The DOI matches its Crossref record; 128 of the 128 references it cites were found in a registry or an index.
Derivation and Systematic Validation of a Refined All-Atom Force Field for Phosphatidylcholine Lipids
Open accessAbstract
An all-atomistic force field (FF) has been developed for fully saturated phospholipids. The parametrization has been largely based on high-level ab initio calculations in order to keep the empirical input to a minimum. Parameters for the lipid chains have been developed based on knowledge about bulk alkane liquids, for which thermodynamic and dynamic data are excellently reproduced. The FFs ability to simulate lipid bilayers in the liquid crystalline phase in a tensionless ensemble was tested in simulations of three lipids: 1,2-diauroyl-sn-glycero-3-phospocholine (DLPC), 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC), and 1,2-dipalmitoyl-sn-glycero-3-phospcholine (DPPC). Computed areas and volumes per lipid, and three different kinds of bilayer thicknesses, have been investigated. Most importantly NMR order parameters and scattering form factors agree in an excellent manner with experimental data under a range of temperatures. Further, the compatibility with the AMBER FF for biomolecules as well as the ability to simulate bilayers in gel phase was demonstrated. Overall, the FF presented here provides the important balance between the hydrophilic and hydrophobic forces present in lipid bilayers and therefore can be used for more complicated studies of realistic biological membranes with protein insertions.
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Cites
Density-functional thermochemistry. III. The role of exact exchange
Becke, A. D. (1993) · The Journal of Chemical Physics · doi:10.1063/1.464913 · Cited by 103,767
Lee, C., Yang, W., & Parr, R. G. (1988) · Physical Review B · doi:10.1103/physrevb.37.785 · Cited by 100,874
VMD: visual molecular dynamics
Humphrey, W., Dalke, A., & Schulten, K. (1996) · Journal of Molecular Graphics · doi:10.1016/0263-7855(96)00018-5 · Cited by 66,952
CRC Handbook of Chemistry and Physics
(2014) · doi:10.1201/b17118 · Cited by 57,706
Comparison of simple potential functions for simulating liquid water
Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W., & Klein, M. L. (1983) · The Journal of Chemical Physics · doi:10.1063/1.445869 · Cited by 41,298
Particle mesh Ewald: An N ⋅log( N ) method for Ewald sums in large systems
Darden, T., York, D., & Pedersen, L. (1993) · The Journal of Chemical Physics · doi:10.1063/1.464397 · Cited by 30,546
Canonical dynamics: Equilibrium phase-space distributions
Hoover, W. G. (1985) · Physical Review A · doi:10.1103/physreva.31.1695 · Cited by 23,465
Stephens, P. J., Devlin, F. J., Chabalowski, C. F., & Frisch, M. J. (1994) · The Journal of Physical Chemistry · doi:10.1021/j100096a001 · Cited by 23,248
A smooth particle mesh Ewald method
Essmann, U., Perera, L., Berkowitz, M. L., Darden, T., Lee, H., & Pedersen, L. G. (1995) · The Journal of Chemical Physics · doi:10.1063/1.470117 · Cited by 22,514
Vosko, S. H., Wilk, L., & Nusair, M. (1980) · Canadian Journal of Physics · doi:10.1139/p80-159 · Cited by 20,768
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Muller, M. P., Jiang, T., Sun, C., Lihan, M., Pant, S., Mahinthichaichan, P., Trifan, A., & Tajkhorshid, E. (2019) · Chemical Reviews · doi:10.1021/acs.chemrev.8b00608 · Cited by 282
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Uusitalo, J. J., Ingólfsson, H. I., Marrink, S. J., & Faustino, I. (2017) · Biophysical Journal · doi:10.1016/j.bpj.2017.05.043 · Cited by 259
Melcr, J., Bonhenry, D., Timr, Š., & Jungwirth, P. (2016) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.5b01202 · Cited by 43
Wang, L., Zhang, J., Wang, D., & Song, C. (2022) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1009972 · Cited by 18
Cryo‐EM structure of the octameric pore of Clostridium perfringens β‐toxin
Bruggisser, J., Iacovache, I., Musson, S. C., Degiacomi, M. T., Posthaus, H., & Zuber, B. (2022) · The EMBO Reports · doi:10.15252/embr.202254856 · Cited by 13
Free Energy of Membrane Pore Formation and Stability from Molecular Dynamics Simulations
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Metadata
- Authors
- Jämbeck, J. P. M., & Lyubartsev, A. P.
- Venue
- The Journal of Physical Chemistry B
- Publisher
- American Chemical Society (ACS)
- Published
- 2012-03-01
- Volume
- 116
- Issue
- 10
- Pages
- 3164-3179
- ISSN
- 1520-5207 (ISSN-L)
- 1520-6106
- OpenAlex
- W1977486075
- Cited by
- 527
- References
- 128
- FWCI
- 11.38
- Type
- journal article
- Language
- en
- Open access
- hybrid
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
