publication . Article . Other literature type . 2015

Toward Atomistic Resolution Structure of Phosphatidylcholine Headgroup and Glycerol Backbone at Different Ambient Conditions

Botan, Alexandru; Favela-Rosales, Fernando; Fuchs, Patrick F. J.; Javanainen, Matti; Kanduč, Matej; Kulig, Waldemar; Lamberg, Antti; Loison, Claire; Lyubartsev, Alexander; Miettinen, Markus S.; ...
  • Published: 25 Nov 2015
  • Country: Finland
Abstract
Phospholipids are essential building blocks of biological membranes. Despite a vast amount of very accurate experimental data, the atomistic resolution structures sampled by the glycerol backbone and choline headgroup in phoshatidylcholine bilayers are not known. Atomistic resolution molecular dynamics simulations have the potential to resolve the structures, and to give an arrestingly intuitive interpretation of the experimental data, but only if the simulations reproduce the data within experimental accuracy. In the present work, we simulated phosphatidylcholine (PC) lipid bilayers with 13 different atomistic models, and compared simulations with NMR experimen...
Subjects
free text keywords: Article, 116 Chemical sciences, [PHYS]Physics [physics], [CHIM]Chemical Sciences, [SPI]Engineering Sciences [physics], Physical and Theoretical Chemistry, Materials Chemistry, Surfaces, Coatings and Films, Lipid bilayer, Solid-state nuclear magnetic resonance, Glycerol, chemistry.chemical_compound, chemistry, Molecule, Chemical physics, Bond vector, Phosphatidylcholine, Biological membrane, Photochemistry, Molecular dynamics, Crystallography
159 references, page 1 of 11

Structure and Dynamics of Membranes; Lipowsky R., Sackmann E., Eds.; Elsevier: New York, 1995.

Tieleman D. P.; Marrink S. J.; Berendsen H. J. C.A computer perspective of membranes: molecular dynamics studies of lipid bilayer systems. Biochim. Biophys. Acta, Rev. Biomembr.1997, 1331, 235–270 10.1016/S0304-4157(97)00008-7. [OpenAIRE] [DOI]

Klauda J. B.; Venable R. M.; MacKerell A. D.Jr.; Pastor R. W. In Computational Modeling of Membrane Bilayers; Feller S. E., Ed.; Current Topics in Membranes; Academic Press: New York, 2008; Vol. 60; pp 1–48.

Edholm O. In Computational Modeling of Membrane Bilayers; Feller S. E., Ed.; Current Topics in Membranes; Academic Press: New York, 2008; Vol. 60; pp 91–110.

Tieleman D. P. In Molecular Simulations and Biomembranes: From Biophysics to Function; Sansom M., Biggin P., Eds.; The Royal Society of Chemistry: London, 2010; pp 1–25.

Piggot T. J.; PiñeiroÁ; Khalid S.Molecular Dynamics Simulations of Phosphatidylcholine Membranes: A Comparative Force Field Study. J. Chem. Theory Comput.2012, 8, 4593–4609 10.1021/ct3003157.26605617 [OpenAIRE] [PubMed] [DOI]

Rabinovich A.; Lyubartsev A.Computer simulation of lipid membranes: Methodology and achievements. Polym. Sci., Ser. C 2013, 55, 162–180 10.1134/S1811238213070060. [OpenAIRE] [DOI]

Marsh D.Handbook of Lipid Bilayers, 2nd ed.;RSC Press: London, 2013.

Israelachvili J. N.; Marcelja S.; Horn R. G.Physical Principles of Membrane Organiz ation. Q. Rev. Biophys.1980, 13, 121–200 10.1017/S0033583500001645.7015403 [PubMed] [DOI]

Seelig J.; Gally H.-U.; Wohlgemuth R.Orientation and flexibility of the choline head group in phosphatidylcholine bilayers. Biochim. Biophys. Acta, Biomembr.1977, 467, 109–119 10.1016/0005-2736(77)90188-2. [OpenAIRE] [DOI]

Skarjune R.; Oldfield E.Physical studies of cell surface and cell membrane structure. Determination of phospholipid head group organization by deuterium and phosphorus nuclear magnetic resonance spectroscopy. Biochemistry 1979, 18, 5903–5909 10.1021/bi00593a022.518875 [OpenAIRE] [PubMed] [DOI]

Jacobs R. E.; Oldfield E.NMR of membranes. Prog. Nucl. Magn. Reson. Spectrosc.1980, 14, 113–136 10.1016/0079-6565(80)80006-9. [OpenAIRE] [DOI]

Davis J. H.The description of membrane lipid conformation, order and dynamics by 2H-NMR. Biochim. Biophys. Acta, Rev. Biomembr.1983, 737, 117–171 10.1016/0304-4157(83)90015-1. [OpenAIRE] [DOI]

Strenk L.; Westerman P.; Doane J.A model of orientational ordering in phosphatidylcholine bilayers based on conformational analysis of the glycerol backbone region. Biophys. J.1985, 48, 765–773 10.1016/S0006-3495(85)83834-0.4074836 [OpenAIRE] [PubMed] [DOI]

Akutsu H.; Nagamori T.Conformational analysis of the polar head group in phosphatidylcholine bilayers: a structural change induced by cations. Biochemistry 1991, 30, 4510–4516 10.1021/bi00232a020.2021641 [OpenAIRE] [PubMed] [DOI]

159 references, page 1 of 11
Abstract
Phospholipids are essential building blocks of biological membranes. Despite a vast amount of very accurate experimental data, the atomistic resolution structures sampled by the glycerol backbone and choline headgroup in phoshatidylcholine bilayers are not known. Atomistic resolution molecular dynamics simulations have the potential to resolve the structures, and to give an arrestingly intuitive interpretation of the experimental data, but only if the simulations reproduce the data within experimental accuracy. In the present work, we simulated phosphatidylcholine (PC) lipid bilayers with 13 different atomistic models, and compared simulations with NMR experimen...
Subjects
free text keywords: Article, 116 Chemical sciences, [PHYS]Physics [physics], [CHIM]Chemical Sciences, [SPI]Engineering Sciences [physics], Physical and Theoretical Chemistry, Materials Chemistry, Surfaces, Coatings and Films, Lipid bilayer, Solid-state nuclear magnetic resonance, Glycerol, chemistry.chemical_compound, chemistry, Molecule, Chemical physics, Bond vector, Phosphatidylcholine, Biological membrane, Photochemistry, Molecular dynamics, Crystallography
159 references, page 1 of 11

Structure and Dynamics of Membranes; Lipowsky R., Sackmann E., Eds.; Elsevier: New York, 1995.

Tieleman D. P.; Marrink S. J.; Berendsen H. J. C.A computer perspective of membranes: molecular dynamics studies of lipid bilayer systems. Biochim. Biophys. Acta, Rev. Biomembr.1997, 1331, 235–270 10.1016/S0304-4157(97)00008-7. [OpenAIRE] [DOI]

Klauda J. B.; Venable R. M.; MacKerell A. D.Jr.; Pastor R. W. In Computational Modeling of Membrane Bilayers; Feller S. E., Ed.; Current Topics in Membranes; Academic Press: New York, 2008; Vol. 60; pp 1–48.

Edholm O. In Computational Modeling of Membrane Bilayers; Feller S. E., Ed.; Current Topics in Membranes; Academic Press: New York, 2008; Vol. 60; pp 91–110.

Tieleman D. P. In Molecular Simulations and Biomembranes: From Biophysics to Function; Sansom M., Biggin P., Eds.; The Royal Society of Chemistry: London, 2010; pp 1–25.

Piggot T. J.; PiñeiroÁ; Khalid S.Molecular Dynamics Simulations of Phosphatidylcholine Membranes: A Comparative Force Field Study. J. Chem. Theory Comput.2012, 8, 4593–4609 10.1021/ct3003157.26605617 [OpenAIRE] [PubMed] [DOI]

Rabinovich A.; Lyubartsev A.Computer simulation of lipid membranes: Methodology and achievements. Polym. Sci., Ser. C 2013, 55, 162–180 10.1134/S1811238213070060. [OpenAIRE] [DOI]

Marsh D.Handbook of Lipid Bilayers, 2nd ed.;RSC Press: London, 2013.

Israelachvili J. N.; Marcelja S.; Horn R. G.Physical Principles of Membrane Organiz ation. Q. Rev. Biophys.1980, 13, 121–200 10.1017/S0033583500001645.7015403 [PubMed] [DOI]

Seelig J.; Gally H.-U.; Wohlgemuth R.Orientation and flexibility of the choline head group in phosphatidylcholine bilayers. Biochim. Biophys. Acta, Biomembr.1977, 467, 109–119 10.1016/0005-2736(77)90188-2. [OpenAIRE] [DOI]

Skarjune R.; Oldfield E.Physical studies of cell surface and cell membrane structure. Determination of phospholipid head group organization by deuterium and phosphorus nuclear magnetic resonance spectroscopy. Biochemistry 1979, 18, 5903–5909 10.1021/bi00593a022.518875 [OpenAIRE] [PubMed] [DOI]

Jacobs R. E.; Oldfield E.NMR of membranes. Prog. Nucl. Magn. Reson. Spectrosc.1980, 14, 113–136 10.1016/0079-6565(80)80006-9. [OpenAIRE] [DOI]

Davis J. H.The description of membrane lipid conformation, order and dynamics by 2H-NMR. Biochim. Biophys. Acta, Rev. Biomembr.1983, 737, 117–171 10.1016/0304-4157(83)90015-1. [OpenAIRE] [DOI]

Strenk L.; Westerman P.; Doane J.A model of orientational ordering in phosphatidylcholine bilayers based on conformational analysis of the glycerol backbone region. Biophys. J.1985, 48, 765–773 10.1016/S0006-3495(85)83834-0.4074836 [OpenAIRE] [PubMed] [DOI]

Akutsu H.; Nagamori T.Conformational analysis of the polar head group in phosphatidylcholine bilayers: a structural change induced by cations. Biochemistry 1991, 30, 4510–4516 10.1021/bi00232a020.2021641 [OpenAIRE] [PubMed] [DOI]

159 references, page 1 of 11
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