Numerical studies of the membrane fluorescent dyes dynamics in ground and excited states

Abstract

Fluorescence methods are widely used in studies of biological and model membranes. The dynamics of membrane fluorescent markers in their ground and excited electronic states and correlations with their molecular surrounding within the fully hydrated phospholipid bilayer are still not well understood. In the present work, Quantum Mechanical (QM) calculations and Molecular Dynamics (MD) simulations are used to characterize location and interactions of two membrane polarity probes (Prodan; 6-propionyl-2-dimethylaminonaphthalene and its derivative Laurdan; 2-dimethylamino-6-lauroylnaphthalene) with the dioleoylphosphatidylcholine (DOPC) lipid bilayer model. MD simulations with fluorophores in ground and excited states are found to be a useful tool to analyze the fluorescent dye dynamics and their immediate vicinity. The results of QM calculations and MD simulations are in excellent agreement with available experimental data. The calculation shows that the two amphiphilic dyes initially placed in bulk water diffuse within 10 ns towards their final location in the lipid bilayer. Analysis of solvent relaxation process in the aqueous phase occurs on the picoseconds timescale whereas it takes nanoseconds at the lipid/water interface. Four different relaxation time constants, corresponding to different relaxation processes, where observed when the dyes were embedded into the membrane.

The complex nature of calcium cation interactions with phospholipid bilayers

“…2A). The fluorophore of Laurdan, located at ~10 Å from the DOPC bilayer center4041, was shown to probe predominantly polarity and mobility of hydrated sn -1 carbonyls of phospholipids42. The fluorophore of Dtmac is located close to the phosphate moieties of lipid headgroups, i.e., ~15 Å from the DOPC bilayer center (A. Olżyńska, personal communication).…”

Atomistic Monte Carlo Simulation of Lipid Membranes

“…Local interaction of membrane proteins and lipids as well as the impact of fluorescent probes on bilayer properties has also been investigated by atomistic MD simulations [30–34]. MD simulations were combined with ab-initio calculation and spectroscopy experiments to determine dynamics of fluorescent dyes in ground and excited states [35]. Finally, using a specially designed supercomputer [36], classical atomistic MD simulations of protein-lipid systems were extended into the μsec-range and used to study voltage gating of a membrane embedded ion channel, to decipher conformational changes of the epidermal growth factor receptor on ligand binding and to characterize specific lipid interactions of receptor subunits [37,38].…”

Relationships between membrane water molecules and Patman equilibration kinetics at temperatures far above the phosphatidylcholine melting point

“…Laurdan also encounters this level of complexity as it equilibrates, although the relationship to temperature differs quantitatively from that experienced by Patman. Based on computer simulations, these equilibration steps probably reflect local environmental responses to the presence of the probe instead of probe migrating into its final location, which should occur on the nanosecond rather than second time scale [24].…”

“…Pr 0 represents an intermediate state in which probe is inserted into the membrane and therefore removed from the aqueous phase. Whether the rate-limiting step represented by k 0 is the actual insertion of probe into the membrane (which in the case of Laurdan, should be very fast [24]) or is governed by behavior external to the membrane such as low aqueous solubility [6] does not matter in the formalism used here and will be the subject of future studies. Pr 0 , however, is not the equilibrium state in this model, and the probe and its interactions with the local microenvironment progress slowly (k R ) to a final relaxed state, Pr R .…”