Force Field Effects in Simulations of Flexible Peptides with Varying Polyproline II Propensity
(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)
Please use this url to cite or link to this publication:
https://lup.lub.lu.se/record/76042a60-9e80-4613-aef4-89d1922db43a
- author
- Jephthah, Stephanie LU ; Pesce, Francesco ; Lindorff-Larsen, Kresten and Skepö, Marie LU
- organization
- publishing date
- 2021-10-12
- 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}}, }