Coarse-Grained Molecular Dynamics Simulations of Membrane-Trehalose Interactions.

It is well established that trehalose (TRH) affects the physical properties of lipid bilayers and stabilizes biological membranes. We present molecular dynamics (MD) computer simulations to investigate the interactions between lipid membranes formed by 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and TRH. Both atomistic and coarse-grained (CG) interaction models were employed, and the coarse graining of DMPC leads to a reduction in the acyl chain length corresponding to a 1,2-dilauroyl-sn-glycero-3-phosphocholine lipid (DLPC). Several modifications of the Martini interaction model, used for CG simulations, were implemented, resulting in different potentials of mean force (PMFs) for DMPC bilayer-TRH interactions. These PMFs were subsequently used in a simple two-site analytical model for the description of sugar binding at the membrane interface. In contrast to that in atomistic MD simulations, the binding in the CG model was not in agreement with the two-site model. Our interpretation is that the interaction balance, involving water, TRH, and lipids, in the CG systems needs further tuning of the force-field parameters. The area per lipid is only weakly affected by TRH concentration, whereas the compressibility modulus related to the fluctuations of the membrane increases with an increase in TRH content. In agreement with experimental findings, the bending modulus is not affected by the inclusion of TRH. The important aspects of lipid bilayer interactions with biomolecules are membrane curvature generation and sensing. In the present investigation, membrane curvature is generated by artificial buckling of the bilayer in one dimension. It turns out that TRH prefers the regions with the highest curvature, which enables the most favorable situation for lipid-sugar interactions.

Molecular dynamics simulations and NMR spectroscopy studies of trehalose-lipid bilayer systems.

The disaccharide trehalose (TRH) strongly affects the physical properties of lipid bilayers. We investigate interactions between lipid membranes formed by 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and TRH using NMR spectroscopy and molecular dynamics (MD) computer simulations. We compare dipolar couplings derived from DMPC/TRH trajectories with those determined (i) experimentally in TRH using conventional high-resolution NMR in a weakly ordered solvent (bicelles), and (ii) by solid-state NMR in multilamellar vesicles (MLV) formed by DMPC. Analysis of the experimental and MD-derived couplings in DMPC indicated that the force field used in the simulations reasonably well describes the experimental results with the exception for the glycerol fragment that exhibits significant deviations. The signs of dipolar couplings, not available from the experiments on highly ordered systems, were determined from the trajectory analysis. The crucial step in the analysis of residual dipolar couplings (RDCs) in TRH determined in a bicelle-environment was access to the conformational distributions derived from the MD trajectory. Furthermore, the conformational behavior of TRH, investigated by J-couplings, in the ordered and isotropic phases is essentially identical, indicating that the general assumptions in the analyses of RDCs are well founded.

Molecular dynamics simulations of membrane-sugar interactions.

It is well documented that disaccharides in general and trehalose (TRH) in particular strongly affect physical properties and functionality of lipid bilayers. We investigate interactions between lipid membranes formed by 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and TRH by means of molecular dynamics (MD) computer simulations. Ten different TRH concentrations were studied in the range wTRH = 0-0.20 (w/w). The potential of mean force (PMF) for DMPC bilayer-TRH interactions was determined using two different force fields, and was subsequently used in a simple analytical model for description of sugar binding at the membrane interface. The MD results were in good agreement with the predictions of the model. The net affinities of TRH for the DMPC bilayer derived from the model and MD simulations were compared with experimental results. The area per lipid increases and the membrane becomes thinner with increased TRH concentration, which is interpreted as an intercalation effect of the TRH molecules into the polar part of the lipids, resulting in conformational changes in the chains. These results are consistent with recent experimental observations. The compressibility modulus related to the fluctuations of the membrane increases dramatically with increased TRH concentration, which indicates higher order and rigidity of the bilayer. This is also reflected in a decrease (by a factor of 15) of the lateral diffusion of the lipids. We interpret these observations as a formation of a glassy state at the interface of the membrane, which has been suggested in the literature as a hypothesis for the membrane-sugar interactions.

Molecular dynamics simulations of membranes composed of glycolipids and phospholipids.

Lipid membranes composed of 1,2-di-(9Z,12Z,15Z)-octadecatrienoyl-3-O-ß-D-galactosyl-sn-glycerol or monogalactosyldiacylglycerol (MGDG) and 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) were studied by means of molecular dynamics (MD) computer simulations. Three lipid compositions were considered: 0%, 20%, and 45% MGDG (by mole) denoted as MG-0, MG-20, and MG-45, respectively. The article is focused on the calculation of NMR dipolar interactions, which were confronted with previously reported experimental couplings. Dynamical processes and orientational distributions relevant for the averaging of dipolar interactions were evaluated. Furthermore, several parameters important for characterization of the bilayer structure, molecular organization, and dynamics were investigated. In general, only a minor change in DMPC properties was observed upon the increased MGDG/DMPC ratio, whereas properties related to MGDG undergo a more pronounced change. This effect was ascribed to the fact that DMPC is a bilayer (L(α)) forming lipid, whereas MGDG prefers a reverse hexagonal (H(II)) arrangement.

Molecular conformations in the pentasaccharide LNF-1 derived from NMR spectroscopy and molecular dynamics simulations.

The conformational dynamics of the human milk oligosaccharide lacto-N-fucopentaose (LNF-1), α-L-Fucp-(1 → 2)-ß-D-Galp-(1 → 3)-ß-D-GlcpNAc-(1 → 3)-ß-D-Galp-(1 → 4)-D-Glcp, has been analyzed using NMR spectroscopy and molecular dynamics (MD) computer simulations. Employing the Hadamard (13)C-excitation technique and the J-HMBC experiment, (1)H,(13)C trans-glycosidic J coupling constants were obtained, and from one- and two-dimensional (1)H,(1)H T-ROESY experiments, proton-proton cross-relaxation rates were determined in isotropic D(2)O solution. In the lyotropic liquid-crystalline medium consisting of ditetradecylphosphatidylcholine, dihexylphosphatidylcholine, N-cetyl-N,N,N-trimethylammonium bromide, and D(2)O, (1)H, (1)H and one-bond (1)H, (13)C residual dipolar couplings (RDCs), as well as relative sign information on homonuclear RDCs, were determined for the pentasaccharide. Molecular dynamics simulations with explicit water were carried out from which the internal isomerization relaxation time constant, τ(N), was calculated for transitions at the ψ torsion angle of the ß-(1 → 3) linkage to the lactosyl group in LNF-1. Compared to the global reorientation time, τ(M), of ∼0.6 ns determined experimentally in D(2)O solution, the time constant for the isomerization relaxation process, τ(N(scaled)), is about one-third as large. The NMR parameters derived from the isotropic solution show very good agreement with those calculated from the MD simulations. The only notable difference occurs at the reducing end, which should be more flexible than observed by the molecular simulation, a conclusion in complete agreement with previous (13)C NMR relaxation data. A hydrogen-bond analysis of the MD simulation revealed that inter-residue hydrogen bonds on the order of ∼30% were present across the glycosidic linkages to sugar ring oxygens. This finding highlights that intramolecular hydrogen bonds might be important in preserving well-defined structures in otherwise flexible molecules. An analysis including generalized order parameters obtained from nuclear spin relaxation experiments was performed and successfully shown to limit the conformational space accessible to the molecule when the number of experimental data are too scarce for a complete conformational analysis.

Carbon-13 NMR chemical shifts in columnar liquid crystals.

In this article, we present quantum chemical density functional theory (DFT) calculations of the NMR (13)C chemical shift (CS) tensors in 2,3,6,7,10,11-hexahexylthiotriphenylene (HHTT). The DFT calculations are performed on a smaller model molecule where the hexyl chains were reduced to methyl groups (HMTT). These tensors are compared with our previously reported experimental results carried out under magic-angle spinning (MAS) conditions. The phase diagram of HHTT is K ↔ H ↔ D(hd) ↔ I, where H is a helical phase and D(hd) is a columnar liquid crystal. The motivation for the present study was to explain experimentally observed and puzzling thermal history effects, which resulted in different behavior in the helical phase upon cooling and heating. In particular, the CS tensors for the aromatic carbons measured in the helical phase upon heating from the solid phase were essentially unaffected, while the cooling from the columnar liquid crystal resulted in a significant averaging. We investigate the effect on the CS tensors of (i) conformational transitions, and (ii) relative molecular orientations within the columns for dimer and trimer configurations. Finally a motional wobbling (PIZZA) model for the dynamic averaging of the CS tensor in the helical phase is suggested.

Quantum chemical modeling of the cardiolipin headgroup.

Cardiolipin is a key lipid component in many biological membranes. Proton conduction and proton-lipid interactions on the membrane surface are thought to be central to mitochondrial energy production. However, details on the cardiolipin headgroup structure are lacking and the protonation state of this lipid at physiological pH is not fully established. Here we present ab initio DFT calculations of the cardiolipin (CL) headgroup and its 2'-deoxy derivative (dCL), with the aim of establishing a connection between structure and acid-base equilibrium in CL. Furthermore, we investigate the effects of solvation on the molecular conformations. In our model, both CL and dCL showed a significant gap between the two pK(a) values, with pK(a2) above the physiological range, and intramolecular hydrogen bonds were found to play a central role in the conformations of both molecules. This behavior was also observed experimentally in CL. Structures derived from the DFT calculations were compared with those obtained experimentally, collected for CL in the Protein Data Bank, and conformations from previous as well as new molecular dynamics simulations of cardiolipin bilayers. Transition states for proton transfer in CL were investigated, and we estimate that protons can exchange between phosphate groups with an approximate 4-5 kcal/mol barrier. Computed NMR and IR spectral properties were found to be in reasonable agreement with experimental results available in the literature.

Mechanical Properties of Coarse-Grained Bilayers Formed by Cardiolipin and Zwitterionic Lipids.

Lipid shape and charge are connected with the physical properties and the biological function of membranes. Cardiolipin, a double phospholipid with four chains and the potential of changing its charge with pH, is crucially connected with mitochondrial inner membrane shape, and recent experiments suggest that local pH changes allow highly curved local geometries. Here, we use a coarse-grained molecular dynamics model to investigate the mechanical properties of cardiolipin bilayers, systematically varying the headgroup charge and the composition in mixtures with zwitterionic 1,2-dioleoyl-glycero-3-phosphatidylcholine (DOPC) or 1,2-dioleoyl-glycero-3-phosphatidylethanolamine (DOPE). Low cardiolipin charge, corresponding to low pH, was found to induce bending moduli on the order of kBT and curved microdomains. On the length scale investigated, in contrast to continuum theoretical models, we found the area modulus and bending modulus to be inversely correlated for mixtures of cardiolipin and DOPC/DOPE, explainable by changes in the effective headgroup volume.

Use of local alignment tensors for the determination of relative configurations in organic compounds.

In this proof of principle the use of local alignment tensors for the determination of relative configurations in moderately flexible molecules is demonstrated. These tensors are derived from residual dipolar couplings. Two methods for the analysis of partly linearly dependent RDCs in a rigid molecular fragment are also presented.

Glucose orientation and dynamics in alpha-, beta-, and gamma-cyclodextrins.

We investigate, using molecular dynamics (MD) computer simulations, the conformational behavior of alpha-, beta-, and gamma-cyclodextrins (CDs). Our analysis of a 30 ns trajectory of CD solution dynamics reveals the underlying conformational behaviours of the CDs that explain their relative flexibility. The distributions of the torsion angles related to the glycosidic linkages, P(phi,psi) were calculated for the three CDs. Most noticeable is the limited range in phi torsion rotations compared with psi rotations for all the CDs. This difference between the three CDs is amplified in the motion and dynamics of their glucose monomers when we monitor their orientational and librational positions relative to the macrocyclic mean plane. The relaxation times of the monomers to their equilibrium orientations follow the pattern gamma-CD > alpha-CD > beta-CD. The root-mean-square deviations of the motion of the monomer centers of mass from the mean macrocyclic planes exhibit the same trend.

Molecular dynamics simulations of cardiolipin bilayers.

Cardiolipin is a key lipid component in the inner mitochondrial membrane, where the lipid is involved in energy production, cristae structure, and mechanisms in the apoptotic pathway. In this article we used molecular dynamics computer simulations to investigate cardiolipin and its effect on the structure of lipid bilayers. Three cardiolipin/POPC bilayers with different lipid compositions were simulated: 100, 9.2, and 0% cardiolipin. We found strong association of sodium counterions to the carbonyl groups of both lipid types, leaving in the case of 9.2% cardiolipin virtually no ions in the aqueous compartment. Although binding occurred primarily at the carbonyl position, there was a preference to bind to the carbonyl groups of cardiolipin. Ion binding and the small headgroup of cardiolipin gave a strong ordering of the hydrocarbon chains. We found significant effects in the water dipole orientation and water dipole potential which can compensate for the electrostatic repulsion that otherwise should force charged lipids apart. Several parameters relevant for the molecular structure of cardiolipin were calculated and compared with results from analyses of coarse-grained simulations and available X-ray structural data.

NMR investigations of interactions between anesthetics and lipid bilayers.

Interactions between anesthetics (lidocaine and short chain alcohols) and lipid membranes formed by dimyristoylphosphatidylcholine (DMPC) were studied using NMR spectroscopy. The orientational order of lidocaine was investigated using deuterium NMR on a selectively labelled compound whereas segmental ordering in the lipids was probed by two-dimensional 1H-13C separated local field experiments under magic-angle spinning conditions. In addition, trajectories generated in molecular dynamics (MD) computer simulations were used for interpretation of the experimental results. Separate simulations were carried out with charged and uncharged lidocaine molecules. Reasonable agreement between experimental dipolar interactions and the calculated counterparts was observed. Our results clearly show that charged lidocaine affects significantly the lipid headgroup. In particular the ordering of the lipids is increased accompanied by drastic changes in the orientation of the P-N vector in the choline group.

NMR studies of molecular conformations in alpha-cyclodextrin.

A new approach for analysis of NMR parameters is proposed. The experimental data set includes scalar couplings, NOEs, and residual dipolar couplings. The method, which aims at construction of the conformational distribution function, is applied to alpha-cyclodextrin in isotropic solution and dissolved in a dilute liquid crystal. An attempt to analyze the experimental data using an average molecular conformation resulted in unacceptable errors. Our approach rests on the maximum entropy method (ME), which gives the flattest possible distribution, consistent with the experimental data. Very good agreement between experimental and calculated NMR parameters was observed. In fact, two conformational states were required in order to obtain a satisfactory agreement between calculated and experimental data. In addition, good agreement with Langevin dynamics computer simulations was obtained.

Molecular conformations in a phospholipid bilayer extracted from dipolar couplings: a computer simulation study.

This paper describes an analysis of NMR dipolar couplings in a bilayer formed by dimyristoylphosphatidylcholine (DMPC). The couplings are calculated from a trajectory generated in a molecular dynamics (MD) simulation based on a realistic atom-atom interaction potential. The analysis is carried out employing a recently developed approach that focuses on the construction of the conformational distribution function. This approach is a combination of two models, the additive potential (AP) model and the maximum entropy (ME) method, and is therefore called APME. In contrast to the AP model, the APME procedure does not require an intuition-based choice of the functional form of the torsional potential and is, unlike the ME method, applicable to weakly ordered systems. The conformational distribution function for the glycerol moiety of the DMPC molecule derived from the APME analysis of the dipolar couplings is in reasonable agreement with the "true" distributions calculated from the trajectory. Analyses of dipolar couplings derived from MD trajectories can, in general, serve as guidelines for experimental investigations of bilayers and other complex biological systems.

NMR studies of membranes composed of glycolipids and phospholipids.

Lipid membranes composed of monogalactosyldiacylglycerol (MGDG) and dimyristoylphosphatidylcholine (DMPC) were studied by means of NMR spectroscopy. The macroscopic phase behaviour was investigated by (31)P NMR under stationary conditions, whereas microscopic properties such as segmental ordering were probed by two-dimensional (1)H-(13)C separated local field experiments under magic-angle spinning conditions. Our results clearly show that ordering/disordering effects occur for the headgroups as well as for the acyl chains when the sample composition is varied. In particular, the (1)H-(13)C dipolar couplings within the galactose headgroup of MGDG exhibited significant concentration dependence.

Dynamical and structural properties of charged and uncharged lidocaine in a lipid bilayer.

Molecular dynamics computer simulations have been performed to investigate dynamical and structural properties of a lidocaine local anesthetic. Both charged and uncharged forms of the lidocaine molecule were investigated. Properties such as membrane area per lipid, diffusion, mass density, bilayer penetration and order parameters have been examined. An analysis of the lidocaine interaction with the lipid surrounding according to a simple mean field theory has also been performed. Almost all examined properties were found to depend on which of the two forms of lidocaine, charged or uncharged, is studied. The overall picture is a rather static behavior determined by the lipids for the charged molecules and more mobile situation of the uncharged form with higher diffusion and lower orientational and positional order.

Mesomorphism in columnar phases studied by solid-state nuclear magnetic resonance.

In this paper, we present 13C and 1H NMR investigations of 2, 3, 6, 7, 10, 11-hexahexyl-thiotriphenylene (HHTT). The measurements were carried out under both static and magic-angle spinning conditions. The phase diagram of HHTT is K<-->H<-->D(hd)<-->I , where H is a helical phase and D(hd) is a columnar liquid crystal. The motivation was to characterize the molecular order and dynamics and to investigate differences at the molecular level between the two mesophases: H and D(hd). It is shown that D(hd) is a conventional columnar liquid crystal, where the molecular core undergoes fast rotation about the symmetry axis. The orientational order in this mesophase is lower and the temperature dependence of the order parameter is steeper than in other triphenylene-based compounds. On the other hand, in the helical phase the core, similarly to the solid phase, is essentially rigid. The difference between the solid and helical phases is mainly manifested in an increased mobility of the aliphatic chains observed in the latter phase. In addition, the sample exhibits thermal history effects, which are observed in the different behavior upon cooling and heating.

Molecular conformations of a disaccharide investigated using NMR spectroscopy.

The molecular structure of alpha-L-Rhap-(1--> 2)-alpha-L-Rhap-OMe has been investigated using conformation sensitive NMR parameters: cross-relaxation rates, scalar 3J(CH) couplings and residual dipolar couplings obtained in a dilute liquid crystalline phase. The order matrices of the two sugar residues are different, which indicates that the molecule cannot exist in a single conformation. The conformational distribution function, P(phi, psi) related to the two glycosidic linkage torsion angles phi and psi was constructed using the APME method, valid in the low orientational order limit. The APME approach is based on the additive potential (AP) and maximum entropy (ME) models. The analyses of the trajectories generated in molecular dynamics and Langevin dynamics (LD) computer simulations gave support to the distribution functions constructed from the experimental NMR parameters. It is shown that at least two conformational regions are populated on the Ramachandran map and that these regions exhibit very different molecular order.

Molecular structure extracted from residual dipolar couplings: diphenylmethane dissolved in a nematic liquid crystal.

This paper describes an analysis of 1H-1H residual dipolar couplings (RDCs) in diphenylmethane (DPM) dissolved in a nematic liquid crystal, reported by Celebre et al. [J. Chem. Phys. 118, 6417 (2003)]. In that article, the conformational distribution function for DPM was extracted from the RDCs, using the additive potential (AP) model which is based on the molecular-field theory. The AP approach is a powerful, and frequently used, tool for analysis of the nuclear-magnetic-resonance (NMR) parameters in liquid crystals. It requires, however, a priori knowledge of the functional form of the torsional potential, which may even for a simple molecule, such as DPM, be complicated to determine. Here, we analyze the same set of the RDCs using our APME procedure, which is a hybrid model based on the AP approach and maximum entropy (ME) theory. The APME procedure does not require any assumptions about the functional form of the torsional potential and, in contrast with the ME method, is applicable to weakly ordered systems. In the investigation reported in the present study, the results from the APME analysis are in good agreement with the AP interpretation, whereas the ME approach essentially fails in the extraction of the conformational distribution function for DPM.