd4cb,

title = "Force Field Effects in Simulations of Flexible Peptides with Varying Polyproline II Propensity",

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 = "St{\'e}phanie Jephthah and Francesco Pesce and Kresten Lindorff-Larsen and Marie Skep{\"o}",

note = "Publisher Copyright: {\textcopyright} 2021 The Authors. Published by American Chemical Society.",

year = "2021",

doi = "10.1021/acs.jctc.1c00408",

language = "English",

volume = "17",

pages = "6634--6646",

journal = "Journal of Chemical Theory and Computation",

issn = "1549-9618",

publisher = "American Chemical Society",

number = "10",

}

RIS

TY - JOUR

T1 - Force Field Effects in Simulations of Flexible Peptides with Varying Polyproline II Propensity

AU - Jephthah, Stéphanie

AU - Pesce, Francesco

AU - Lindorff-Larsen, Kresten

AU - Skepö, Marie

PY - 2021

Y1 - 2021

N2 - 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.

AB - 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.

U2 - 10.1021/acs.jctc.1c00408

DO - 10.1021/acs.jctc.1c00408

M3 - Journal article

C2 - 34524800

AN - SCOPUS:85115937402

VL - 17

SP - 6634

EP - 6646

JO - Journal of Chemical Theory and Computation

JF - Journal of Chemical Theory and Computation

SN - 1549-9618

IS - 10

ER -

ID: 283211295

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