United-atom Acyl Chains for CHARMM Phospholipids

Overview

Journal J Phys Chem B

Publisher American Chemical Society

Specialty Chemistry

Date 2008 May 17

PMID 18481889

Citations 32

Authors

Jerome Henin

Wataru Shinoda

Michael L Klein

Affiliations

Soon will be listed here.

Abstract

In all-atom simulations of lipid membranes, explicit hydrogen atoms contained in the hydrocarbon region are described by a large number of degrees of freedom, although they convey only limited physical information. We propose an implicit-hydrogen model for saturated and monounsaturated acyl chains, aimed at complementing the all-atom CHARMM27 model for phospholipid headgroups. Torsional potentials and nonbonded parameters were fitted to reproduce experimental data and free energy surfaces of all-atom model systems. Comparative simulations of fluid-phase POPC bilayers were performed using the all-hydrogen force field and the present model. The hybrid model accelerates a typical bilayer simulation by about 50% while sacrificing a minimal amount of detail with respect to the fully atomistic description. In addition, the united-atom description is energetically compatible with all-atom CHARMM models, making it suitable for simulations of complex membrane systems.

Citing Articles

CHARMM36 Lipid Force Field with Explicit Treatment of Long-Range Dispersion: Parametrization and Validation for Phosphatidylethanolamine, Phosphatidylglycerol, and Ether Lipids.

Yu Y, Kramer A, Venable R, Brooks B, Klauda J, Pastor R J Chem Theory Comput. 2021; 17(3):1581-1595.

PMID: 33620194 PMC: 8130185. DOI: 10.1021/acs.jctc.0c01327.

Phospholipid-Based Reverse Micelle Structures in Vegetable Oil Modified by Water Content, Free Fatty Acid, and Temperature.

Penttila P, Vierros S, Utriainen K, Carl N, Rautkari L, Sammalkorpi M Langmuir. 2019; 35(25):8373-8382.

PMID: 31141381 PMC: 6750831. DOI: 10.1021/acs.langmuir.9b01135.

Molecular mechanism of substrate selectivity of the arginine-agmatine Antiporter AdiC.

Krammer E, Gibbons A, Roos G, Prevost M Sci Rep. 2018; 8(1):15607.

PMID: 30353119 PMC: 6199258. DOI: 10.1038/s41598-018-33963-1.

Propofol inhibits the voltage-gated sodium channel NaChBac at multiple sites.

Wang Y, Yang E, Wells M, Bondarenko V, Woll K, Carnevale V J Gen Physiol. 2018; 150(9):1317-1331.

PMID: 30018039 PMC: 6122922. DOI: 10.1085/jgp.201811993.

Lipidated apolipoprotein E4 structure and its receptor binding mechanism determined by a combined cross-linking coupled to mass spectrometry and molecular dynamics approach.

Henry N, Krammer E, Stengel F, Adams Q, Van Liefferinge F, Hubin E PLoS Comput Biol. 2018; 14(6):e1006165.

PMID: 29933361 PMC: 6033463. DOI: 10.1371/journal.pcbi.1006165.

References

Chiu S, Vasudevan S, Jakobsson E, Mashl R, Scott H . Structure of sphingomyelin bilayers: a simulation study. Biophys J. 2003; 85(6):3624-35. PMC: 1303667. DOI: 10.1016/S0006-3495(03)74780-8. View

Chandrasekhar I, Kastenholz M, Lins R, Oostenbrink C, Schuler L, Tieleman D . A consistent potential energy parameter set for lipids: dipalmitoylphosphatidylcholine as a benchmark of the GROMOS96 45A3 force field. Eur Biophys J. 2003; 32(1):67-77. DOI: 10.1007/s00249-002-0269-4. View

Duque D, Vega L . Some issues on the calculation of interfacial properties by molecular simulation. J Chem Phys. 2004; 121(17):8611-7. DOI: 10.1063/1.1802672. View

Berger O, Edholm O, Jahnig F . Molecular dynamics simulations of a fluid bilayer of dipalmitoylphosphatidylcholine at full hydration, constant pressure, and constant temperature. Biophys J. 1997; 72(5):2002-13. PMC: 1184396. DOI: 10.1016/S0006-3495(97)78845-3. View

Egberts E, Marrink S, Berendsen H . Molecular dynamics simulation of a phospholipid membrane. Eur Biophys J. 1994; 22(6):423-36. DOI: 10.1007/BF00180163. View

Knecht V, Marrink S . Molecular dynamics simulations of lipid vesicle fusion in atomic detail. Biophys J. 2007; 92(12):4254-61. PMC: 1877782. DOI: 10.1529/biophysj.106.103572. View

Deol S, Bond P, Domene C, Sansom M . Lipid-protein interactions of integral membrane proteins: a comparative simulation study. Biophys J. 2004; 87(6):3737-49. PMC: 1304887. DOI: 10.1529/biophysj.104.048397. View

Tieleman D, MacCallum J, Ash W, Kandt C, Xu Z, Monticelli L . Membrane protein simulations with a united-atom lipid and all-atom protein model: lipid-protein interactions, side chain transfer free energies and model proteins. J Phys Condens Matter. 2011; 18(28):S1221-34. DOI: 10.1088/0953-8984/18/28/S07. View

Tarek M . Membrane electroporation: a molecular dynamics simulation. Biophys J. 2005; 88(6):4045-53. PMC: 1305635. DOI: 10.1529/biophysj.104.050617. View

10.

Kandt C, Ash W, Tieleman D . Setting up and running molecular dynamics simulations of membrane proteins. Methods. 2007; 41(4):475-88. DOI: 10.1016/j.ymeth.2006.08.006. View

11.

Kucerka N, Tristram-Nagle S, Nagle J . Structure of fully hydrated fluid phase lipid bilayers with monounsaturated chains. J Membr Biol. 2006; 208(3):193-202. DOI: 10.1007/s00232-005-7006-8. View

12.

Scott H . Modeling the lipid component of membranes. Curr Opin Struct Biol. 2002; 12(4):495-502. DOI: 10.1016/s0959-440x(02)00353-6. View

13.

Feller S, Yin D, Pastor R, MacKerell Jr A . Molecular dynamics simulation of unsaturated lipid bilayers at low hydration: parameterization and comparison with diffraction studies. Biophys J. 1997; 73(5):2269-79. PMC: 1181132. DOI: 10.1016/S0006-3495(97)78259-6. View

14.

Nagle J, Tristram-Nagle S . Structure of lipid bilayers. Biochim Biophys Acta. 2000; 1469(3):159-95. PMC: 2747654. DOI: 10.1016/s0304-4157(00)00016-2. View

15.

Marrink S, Lindahl E, Edholm O, Mark A . Simulation of the spontaneous aggregation of phospholipids into bilayers. J Am Chem Soc. 2001; 123(35):8638-9. DOI: 10.1021/ja0159618. View

16.

Kucerka N, Liu Y, Chu N, Petrache H, Tristram-Nagle S, Nagle J . Structure of fully hydrated fluid phase DMPC and DLPC lipid bilayers using X-ray scattering from oriented multilamellar arrays and from unilamellar vesicles. Biophys J. 2005; 88(4):2626-37. PMC: 1305359. DOI: 10.1529/biophysj.104.056606. View

17.

Klauda J, Pastor R, Brooks B . Adjacent gauche stabilization in linear alkanes: implications for polymer models and conformational analysis. J Phys Chem B. 2006; 109(33):15684-6. PMC: 1540463. DOI: 10.1021/jp0527608. View

18.

Wang J, Wolf R, Caldwell J, Kollman P, Case D . Development and testing of a general amber force field. J Comput Chem. 2004; 25(9):1157-74. DOI: 10.1002/jcc.20035. View

19.

Lee A . How lipids affect the activities of integral membrane proteins. Biochim Biophys Acta. 2004; 1666(1-2):62-87. DOI: 10.1016/j.bbamem.2004.05.012. View

20.

MacKerell Jr A, Feig M, Brooks 3rd C . Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations. J Comput Chem. 2004; 25(11):1400-15. DOI: 10.1002/jcc.20065. View