Oana Cramariuc

Refined OPLS all-atom force field for saturated phosphatidylcholine bilayers at full hydration.

We report parametrization of dipalmitoyl-phosphatidylcholine (DPPC) in the framework of the Optimized Parameters for Liquid Simulations all-atom (OPLS-AA) force field. We chose DPPC as it is one of the most studied phospholipid species and thus has plenty of experimental data necessary for model validation, and it is also one of the highly important and abundant lipid types, e.g., in lung surfactant. Overall, PCs have not been previously parametrized in the OPLS-AA force field; thus, there is a need to derive its bonding and nonbonding parameters for both the polar and nonpolar parts of the molecule. In the present study, we determined the parameters for torsion angles in the phosphatidylcholine and glycerol moieties and in the acyl chains, as well the partial atomic charges. In these calculations, we used three methods: (1) Hartree-Fock (HF), (2) second order Møller-Plesset perturbation theory (MP2), and (3) density functional theory (DFT). We also tested the effect of the polar environment by using the polarizable continuum model (PCM), and for acyl chains the van der Waals parameters were also adjusted. In effect, six parameter sets were generated and tested on a DPPC bilayer. Out of these six sets, only one was found to be able to satisfactorily reproduce experimental data for the lipid bilayer. The successful DPPC model was obtained from MP2 calculations in an implicit polar environment (PCM).

Atomistic simulations indicate cardiolipin to have an integral role in the structure of the cytochrome bc1 complex.

The reaction mechanism of the cytochrome (cyt) bc1 complex relies on proton and electron transfer to/from the substrate quinone/quinol, which in turn generate a proton gradient across the mitochondrial membrane. Cardiolipin (CL) have been suggested to play an important role in cyt bc1 function by both ensuring the structural integrity of the protein complex and also by taking part in the proton uptake. Yet, the atom-scale understanding of these highly charged four-tail lipids in the cyt bc1 function has remained quite unclear. We consider this issue through atomistic molecular dynamics simulations that are applied to the entire cyt bc1 dimer of the purple photosynthetic bacterium Rhodobacter capsulatus embedded in a lipid bilayer. We find CLs to spontaneously diffuse to the dimer interface to the immediate vicinity of the higher potential heme b groups of the complexs catalytic Qi-sites. This observation is in full agreement with crystallographic studies of the complex, and supports the view that CLs are key players in the proton uptake. The simulation results also allow us to present a refined picture for the dimer arrangement in the cyt bc1 complex, the novelty of our work being the description of the role of the surrounding lipid environment: in addition to the specific CL-protein interactions, we observe the protein domains on the positive side of the membrane to settle against the lipids. Altogether, the simulations discussed in this article provide novel views into the dynamics of cyt bc1 with lipids, complementing previous experimental findings.

Mechanism for translocation of fluoroquinolones across lipid membranes

Classical atom-scale molecular dynamics simulations, constrained free energy calculations, and quantum mechanical (QM) calculations are employed to study the diffusive translocation of ciprofloxacin (CPFX) across lipid membranes. CPFX is considered here as a representative of the fluoroquinolone antibiotics class. Neutral and zwitterionic CPFX coexist at physiological pH, with the latter being predominant. Simulations reveal that only the neutral form permeates the bilayer, and it does so through a novel mechanism that involves dissolution of concerted stacks of zwitterionic ciprofloxacins. Subsequent QM analysis of the observed molecular stacking shows the important role of partial charge neutralization in the stacks, highlighting how the zwitterionic form of the drug is neutralized for translocation. The findings propose a translocation mechanism in which zwitterionic CPFX molecules approach the membrane in stacks, but they diffuse through the membrane as neutral CPFX monomers due to intermolecular transfer of protons favored by partial solvation loss. The mechanism is expected to be of importance in the permeation and translocation of a variety of ampholitic drugs with stacking tendencies.

Indocyanine Green-Loaded Liposomes for Light-Triggered Drug Release

Light-triggered drug delivery systems enable site-specific and time-controlled drug release. In previous work, we have achieved this with liposomes containing gold nanoparticles in the aqueous core. Gold nanoparticles absorb near-infrared light and release the energy as heat that increases the permeability of the liposomal bilayer, thus releasing the contents of the liposome. In this work, we replaced the gold nanoparticles with the clinically approved imaging agent indocyanine green (ICG). The ICG liposomes were stable at storage conditions (4-22 °C) and at body temperature, and fast near-infrared (IR) light-triggered drug release was achieved with optimized phospholipid composition and a 1:50 ICG-to-lipid molar ratio. Encapsulated small molecular calcein and FITC-dextran (up to 20 kDa) were completely released from the liposomes after light exposure for 15 s. Location of ICG in the PEG layer of the liposomes was simulated with molecular dynamics. ICG has important benefits as a light-triggering agent in liposomes: fast content release, improved stability, improved possibility of liposomal size control, regulatory approval to use in humans, and the possibility of imaging the in vivo location of the liposomes based on the fluorescence of ICG. Near-infrared light used as a triggering mechanism has good tissue penetration and safety. Thus, ICG liposomes are an attractive option for light-controlled and efficient delivery of small and large drug molecules.

A TDDFT study of the fluorescence properties of three alkoxypyridylindolizine derivatives.

The fluorescence properties of three pyridylindolizine derivatives (one tricarbomethoxy-7-pyridyl-pyrrolopyridine and two dicarboethoxy-3-bromobenzoyl-7-pyridyl-pyrrolopyridines) have been investigated by applying density functional theory (DFT) and the time-dependent DFT (TDDFT). Performances of two hybrid-type functionals (BH&HLYP and B3LYP) and one generalized gradient approximation (GGA) functional (PBE) as well as three basis sets (SV(P), DZP, and TZVP) have been assessed. The solvent environment has been modeled with the conductor-like screening model (COSMO). Of the three functionals only BH&HLYP is able to yield reasonable estimates for all the studied indolizine derivatives whereas the success of the PBE and B3LYP functionals is highly dependent on the structure of the studied molecule. The SV(P) basis set provides geometrical changes as well as fluorescence maxima and Stokes shifts that agree with those obtained with DZP and TZVP. When a nonpolar solvent is used, COSMO is able to reproduce the experimental fluorescence maxima and Stokes shifts well. However, the agreement between the calculations and experiments is not as good when a solvent with higher polarity is used.

Porphyrin adsorbed on the (101[combining macron]0) surface of the wurtzite structure of ZnO--conformation induced effects on the electron transfer characteristics.

Electron transfer at the adsorbate-surface interface is crucial in many applications but the steps taking place prior to and during the electron transfer are not always thoroughly understood. In this work a model system of 4-(porphyrin-5-yl)benzoic acid adsorbed as a corresponding benzoate on the ZnO wurtzite (101[combining macron]0) surface is studied using density functional theory (DFT) and time-dependent DFT. Emphasis is on the initial photoexcitation of porphyrin and on the strength of coupling between the porphyrin LUMO or LUMO + 1 and the ZnO conduction band that plays a role in the electron transfer. Firstly, ZnO wurtzite bulk is optimized to minimum energy geometry and the properties of the isolated ZnO (101[combining macron]0) surface model and the porphyrin model are discussed to gain insight into the combined system. Secondly, various orientations of the model porphyrin on the ZnO surface are studied: the porphyrin model standing perpendicularly to the surface and gradually brought close to the surface by tilting the linker in a few steps. The porphyrin model approaches the surface either sideways with hydrogen atoms of the porphyrin ring coming down first or twisted in a ca. 45° angle, giving rise to π-interactions of the porphyrin ring with ZnO. Because porphyrins are closely packed and near the surface, emerging van der Waals (vdW) interactions are examined using Grimmes D2 method. While the orientation affects the initial excitation of porphyrin only slightly, the coupling between the LUMO and LUMO + 1 of porphyrin and the conduction band of ZnO increases considerably if porphyrin is close to the surface, especially if the π-electrons are interacting with the surface. Based on the results of coupling studies, not only the distance between porphyrin and the ZnO surface but also the orientation of porphyrin can greatly affect the electron transfer.

Parameterization of the prosthetic redox centers of the bacterial cytochrome bc 1 complex for atomistic molecular dynamics simulations

Cytochrome (cyt) bc1 is a multi-subunit membrane protein complex that is a vital component of the respiratory and photosynthetic electron transfer chains both in bacteria and eukaryotes. Although the complex’s dimer structure has been solved using X-ray crystallography, it has not yet been studied in large-scale classical molecular dynamics (MD) simulations. In part, this is due to lack of suitable force field parameters, centered atomic point charges in particular, for the complex’s prosthetic redox centers. Accurate redox center charges are needed to depict realistically the inter-molecular interactions at different redox stages of the cytbc1 complex. Accordingly, here we present high-precision atomic point charges for the metal centers of the cyt bc1 complex of Rhodobacter capsulatus derived from extensive density functional theory calculations, fitted using the restrained electrostatic potential methodology and combined with the CHARMM force field parameters. We also provide the Hartree–Fock charges for all substrate forms (quinol, quinone, and semiquinone) and the inhibitors antimycin and stigmatellin of the bacterial bc1 complex. The accuracy of the parameterization scheme was verified by running a 200-ns MD simulation encompassing the entire cyt bc1 complex embedded in a lipid bilayer and solvated with explicit water. The results indicate that these meticulously derived parameters are ready for running extensive MD simulations encompassing all biologically relevant stages of the cyt bc1 complex reaction cycle.

Phase Partitioning of GM1 and Its Bodipy-Labeled Analog Determine Their Different Binding to Cholera Toxin

Driven by interactions between lipids and proteins, biological membranes display lateral heterogeneity that manifests itself in a mosaic of liquid-ordered (Lo) or raft, and liquid-disordered (Ld) or non-raft domains with a wide range of different properties and compositions. In giant plasma membrane vesicles and giant unilamellar vesicles, specific binding of Cholera Toxin (CTxB) to GM1 glycolipids is a commonly used strategy to label raft domains or Lo membrane environments. However, these studies often use acyl-chain labeled bodipy-GM1 (bdGM1), whose headgroup accessibility and membrane order or phase partitioning may differ from those of GM1, rendering the interpretation of CTxB binding data quite problematic. To unravel the molecular basis of CTxB binding to GM1 and bdGM1, we explored the partitioning and the headgroup presentation of these gangliosides in the Lo and Ld phases using atomistic molecular dynamics simulations complemented by CTxB binding experiments. The conformation of both GM1 and bdGM1 was shown to be largely similar in the Lo and Ld phases. However, bdGM1 showed reduction in receptor availability when reconstituted into synthetic bilayer mixtures, highlighting that membrane phase partitioning of the gangliosides plays a considerable role in CTxB binding. Our results suggest that the CTxB binding is predominately modulated by the partitioning of the receptor to an appropriate membrane phase. Further, given that the Lo and Ld partitioning of bdGM1 differs from those of GM1, usage of bdGM1 for studying GM1 behavior in cells can lead to invalid interpretation of experimental data.

Electric-Field-Assisted Electron Transfer in a Porphine-Quinone Complex: A Theoretical Study.

The effects of a static external electric field on the ground state electronic structure of a porphine-quinone (PQ) complex have been studied by using density functional theory (DFT). The energies of the excited states have been calculated with time-dependent density functional theory (TDDFT) and with the approximate coupled cluster singles and doubles (CC2) method. The geometries of porphine and quinone have been optimized with B3LYP. The influence of the external electric field on the PQ complex has been studied at six different intermolecular distances between 2.5 and 5.0 Å with the BH&HLYP functional. An external electric field clearly affects the orbitals localized mostly on quinone but not the orbitals localized on porphine. Additionally, the effect of the external field increases with the increasing intermolecular distance. The optical absorption spectrum of porphine obtained by using the BH&HLYP functional is consistent with the Gouterman model and with the spectrum previously calculated with CAM-B3LYP. The potential energy curves of the Q and B states and the lowest charge transfer (CT) states of the PQ complex calculated by using the BH&HLYP with TDDFT functional have also been compared with those obtained with the CC2 method. Both methods show that the lowest CT state is clearly above the Q states when no external field is applied. Therefore, when the Q states of a porphine-quinone system are excited, the conical intersection is not possible and cannot thus provide a path for electron transfer (ET). The calculations show that the Q and B states are affected by the field much less than the lowest CT state. Consequently, the calculations show that the CT state crosses the Q and B states at certain field strengths. Thus, it is possible that the external electric field triggers ET in porphine-quinone systems via conical intersection.

Ab initio description of photoabsorption and electron transfer in a doubly‐linked porphyrin‐fullerene dyad

Structure, photoabsorption and excited states of two representative conformations obtained from molecular dynamics (MD) simulations of a doubly‐linked porphyrin‐fullerene dyad DHD6ee are studied by using both DFT and wavefunction based methods. Charge transfer from the donor (porphyrin) to the acceptor (fullerene) and the relaxation of the excited state are of special interest. The results obtained with LDA, GGA, and hybrid functionals (SVWN, PBE, and B3LYP, respectively) are analyzed with emphasis on the performance of used functionals as well as from the point of view of their comparison with wavefunction based methods (CCS, CIS(D), and CC2). Characteristics of the MD structures are retained in DFT optimization. The relative orientation of porphyrin and fullerene is significantly influencing the MO energies, the charge transfer (CT) in the ground state of the dyad and the excitation of ground state CT complex (g‐CTC). At the same time, the excitation to the locally excited state of porphyrin is only little influenced by the orientation or cc distance. TD‐DFT underestimates the excitation energy of the CT state, however for some cases (with relatively short donor‐acceptor separations), the use of a hybrid functional like B3LYP alleviates the problem. Wavefunction based methods and CC2 in particular appear to overestimate the CT excitation energies but the inclusion of proper solvation models can significantly improve the results.