A computer simulation of functional group contributions to free energy in water and a DPPC lipid bilayer

A series of all-atom molecular dynamics simulations has been performed to evaluate the contributions of various functional groups to the free energy of solvation in water and a dipalmitoylphospatidylcholine lipid bilayer membrane and to the free energies of solute transfer (Delta(DeltaG(o))X) from water into the ordered-chain interior of the bilayer. Free energies for mutations of the alpha-H atom in p-toluic acid to six different substituents (-CH3, -Cl, -OCH3, -CN, -OH, -COOH) were calculated by a combined thermodynamic integration and perturbation method and compared to literature results from vapor pressure measurements, partition coefficients, and membrane transport experiments. Convergence of the calculated free energies was indicated by substantial declines in standard deviations for the calculated free energies with increased simulation length, by the independence of the ensemble-averaged Boltzmann factors to simulation length, and the weak dependence of hysteresis effects on simulation length over two different simulation lengths and starting from different initial configurations. Calculated values of Delta(DeltaG(o))X correlate linearly with corresponding values obtained from lipid bilayer transport experiments with a slope of 1.1 and from measurements of partition coefficients between water and hexadecane or decadiene, with slopes of 1.1 and 0.9, respectively. Van der Waals interactions between the functional group of interest and the acyl chains in the ordered chain region account for more than 95% of the overall potential energy of interaction. These results support the view that the ordered chain region within the bilayer interior is the barrier domain for transport and that solvation interactions within this region resemble those occurring in a nonpolar hydrocarbon.     

Amine spin probe permeability in sonicated liposomes

Summary Permeabilities for an homologous series of amine nitroxide spin probes were measured in liposomes of varying composition by an electron paramagnetic resonance (EPR) method. Results show that the rate-limiting step in permeation is not adsorption/desorption at the aqueous/membrane interface for two probes in phosphatidylcholine/phosphatidic acid liposomes and for one probe in phosphatidylcholine/cholesterol/phosphatidic acid liposomes. Accordingly, we interpret observed selectivity patterns for the entire series of probes in liposomes and red cells in terms of the properties of the bilayer interior.Results are inconsistent with simple applications of either free volume or hydrocarbon sheet models of nonelectrolyte permeation. In the former case, it was found that liposomes do not select against these probes on the basis of molecular volume. In the latter case, probe permeabilities are all much lower than would be predicted for a sheet of bulk hydrocarbon and the polarity of the rate-limiting region is shown to be greater than bulk hydrocarbon. Together with the results of previous studies of spin-labeled solutes in membranes, as well as studies of lipid dynamics in membranes, these latter results suggest that the rate-limiting region in nonelectrolyte permeation is not in the center of the bilayer, but in the relatively ordered acyl chain segments near the glycerol backbone.     

Free volume model for lipid lateral diffusion coefficients. Assessment of the temperature dependence in phosphatidylcholine and phosphatidylethanolamine bilayers

The lipid lateral diffusion coefficients, DT, in fluid-phase phosphatidylcholine and phosphatidylethanolamine bilayers have been analysed in terms of the free-volume diffusion model by fitting the expression: DT = AT exp[- B/(T - T0)] to the observed temperature dependence, where A, B and T0 are the parameters to be optimized. Application of an unconstrained optimization procedure to data obtained from excimer formation (Galla et al. (1979) J. Membrane Biol. 48, 215-236) and from fluorescence photobleaching (Vaz et al. (1985) Biochemistry 24, 781-786) provides statistical evidence for a free-volume model as opposed to a simple Stokes-Einstein model (T0 = 0), only in certain cases. In the instances for which the parameter T0 can be determined with a reasonable degree of accuracy, it is found that this characteristic temperature at which the free volume extrapolates to zero lies below the bilayer gel-to-fluid phase transition temperature and does not coincide with the pre-transition temperature for phosphatidylcholines.     

The order of cyanogen-bromide peptides and location of carbohydrate in the alpha2 chain of guinea-pig skin collagen.

The alpha2 chain of guinea pig skin collagen contains two additional methionyl residues in comparison with the alpha2 chain of other vertebrate species. The order of the three CNBr peptides unique to the alpha2 chain was established on the basis of the homology of their primary structures to sequences of previously ordered regions in the alpha1 and alpha2 chains of other colagens. The two larger peptides, 4A + 4B, were found to correspond to the region homologous to alpha2-CB4 of other species, while the smaller peptide, 3A, was homologous to the NH2-terminal portion of alpha2-CB3. Thus, the order of the peptides in the alpha2 chain of this collagen is 1-O-4A-4B-2-3A-3B-5. Periodate oxidation and alkaline or acid hydrolysis of the CNBr fragments showed that all of the hydroxlysine-linked carbohydrate in the alpha2 chain was present in alpha2-CB4B. Carbohydrate analyses were most consistent with the existence of single monosaccharide and disaccharide units in this region.     

Distribution of halothane in a dipalmitoylphosphatidylcholine bilayer from molecular dynamics calculations

We report a 2-ns constant pressure molecular dynamics simulation of halothane, at a mol fraction of 50%, in the hydrated liquid crystal bilayer phase of dipalmitoylphosphatidylcholine. Halothane molecules are found to preferentially segregate to the upper part of the lipid acyl chains, with a maximum probability near the C(5) methylene groups. However, a finite probability is also observed along the tail region and across the methyl trough. Over 95% of the halothane molecules are located below the lipid carbonyl carbons, in agreement with photolabeling experiments. Halothane induces lateral expansion and a concomitant contraction in the bilayer thickness. A decrease in the acyl chain segment order parameters, S(CD), for the tail portion, and a slight increase for the upper portion compared to neat bilayers, are in agreement with several NMR studies on related systems. The decrease in S(CD) is attributed to a larger accessible volume per lipid in the tail region. Significant changes in the electric properties of the lipid bilayer result from the structural changes, which include a shift and broadening of the choline headgroup dipole (P-N) orientation distribution. Our findings reconcile apparent controversial conclusions from experiments on diverse lipid systems.     

Protein-ligand dynamics. A 96 picosecond simulation of a myoglobin-xenon complex

A 96 picosecond dynamics trajectory of myoglobin with five xenon-probe ligands in internal cavities is examined to study the effect of protein motions on ligand motion and internal cavity fluctuations. Average structural and energetic properties indicate that the simulation is well behaved. The average protein volume is similar to the volume of the X-ray model and the main-chain atom root-mean-square deviation between the X-ray model and the average dynamical structure is 1.25 A. The protein volume oscillates 3 to 4% around the volume of the X-ray structure. These fluctuations lead to changes in the internal free volume and in the size, shape and location of atom-sized cavity features. Transient cavities produced in the simulation have a crucial role in the movement of two of the ligands. One of the ligands escapes to the protein surface, whilst a second ligand travels through the protein interior. Complex gating processes involving several protein residues are responsible for producing the necessary pores through which the ligand passes between transient cavities or packing defects.     

Distribution of Pentachlorophenol in Phospholipid Bilayers: A Molecular Dynamics Study

Molecular dynamics computer simulations of pentachlorophenol (PCP) in palmitoyl-oleoyl-phosphatidylethanolamine and palmitoyl-oleoyl-phosphatidylcholine lipid bilayers were carried out to investigate the distribution of PCP and the effects of PCP on the phospholipid bilayer structure. Starting from two extreme starting structures, including PCP molecules outside the lipid bilayer, the PCP distribution converges in simulations of up to 50 ns. PCP preferentially occupies the region between the carbonyl groups and the double bonds in the acyl chains of the lipid molecules in the bilayer. In the presence of PCP, the lipid chain order increases somewhat in both chains, and the average tilt angle of the lipid chains decreases. The increase in the lipid chain order in the presence of PCP was more pronounced in the palmitoyl-oleoyl-phosphatidylcholine bilayer compared to the palmitoyl-oleoyl-phosphatidylethanolamine bilayer. The number of trans conformations of lipid chain dihedrals does not change significantly. PCP aligns parallel to the alkyl chains of the lipid to optimize the packing in the dense ordered chain region of the bilayer. The hydroxyl group of PCP forms hydrogen bonds with both water and lipid oxygen atoms in the water/lipid interface region.     

Structure of polymerizable lipid bilayers. I--1,2-bis(10,12-tricosadiynoyl)-sn-glycero-3-phosphocholine, a tubule-forming phosphatidylcholine

This report presents the first X-ray diffraction data on diacetylenic phospholipids. The tubule-forming polymerizable lipid, 1,2-bis(10,12-tricosadiynoyl)-sn-glycero-3-phosphocholine (DC8,9PC), was studied by low angle X-ray diffraction from partially dehydrated oriented multibilayers in both polymerized and unpolymerized form. Bilayers of this material were found to be highly ordered, yielding as many as 16 orders of lamellar diffraction, in both the polymerized and unpolymerized states. The unit cell dimension was very small for a lipid of this size. In addition to the features usually observed in the electron density profile structure of phospholipid bilayers, the electron-dense diacetylenic portions of the fatty acyl chain produced electron density maxima at two well-defined levels on each side of the bilayer approximately 15 A and 9 A from the bilayer midplane. A model molecular conformation deduced from the one-dimensional electron density map features all-trans acyl chains tilted at approximately 28 degrees from the bilayer normal that are interdigitated with chains of the opposing monolayer by approximately two carbons at the bilayer center. The linear diacetylene moieties on beta- and gamma-chains appear at different positions along the bilayer normal axis and are roughly parallel to the bilayer surface. This model is discussed in terms of a polymerization mechanism.     

Analysis of the life cycle of Mycoplasma gallisepticum

Morowitz, Harold J. (Yale University, New Haven, Conn.), and Jack Maniloff. Analysis of the life cycle of Mycoplasma gallisepticum. J. Bacteriol. 91:1638-1644. 1966.-A series of electron microscope observations on Mycoplasma gallisepticum strain A5969 have been made by use of thin-section techniques and negative staining. The methods presented a consistent picture of a postdivision cell, which contains a fibrillar nuclear region, surrounding ribosomal region, highly organized bleb at one end of the cell, granular infrableb region, and bounding unit membrane. Cell division commenced with the appearance of a second infrableb area at the end of the cell opposite the original bleb. A new bleb grew in this area, and the cell then elongated. The nuclear material segregated into two parts separated by a band of ribosomes. A constriction appeared, in this central ribosome-packed area, leading to the formation of two daughter cells. The following was noted: the cells were very small (volume, 5 x 10(-14) cm(3)); each cell was highly structured and strongly ordered; and the replication appeared to be a very precisely programmed series of events.     

Molecular motions and dynamics of a diunsaturated acyl chain in a lipid bilayer: implications for the role of polyunsaturation in biological membranes.

The nature and dynamics of the motions of a diunsaturated fatty acyl chain in a lipid bilayer were examined using a comprehensive simulation program for 2H NMR line shapes developed by Wittebort et al. [Wittebort, R. J., Olejniczak, E. T., & Griffin, R. G. (1987) J. Chem. Phys. 36, 5411-5420]. A motional model in which the isolinoleoyl chain (18:2 delta 6,9) adopts two conformations consistent with the low energy structures proposed for 1,4-pentadiene [Applegate, K. R., & Glomset, J. A. (1986) J. Lipid Res. 27, 658-680], but undergoes a rapid jump between these states, is sufficient to account for the experimentally observed quadrupolar couplings, the 2H-2H and 1H-2H dipolar couplings, the longitudinal relaxation times, and the changes in the average conformation of the chain that occur with a variation in temperature. The jump motion originates via rotations about the C7-C8 and the C8-C9 carbon bonds and leads to the low order parameters assigned to the C8 methylene segment (0.18) and the C9-C10 double bond (0.11). In contrast, the C6-C7 double bond, which is not involved in the two-site jump, characterized by a relatively large order parameter (0.56). Fatty acyl chains containing three or more double bonds likely cannot undergo the same jump motion and consequently will be highly ordered structures. Correlation times for diffusion of the molecular long axis of the diunsaturated acyl chain about the bilayer normal (approximately 10(-10) s) and for the local jump motion (approximately 10(-10) s) were calculated.(ABSTRACT TRUNCATED AT 250 WORDS)     

Characterization of lipid membrane dynamics by simulation: I. Torsion angle motions of the linear chains

The torsion angle motions, generated from molecular dynamics (MD) simulations, of the two aliphatic chains of 1,2-dimyristoyl-sn-glycero-3-phosphatidylcholine (DMPC) in its lipid monolayer were evaluated by comparing these motions to those of an equivalent isolated (free) n-alkane chain, and the same n-alkane chain in its crystal lattice. The time-dependent autocorrelation and (1,2)-, (1,3)-, (1,4)-, and (1,5)-cross-correlation functions were constructed to analyze the torsion angle motions. It was found that the torsion angle motions of the DMPC lipid monolayer aliphatic chains are intermediate to those of the free n-alkane chain and the same n-alkane chain in its crystal lattice, particularly for short correlation times. The torsion angle motions of the aliphatic chains of DMPC are also found to be essentially independent of the charge state on the head group. The linear aliphatic chains of a DMPC lipid monolayer behave most like the isolated n-alkane chains with respect to torsion angle flexibility, even though the pairs of aliphatic chains of each DMPC are part of an ordered monolayer assembly. The aliphatic chains of the DMPC molecules in their monolayer exhibit at least two types of wave motions. One of the wave motions is the same in form, though somewhat more diffuse, as a traveling wave found in n-alkane crystals. The other wave motion involves major torsion angle transitions, and has some characteristics of the soliton properties observed in n-alkane crystals near their respective melt transition temperatures. © 1997 John Wiley & Sons, Inc.     

Analytical derivation of thermodynamic properties of bilayer membrane with interdigitation

We consider a model of bilayer lipid membrane with interdigitation, in which the lipid tails of the opposite monolayers interpenetrate. The interdigitation is modeled by linking tails of the hydrophobic chains in the opposite monolayers within bilayer as a first approximation. This model corresponds to the types of interdigitation that are not related with the areal “hydrophobic” dilation of the membrane. A number of essential thermodynamical characteristics are calculated analytically and compared with the ones of a regular bilayer membrane without interdigitation. Important difference between lateral pressure profiles at the layers interface for linked and regular bilayer models is found. In the linked case, the lateral pressure mid-plane peak disappears, while the entropy decreases and the free energy per chain increases. Within our model we found that in case of elongation of the chains inside a nucleus of, e.g., liquid-condensed phase, homogeneous interdigitation would be more costly for the membrane’s free energy than energy of the hydrophobic mismatch between the elongated chains and the liquid-expanded surrounding. Nonetheless, an inhomogeneous interdigitation along the nucleus boundary may occur inside a “belt” of a width that varies approximately with the hydrophobic mismatch amplitude.     

A 2H-NMR analysis of dihydrosterculoyl-containing lipids in model membranes: structural effects of a cyclopropane ring

The molecular properties of lipid multilayers of 1-palmitoyl-2-[dideutero]dihydrosterculoyl-sn-glycero-3-phosphocholine (PDSPC) were investigated by means of 2H-NMR. The transition from the liquid-crystalline phase to a more highly ordered phase was found to take place between -10 degrees C and -15 degrees C. The temperature variation of the quadrupolar splittings of specifically dideuterated PDSPC molecules was analyzed in terms of 'segmental' and 'geometrical' order parameters: the lower half of the sn-2 chain (from the site of the cyclopropane ring to the terminal methyl group) was more conformationally disordered than the upper half. The apparently abnormal increase of the quadrupolar splitting of the pro-S deuteron at the C-2' position, with increasing temperature, was attributed to a change in the average orientation of that C-2H bond with respect to the axis of motion, resulting in an increase of the 'geometrical' order parameter, S gamma. The molecular order parameter matrix elements, Sij, of the cyclopropane ring were derived from the experimental SC-2H order parameters using similarity transformations. The matrix S was diagonalized and the molecular order parameter of the cyclopropane ring, Smol (or S*33), was determined by assuming axial symmetry for such matrices associated with molecules in a liquid-crystal medium. A value of Smol = 0.59 +/- 0.04 at 25 degrees C was thus calculated. This value represents a discontinuity in the positional dependence of the molecular order parameter for the sn-2 chain of PDSPC, indicating that the cyclopropane ring provides a rigid barrier separating the lipid bilayer into two regions: an ordered region from the bilayer surface to the site of the cyclopropane ring and a much more disordered region thereafter to the center of the bilayer.     

Mean-field calculations of chain packing and conformational statistics in lipid bilayers: comparison with experiments and molecular dynamics studies.

A molecular, mean-field theory of chain packing statistics in aggregates of amphiphilic molecules is applied to calculate the conformational properties of the lipid chains comprising the hydrophobic cores of dipalmitoyl-phosphatidylcholine (DPPC), dioleoyl-phosphatidylcholine (DOPC), and palmitoyl-oleoyl-phosphatidylcholine (POPC) bilayers in their fluid state. The central quantity in this theory, the probability distribution of chain conformations, is evaluated by minimizing the free energy of the bilayer assuming only that the segment density within the hydrophobic region is uniform (liquidlike). Using this distribution we calculate chain conformational properties such as bond orientational order parameters and spatial distributions of the various chain segments. The lipid chains, both the saturated palmitoyl (-(CH2)14-CH3) and the unsaturated oleoyl (-(CH2)7-CH = CH-(CH2)7-CH3) chains are modeled using rotational isomeric state schemes. All possible chain conformations are enumerated and their statistical weights are determined by the self-consistency equations expressing the condition of uniform density. The hydrophobic core of the DPPC bilayer is treated as composed of single (palmitoyl) chain amphiphiles, i.e., the interactions between chains originating from the same lipid headgroup are assumed to be the same as those between chains belonging to different molecules. Similarly, the DOPC system is treated as a bilayer of oleoyl chains. The POPC bilayer is modeled as an equimolar mixture of palmitoyl and oleoyl chains. Bond orientational order parameter profiles, and segment spatial distributions are calculated for the three systems above, for several values of the bilayer thickness (or, equivalently, average area/headgroup) chosen, where possible, so as to allow for comparisons with available experimental data and/or molecular dynamics simulations. In most cases the agreement between the mean-field calculations, which are relatively easy to perform, and the experimental and simulation data is very good, supporting their use as an efficient tool for analyzing a variety of systems subject to varying conditions (e.g., bilayers of different compositions or thicknesses at different temperatures).     

Shear rate dependence of free energy barrier height for phenyl ring rotations in polystyrene based on non-equilibrium molecular dynamics simulations

Polystyrene properties are influenced by ring motions in side groups. The main chain conformation and interaction with the surroundings dominate the ring rotations. It is known that shear flow affects linear chain conformation and molecular distribution. However, shear-induced variations in the ring rotations have yet to be studied. This study presents a shear flow system of polystyrene via non-equilibrium molecular dynamics simulations. The free energy barrier of the phenyl ring rotations was obtained from the distribution of angle χ between the ring and main chain based on the Boltzmann distribution law. The results showed that the barrier height approaches a constant value at a shear rate less than 10¹⁰ s^? 1, but decreases with an increase in shear rate higher than 10^10.5 s^? 1. Furthermore, the radial distribution function and potential energies were compared. Remarkably, the shear flow reduced the bond vibrations of the phenyl rings, but increased the separation between intermolecular particles. Hence, a smaller cavity is necessary for the rings to rotate once but more volume is occupied by the rings. The smaller volume obtained via main chain motions needed to construct the cavity lowers the energy barrier height at shear rate higher than 10^10.5 s^? 1.     

Mapping backbone dynamics in solution with site-directed spin labeling: GCN4-58 bZip free and bound to DNA

In site-directed spin labeling, a nitroxide-containing side chain is introduced at selected sites in a protein. The EPR spectrum of the labeled protein encodes information about the motion of the nitroxide on the nanosecond time scale, which has contributions from the rotary diffusion of the protein, from internal motions in the side chain, and from backbone fluctuations. In the simplest model for the motion of noninteracting (surface) side chains, the contribution from the internal motion is sequence independent, as is that from protein rotary diffusion. Hence, differences in backbone motions should be revealed by comparing the sequence-dependent motions of nitroxides at structurally homologous sites. To examine this model, nitroxide side chains were introduced, one at a time, along the GCN4-58 bZip sequence, for which NMR (15)N relaxation experiments have identified a striking gradient of backbone mobility along the DNA-binding region [Bracken et al. (1999) J. Mol. Biol. 285, 2133]. Spectral simulation techniques and a simple line width measure were used to extract dynamical parameters from the EPR spectra, and the results reveal a mobility gradient similar to that observed in NMR relaxation, indicating that side chain motions mirror backbone motions. In addition, the sequence-dependent side chain dynamics were analyzed in the DNA/protein complex, which has not been previously investigated by NMR relaxation methods. As anticipated, the backbone motions are damped in the DNA-bound state, although a gradient of motion persists with residues at the DNA-binding site being the most highly ordered, similar to those of helices on globular proteins.     

Comparisons of lipid dynamics and packing in fully interdigitated monoarachidoylphosphatidylcholine and non-interdigitated dipalmitoylphosphatidylcholine bilayers: cross polarization/magic angle spinning 13C-NMR studies

13C-NMR spectra have been obtained at 50.3 MHz for monoarachidoylphosphatidylcholine (MAPC) and dipalmitoylphosphatidylcholine (DPPC) dispersions from 25 degrees C to 55 degrees C and for DPPC polycrystals at 25 degrees C using the cross polarization/magic angle spinning technique. Differential scanning calorimetric studies on DPPC and MAPC dispersions show comparable lipid phase transitions with transition temperatures at 41 degrees C and 45 degrees C, respectively, and thus enable the comparison of thermal, structural and dynamic differences between these two systems at corresponding temperatures. Conformational-dependent 13C chemical shift studies on DPPC dispersions demonstrate not only the coexistence of the tilted gel (L beta') and liquid-crystalline (L alpha) phases in the rippled gel (P beta') phase, but also the presence of an intermediate third microscopic phase as evidenced by three resolvable peaks for omega - 1 methylene carbon signals at the temperature interval between Tp and Tm. By comparing chemical shifts of MAPC in the hydrocarbon chain region with those of DPPC at similar reduced temperatures, it can be concluded that the packings are perturbed markedly in the middle segment of the fatty acyl chain during the lamellar to micellar transition. However, terminal methylene and methyl groups of interdigitated MAPC lamellae were found to be more ordered than those of non-interdigitated DPPC bilayers in the gel state. Interestingly, the terminal methyl groups of MAPC in the micelles remain to be relatively ordered; in fact, they are more ordered than the corresponding acyl chain end of DPPC in the liquid-crystalline state. Analysis of data obtained from rotating frame proton spin-lattice relaxation measurements shows a highly mobile phosphocholine headgroup, a rigid carbonyl group and an ordered hydrocarbon chain for lamellar MAPC in the interdigitated state. Furthermore, results suggest that free rotations of the glycerol C2-C3 bond within MAPC molecules may occur in the interdigitated bilayer, whereas intramolecular exchange between two conformations of the glycerol backbone in DPPC become possible at temperatures close to the pretransition temperature. Without isotope enrichment, we conclude that high-resolution solid-state 13C-NMR is indeed a useful technique which can be employed to study the packing and dynamics of phospholipids.