Molecular Dynamics Generation of Nonarbitrary Membrane Models Reveals Lipid Orientational Correlations
This report addresses the following problems associated with the generation of computer models of phospholipid bilayer membranes using molecular dynamics simulations: arbitrary initial structures and short equilibration periods, an Ewald-induced strong coupling of phospholipids, uncertainty regardin...
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| Published in | Biophysical journal Vol. 79; no. 6; pp. 3118 - 3138 |
|---|---|
| Main Authors | , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
United States
Elsevier Inc
01.12.2000
Biophysical Society |
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| Online Access | Get full text |
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| Abstract | This report addresses the following problems associated with the generation of computer models of phospholipid bilayer membranes using molecular dynamics simulations: arbitrary initial structures and short equilibration periods, an Ewald-induced strong coupling of phospholipids, uncertainty regarding which value should be used for surface tension to alleviate the problem of the small size of the membrane, and simultaneous realization of both order parameters and the surface area. We generated a computer model of the liquid-crystalline
l-
α-dimyristoylphosphatidylcholine (DMPC) bilayer, starting from a configuration based on a crystal structure (rather than from an arbitrary structure). To break the crystalline structure, a 20-ps high-temperature pulse of 510
K (but not 450 or 480
K) was effective. The system finally obtained is an all-atom model, with Ewald summation to evaluate Coulombic interactions and a constant surface tension of 35 dynes/cm/water-membrane interface, equilibrated for 12
ns (over 50
ns total calculation time), which reproduces all of the experimentally observed parameters examined in this work. Furthermore, this model shows the presence of significant orientational correlations between neighboring alkyl chains and between shoulder vectors (which show the orientations of the lipids about their long axes) of neighboring DMPCs. |
|---|---|
| AbstractList | This report addresses the following problems associated with the genreation of computer models of phospholipid bilayer membranes using molecular dynamics simulations: arbitrary initial structures and short equilibration periods, an Ewald-induced strong coupling of phospholipids, uncertainty regarding which value should be used or surface tension to alleviate the problem of the small size of the membrane, and simultaneous realization of both order parameters and the surface area. This report addresses the following problems associated with the generation of computer models of phospholipid bilayer membranes using molecular dynamics simulations: arbitrary initial structures and short equilibration periods, an Ewald-induced strong coupling of phospholipids, uncertainty regarding which value should be used for surface tension to alleviate the problem of the small size of the membrane, and simultaneous realization of both order parameters and the surface area. We generated a computer model of the liquid-crystalline L-alpha-dimyristoylphosphatidylcholine (DMPC) bilayer, starting from a configuration based on a crystal structure (rather than from an arbitrary structure). To break the crystalline structure, a 20-ps high-temperature pulse of 510 K (but not 450 or 480 K) was effective. The system finally obtained is an all-atom model, with Ewald summation to evaluate Coulombic interactions and a constant surface tension of 35 dynes/cm/water-membrane interface, equilibrated for 12 ns (over 50 ns total calculation time), which reproduces all of the experimentally observed parameters examined in this work. Furthermore, this model shows the presence of significant orientational correlations between neighboring alkyl chains and between shoulder vectors (which show the orientations of the lipids about their long axes) of neighboring DMPCs. This report addresses the following problems associated with the generation of computer models of phospholipid bilayer membranes using molecular dynamics simulations: arbitrary initial structures and short equilibration periods, an Ewald-induced strong coupling of phospholipids, uncertainty regarding which value should be used for surface tension to alleviate the problem of the small size of the membrane, and simultaneous realization of both order parameters and the surface area. We generated a computer model of the liquid-crystalline l- α-dimyristoylphosphatidylcholine (DMPC) bilayer, starting from a configuration based on a crystal structure (rather than from an arbitrary structure). To break the crystalline structure, a 20-ps high-temperature pulse of 510 K (but not 450 or 480 K) was effective. The system finally obtained is an all-atom model, with Ewald summation to evaluate Coulombic interactions and a constant surface tension of 35 dynes/cm/water-membrane interface, equilibrated for 12 ns (over 50 ns total calculation time), which reproduces all of the experimentally observed parameters examined in this work. Furthermore, this model shows the presence of significant orientational correlations between neighboring alkyl chains and between shoulder vectors (which show the orientations of the lipids about their long axes) of neighboring DMPCs. |
| Author | Takaoka, Yuji Tamura, Yoshiyasu Pasenkiewicz-Gierula, Marta Kitamura, Kunihiro Miyagawa, Hiroh Kusumi, Akihiro |
| AuthorAffiliation | Department of Molecular Science, Research Center, Taisho Pharmaceutical Co. Ltd., Omiya, Saitama 330-8530, Japan |
| AuthorAffiliation_xml | – name: Department of Molecular Science, Research Center, Taisho Pharmaceutical Co. Ltd., Omiya, Saitama 330-8530, Japan |
| Author_xml | – sequence: 1 givenname: Yuji surname: Takaoka fullname: Takaoka, Yuji organization: Department of Molecular Science, Research Center, Taisho Pharmaceutical Co. Ltd., Omiya, Saitama 330-8530, Japan – sequence: 2 givenname: Marta surname: Pasenkiewicz-Gierula fullname: Pasenkiewicz-Gierula, Marta organization: Department of Molecular Science, Research Center, Taisho Pharmaceutical Co. Ltd., Omiya, Saitama 330-8530, Japan – sequence: 3 givenname: Hiroh surname: Miyagawa fullname: Miyagawa, Hiroh organization: Department of Molecular Science, Research Center, Taisho Pharmaceutical Co. Ltd., Omiya, Saitama 330-8530, Japan – sequence: 4 givenname: Kunihiro surname: Kitamura fullname: Kitamura, Kunihiro organization: Department of Molecular Science, Research Center, Taisho Pharmaceutical Co. Ltd., Omiya, Saitama 330-8530, Japan – sequence: 5 givenname: Yoshiyasu surname: Tamura fullname: Tamura, Yoshiyasu organization: Section of Software Development, Statistical Data Analysis Center, The Institute of Statistical Mathematics, Minato-ku, Tokyo 106-8569, Japan – sequence: 6 givenname: Akihiro surname: Kusumi fullname: Kusumi, Akihiro email: akusumi@bio.nagoya-u.ac.jp organization: Department of Biological Science, Graduate School of Science, Nagoya University, Nagoya 464-8602, and Kusumi Membrane Organizer Project, Exploratory Research on Advanced Technology Organization, Japan Science and Technology Cooperation, Nagoya 460-0012, Japan |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/11106617$$D View this record in MEDLINE/PubMed |
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Simul. contributor: fullname: Takaoka |
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| SubjectTerms | Cells Computer based modeling Computer Simulation Dimyristoylphosphatidylcholine - chemistry Hot Temperature Kinetics Lipid Bilayers - chemistry Lipids Membranes Models, Molecular Molecular biology Molecular Conformation Molecules Thermodynamics Water |
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| Title | Molecular Dynamics Generation of Nonarbitrary Membrane Models Reveals Lipid Orientational Correlations |
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