Developing and Testing of Lipid Force Fields with Applications to Modeling Cellular Membranes

Chemical Reviews
Alison N LeonardJeffery B Klauda

Abstract

The amphipathic nature of the lipid molecule (hydrophilic head and hydrophobic tails) enables it to act as a barrier between fluids with various properties and to sustain an environment where the processes critical to life may proceed. While computer simulations of biomolecules primarily investigate protein conformation and binding to drug-like molecules, these interactions often occur in the context of a lipid membrane. Chemical specificity of lipid models is essential to accurately represent the complex environment of the lipid membrane. This review discusses the development and performance of currently used chemically specific lipid force fields (FF) such as the CHARMM, AMBER, GROMOS, OPLS, and MARTINI families. Considerations in lipid FF development including lipid diversity, temperature dependence, phase behavior, and effects of atomic polarizability are considered, as well as methods and goals of parametrization. Applications of these FFs to complex and diverse models for cellular membranes are summarized. Lastly, areas for future development, such as efficient inclusion of long-range Lennard-Jones interactions (significant in transitions from polar to apolar media), accurate transmembrane dipole potential, and diffusion ...Continue Reading

References

Apr 1, 1978·Proceedings of the National Academy of Sciences of the United States of America·J C OwickiH M McConnell
Sep 21, 1979·Biochimica Et Biophysica Acta·J LauterweinK Wüthrich
Aug 1, 1975·Proceedings of the National Academy of Sciences of the United States of America·P G Saffman, M Delbrück
Nov 1, 1973·Zeitschrift Für Naturforschung. Teil C: Biochemie, Biophysik, Biologie, Virologie·W Helfrich
Feb 18, 1972·Science·S J Singer, G L Nicolson
May 10, 1972·Nature: New Biology·J E Rothman, D M Engelman
Jan 1, 1994·European Biophysics Journal : EBJ·E EgbertsH J Berendsen
Mar 19, 1993·Science·L M ObeidY A Hannun
Oct 1, 1995·Biophysical Journal·Z W Yu, P J Quinn
May 20, 1996·Biochimica Et Biophysica Acta·J A BouwstraM Ponec
Jun 5, 1997·Nature·K Simons, E Ikonen
Jul 25, 1997·Biochimica Et Biophysica Acta·R J Clarke
Apr 29, 1998·Annual Review of Physiology·R N Kolesnick, M Krönke
Sep 15, 1988·Physical Review A: General Physics·A D Becke
Mar 1, 1985·Physical Review. B, Condensed Matter·K Toukan, A Rahman
Apr 23, 1990·Physical Review Letters·E Evans, W Rawicz
Feb 29, 2000·Biophysical Journal·M Pasenkiewicz-GierulaA Kusumi
Jun 27, 2000·Biophysical Journal·W RawiczE Evans
Nov 7, 2000·Biochimica Et Biophysica Acta·J F Nagle, S Tristram-Nagle
Dec 2, 2000·Science·K Simons, E Ikonen
Feb 24, 2001·Advances in Colloid and Interface Science·R J Clarke
Jul 4, 2001·The Journal of Biological Chemistry·S H WhiteK Hristova
Mar 28, 2002·Biophysical Journal·Sagar A Pandit, Max L Berkowitz
Apr 20, 2002·Biophysical Journal·Elizabeth A DolanBernard R Brooks
Jun 19, 2002·Accounts of Chemical Research·Richard W PastorScott E Feller
Aug 7, 2002·Current Opinion in Structural Biology·H Larry Scott
Jan 18, 2003·Biochimica Et Biophysica Acta·Benjamin J PettusYusuf A Hannun
Mar 1, 2003·Biophysical Journal·Tomasz Róg, Marta Pasenkiewicz-Gierula
Mar 13, 2003·European Biophysics Journal : EBJ·Indira ChandrasekharWilfred F van Gunsteren
Apr 2, 2003·Biophysical Journal·Christofer HofsässOlle Edholm
May 6, 2003·Biochimica Et Biophysica Acta·A G Lee
Jun 5, 2003·Cell Biochemistry and Biophysics·Tommy S Tillman, Michael Cascio

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Citations

Sep 29, 2019·Journal of Materials Chemistry. B, Materials for Biology and Medicine·Morteza Vatanparast, Zahra Shariatinia
Oct 10, 2019·Physical Chemistry Chemical Physics : PCCP·Abhilash Sahoo, Silvina Matysiak
Aug 31, 2020·Chemical Science·Giuseppe LicariEmad Tajkhorshid
May 23, 2020·Advanced Science·Samuel CheesemanAaron Elbourne
Feb 24, 2021·Journal of Chemical Theory and Computation·Yalun YuBernard R Brooks
Mar 8, 2021·Chemistry and Physics of Lipids·Jacob Olondo KubaJeffery B Klauda
Mar 13, 2021·Journal of Computational Chemistry·Jean-Marc CrowetManuel Dauchez
Feb 20, 2021·Annual Review of Biophysics·Tamar SchlickEva Xue
May 29, 2021·The Journal of Physical Chemistry. B·Jeffery B Klauda
Mar 16, 2021·Current Opinion in Cell Biology·Weria Pezeshkian, Siewert J Marrink
Aug 1, 2019·Accounts of Chemical Research·Stefano VanniMarco De Vivo
May 10, 2020·Journal of Chemical Theory and Computation·Nozomu KamiyaKeiko Shinoda
Aug 14, 2020·The Journal of Physical Chemistry. B·Helgi I IngólfssonTimothy S Carpenter
Sep 25, 2019·Journal of the American Chemical Society·Eric Wang, Jeffery B Klauda
Sep 15, 2020·The Journal of Physical Chemistry. B·Fredrik Grote, Alexander P Lyubartsev
Aug 19, 2021·Journal of Chemical Information and Modeling·Sachini P Kadaoluwa PathirannahalageAndrew J Christofferson
Apr 26, 2019·Chemical Reviews·Ana-Nicoleta Bondar, M Joanne Lemieux
Feb 24, 2019·The Journal of Physical Chemistry. B·Eric Wang, Jeffery B Klauda
Jul 9, 2020·The Journal of Physical Chemistry. B·Yalun Yu, Jeffery B Klauda
Mar 21, 2020·The Journal of Physical Chemistry. B·Alexander YangClare McCabe
Aug 25, 2021·Computers in Biology and Medicine·Maria C OliveiraAnnemie Bogaerts
Sep 28, 2021·Langmuir : the ACS Journal of Surfaces and Colloids·Song-Di NiHong-Ming Ding
Dec 24, 2021·Journal of Chemical Theory and Computation·Klemen BohincSimone Spada
Dec 29, 2021·The Journal of Physical Chemistry. B·Min-Kang Hsieh, Jeffery B Klauda
Dec 29, 2021·Langmuir : the ACS Journal of Surfaces and Colloids·Min-Kang HsiehJeffery B Klauda
Jan 13, 2022·Journal of Chemical Theory and Computation·Wanling SongMark S P Sansom

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