Mr
Daniel Holý
(Institute of Organic Chemsitry and Biochemistry, Czech Academy of Sciences`)
Cells interact with the environment through plasma membranes. Because of their complexity simpler lipid bilayers are use as models to study their properties. An important component which modulates plasma membranes is the calcium ion which is for example involved in a number of processes, such as neurotransmitter release and membrane fusion. Calcium is also known to modulate the physical properties of plasma membranes and to accelerate the process of membrane fusion. Previous research suggests that calcium binds more strongly to positively curved bilayers than to flat ones.
We build on this finding and extend the investigations by using an improved lipid force field for POPC in our simulations. Using this ECC-POPC force filed[1], which provides a better description of ion-lipid interaction, we characterize the influence that the lipid bilayer shape has on the binding of the calcium ions to the bilayer. To describe the way calcium binds to the bilayer, we first carry out molecular dynamics simulations of flat POPC bilayers at different calcium concentrations and analyze the calcium density distributions in a manner which can be extended to curved systems. After adequately describing the flat bilayer system, we apply the same methodology to bilayers of varying curvatures. We also compare the results of this approach to the calcium density profiles calculated using the instantaneous liquid interface approach. The results of this project will allow us to comment on the mechanisms the cells use to regulate calcium concentration related to curvature of the membrane.
References
Reinhard Jahn, Thorsten Lang, Thomas C Südhof, Membrane Fusion, Cell, Volume 112, Issue 4, 21 February 2003, Pages 519-533, ISSN 0092-8674, http://dx.doi.org/10.1016/S0092-8674(03)00112-0.
Sascha Martens and Harvey T. McMahon, Mechanism of membrane fusion: disparate players and common principles, Nature Reviews Molecular Cell Biology 9, 543-556, 2008, DOI: http://dx.doi.org/10.1038/nrm2417
Mark James Abraham, Teemu Murtola, Roland Schulz, Szilárd Páll, Jeremy C. Smith, Berk Hess, Erik Lindahl, GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers, SoftwareX, Volumes 1–2, September 2015, Pages 19-25, ISSN 2352-7110, http://dx.doi.org/10.1016/j.softx.2015.06.001.
Kohagen, M.; Mason, P. E.; Jungwirth, P. Accounting for Electronic Polarization Effects in Aqueous Sodium Chloride via Molecular Dynamics Aided by Neutron Scattering. J. Phys Chem. B 2016, 120 (8), 1454–1460.
Melcr, J.; Martinez-Seara, H.; Nencini, R.; Kolafa, J.; Jungwirth, P.; Ollila, O. H. S. Accurate Binding of Sodium and Calcium to a POPC Bilayer by Effective Inclusion of Electronic Polarization. J. Phys. Chem. B 2018, 122 (16), 4546–4557.
Summary
Cells interact with the environment through plasma membranes. Because of their complexity simpler lipid bilayers are use as models to study their properties. An important component which modulates plasma membranes is the calcium ion which is for example involved in a number of processes, such as neurotransmitter release and membrane fusion. Calcium is also known to modulate the physical properties of plasma membranes and to accelerate the process of membrane fusion.
Mr
Daniel Holý
(Institute of Organic Chemsitry and Biochemistry, Czech Academy of Sciences`)
