Theoretical conformational analysis of phospholipids: I. Study of the interactions between phospholipid molecules by use of semi-empirical methods with the explicit introduction of polar headgroup interactions

We present a theoretical conformational analysis of a system composed of seven dipalmitoylphosphatidylethanolamine molecules in interaction. The combined use of classical semi-empirical methods for the polar headgroup region with mechanical statistical calculations for the aliphatic chains permits the evaluation of the free energy for a phospholipids molecule. The free energy variation in function of the mean intermolecular interchain distance gives information about the main lipid bilayer phase transition. It appears, however, necessary to take into account the hydration of the polar headgroups.     

Kinetics and mechanism of the spontaneous transfer of fluorescent phospholipids between apolipoprotein-phospholipid recombinants. Effect of the polar headgroup

Fluorescent derivatives of a phosphatidylglycerol, phosphatidylserine, phosphatidic acid, phosphatidylcholine, phosphatidylethanolamine, and diacylglycerol have been studied to establish the effect of different polar headgroups on the mechanism and kinetics of spontaneous phospholipid transfer between recombinants of human plasma apolipoprotein A-II and dimyristoylphosphatidylcholine. The fluorescent lipids are all 1-myristoyl-2-[9-(1-pyrenyl)nonanoyl] glycerides. The transfer of the lipids is a first order process where the rate is independent of the concentration over a 50 fold range of the acceptor recombinants. These results are consistent with the lipids transferring as monomers being a water-soluble intermediate. The rate of transfer of the different phospholipids are slightly slower than phosphatidylcholine, with that of phosphatidylethanolamine being about 4 times slower. The transfer of phospholipids with a titratable headgroup is pH-dependent. The difference in the rates and pH dependence may be a function of the interactions (hydrogen bonding) between polar headgroups. The rate of transfer of the diacylglycerol is 20 times slower than phosphatidylcholine, but its activation energy (21 kcal/mol) is only 2 to 3 kcal less than most of the phospholipids (23 kcal/mol). These results suggest that the rate and activation energy for the spontaneous transfer of phospholipids can be predicted to a first approximation on the basis of its hydrophobic content, irrespective of the pH or identity of the polar headgroup.     

Theoretical conformational analysis of phospholipids. II. Role of hydration in the gel to liquid crystal transition of phospholipids

To obtain a satisfactory agreement between computed transition temperatures and those determined experimentally, we introduce explicitly water molecules which hydrate the polar headgroup of dipalmitoylphosphatidylethanolamine molecules. The calculated free energy curves as a function of the intermolecular interchain distance and the degree of hydration of the polar groups permit the determination of the transition of the phospholipid system from the gel to the liquid crystalline phase. The detailed structure of the hydration shell is defined using the supermolecular approach.     

Structure-function organization of neurokinin A and neurokinin B molecules. I. Theoretical conformational analysis of neurokinin A

The spatial structure of the neurokinin A molecule was studied by the method of theoretical conformational analysis. On the basis of fragmental analysis, stable structures of the neurokinin A molecule under polar conditions were determined. The structures can be described by four families of low-energy conformations having a relatively labile tripeptide at the C-end and a conformationally rigid heptapeptide at the N-end. It was shown that two of these conformations are virtually isoenergetic structures. One of these is an alpha-helical structure and the other forms two beta-turns at the N-terminus, which change to the turn of the alpha-helix at the C-end.     

Theoretical conformational analysis of phospholipids II. Role of hydration in the gel to liquid crystal transition of phospholipids

To obtain a satisfactory agreement between computed transition temperatures and those determined experimentally, we introduce explicitly water molecules which hydrate the polar headgroup of dipalmitoylphosphatidylethanolamine molecules. The calculated free energy curves as a function of the intermolecular interchain distance and the degree of hydration of the polar groups permit the determination of the transition of the phospholipid system from the gel to the liquid crystalline phase. The detailed structure of the hydration shell is defined using the supermolecular approach.     

Quantum-chemical and empirical calculations on phospholipids. VII. The conformational behaviour of the phosphatidylcholine headgroup in layer systems

Starting from single molecule calculations the intermolecular interactions of the glycerophosphatidylcholine (GPC) headgroup with its nearest neighbours in a layer crystal were taken into account using 1-6-12 interatomic potential functions. By use of a steepest descent energy minimisation procedure over all variable torsion angles (θ₁, α₁ … α₆) of the GPC headgroup the minima of the seven-dimensional energy hypersurface were calculated. The torsion angles and the energies of the most stable conformations are given in polar coordinates. The components of the headgroup dipolar moment of these conformations were calculated to be μ₆ = 3.0 … 9.5 D, μ_⊥ = 17.5 … 24 D, μ = 18.5 … 25 D using the net atomic charge distribution in space. The results demonstrate a high flexibility of the GPC headgroup. Around the C-1O-11 bond (α₁), only antiperiplanar conformations are allowed. The $\text{α}{}_4\text{α}{}_5\text{(α}{}_6\text{)}$ correlation diagram shows that the choline group exists in mirror-image enantiomeric conformations. Our results yield a foundation of models of the dynamical behaviour of the phosphatidylcholine headgroup at the level of conformational behaviour and are in agreement with experimental data.     

A semi-empirical conformational analysis of the interaction of n-alkanols with dipalmitoylphosphatidylcholine

The interaction of a homologous series of saturated aliphatic n-alkanols (containing 1–13 carbon atoms) with dipalmitoylphosphatidylcholine was studied by a semi-empirical conformational analysis. The minimal conformational energy of the isolated molecule at the hydrocarbon-water interface was calculated as the sum of the contributions resulting from the Van der Waals, torsional, electrostatic and transfer energies. From the conformers of minimal energies were calculated the hydrophilic-hydrophobic balance, the distance between hydrophilic and hydrophobic centres and the energies of interaction between homologous alkanols and between alkanols and lipids. Using these parameters, different modes of conformation, orientation and interaction of n-alkanols and dipalmitoylphosphatidylcholine were described. For methanol, ethanol and n-propanol, the gauche conformers were the most probable interacting only with the lipid polar heads. Only all-trans conformers were obtained for alkanols with longer acyl chains. n-Butanol to n-octanol form clusters in the lipid matrix. Longer n-alkanols are randomly distributed in the lipid layer. However, due to the increase in hydrocarbon chain-length, n-nonanol and higher alkanols have an interaction energy identical or superior to that found in a pure lipid monolayer, leading to a more ordered alkanol-lipid organization.     

Raman spectroscopic study of the conformational changes of thyroxine induced by interactions with phospholipid

Comparison of the Raman spectra of thyroxine ( L-3,3',5,5'-tetraiodothyronine) in the pure state and in a 1:5 mixture with phosphatidylcholine reveals spectral differences that reflect structural changes of thyroxine induced by interactions with the phospholipid. These structural changes could be localized in specific parts of the thyroxine molecule on the basis of a vibrational analysis that was carried out by density functional calculations with the B3LYP hybrid functional applying the SDD effective core potential basis set. The calculated (and subsequently scaled) frequencies reveal a good agreement with the experimental data, which together with calculated IR and Raman intensities allow a plausible assignment of most of the IR and Raman bands. Thus, it is found that modes localized in the aromatic beta-ring and in the ether group as well as the C-I stretching modes of ring alpha are affected upon lipid interactions, indicating that thyroxine interacts with the phosphatidylcholine bilayer via penetration of the hydrophobic part of the molecule.     

Theoretical studies of nucleic acid interactions. I. Estimates of conformational mobility in intercalated chains

A combined geometric and potential-energy analysis has been carried out to identify the torsional arrangements of the nucleic acid chain that can accommodate the intercalation of small planar moieties. In contrast to previous theoretical efforts, which detail local conformations after adjacent bases are positioned in space, the likely geometries are found here on the basis of the base orientations that result from all feasible combinations of the nine torsional variables of the basic dinucleotide intercalation unit. The relatively mobile nature of the sugar-phosphate backbone, together with the fairly long stretches of chemical bonds between adjacent units, is apparently responsible for the large number of feasible binding geometries. Some previously overlooked conformations with unusual sugar-puckering combinations and various phosphodiester arrangements are found in the survey. A large proportion of the energetically favored intercalation states are closely related to the backbone conformations of familiar double-helical models such as A-, B-, and Z-DNA, as well as the Watson-Crick model. Moreover, the intercalated forms are found to interconvert smoothly along a continuous conformational pathway. The intercalation structures derived from x-ray crystallographic analyses of drug-oligonucleotide complexes, in contrast, are stiff three-dimensional forms essentially frozen in a single domain of conformation space. Specific ligand-nucleic acid interactions that may be responsible for the experimental observations are not included in this study. The classical intramolecular potential energies reported here are highly approximate, providing only rough gauges of the relative importance of the many competing conformations.     

Comparative conformational analysis of nucleosides by NMR, X-ray, and semi-empirical (PM3 VS. AM1) methods

The 2'-deoxy-2'-fluoro-beta-D-arabinofuranosyl ortho-aza-purine and -pyrimidine nucleosides manifest an unusually rigid sugar N conformation in solution.     

Factors affecting the motion of the polar headgroup in phospholipid bilayers. A 31P NMR study of unsonicated phosphatidylcholine liposomes.

(1) The 129 MHZ and 36.4 MHZ 31 P NMR spectra of unsonicated liposomes consisting of phosphatidylcholines of varying chain length and unsaturation have been investigated. (2) In the liquid crystalline state the 31 P NMR liposome spectra are similar for both saturated and unsaturated phosphatidylcholines, demonstrating that the motion of the polar headgroup is not sensitive to the fatty acid composition in the disordered liquid crystalline state. (3) Below the hydrocarbon phase transition temperature there is a marked increase in the linewidth of the 31P NMR liposome spectra, indicating a reduction in the motion of the polar headgroup. (4) The addition of equimolar concentrations of cholesterol to phosphatidylcholine eliminates phase transition effects experienced by the polar headgroup. The motion of the polar headgroup is then very similar to that obtained in the liquid crystalline state for pure phosphatidylcholine bilayers. (5) In the liquid crystalline state the motion of the polar headgroup in the phosphate region is insensitive to changes in the available area per phosphatidy-choline molecule.     

Quantum-chemical and empirical calculations on phospholipids. II. A conformational analysis of model headgroups of phospholipids obtained by the PCILO-procedure.

The conformational behaviour and the charge distribution of methylphosphorylcholine has been analyzed within the framework of the PCILO method including phosphorus-oxygen σ- and π-bonds. In the global minimum of energy the OPOCC chain has a (?synclinal, ?synclinal, ?syn/anticlinal, +anticlinal) conformation.     

Solution conformational study of Scyliorhinin I analogues with conformational constraints by two-dimensional NMR and theoretical conformational analysis.

Two analogues of Scyliorhinin I (Scyl), a tachykinin with N-MeLeu in position 8 and a 1,5-disubstituted tetrazole ring between positions 7 and 8, introduced in order to generate local conformational constraints, were synthesized using the solid-phase method. Conformational studies in water and DMSO-d6 were performed on these peptides using a combination of the two-dimensional NMR technique and theoretical conformational analysis. The algorithm of conformational search consisted of the following three stages: (i) extensive global conformational analysis in order to find all low-energy conformations; (ii) calculation of the NOE effects and vicinal coupling constants for each of the low energy conformations; (iii) determining the statistical weights of these conformations by means of a nonlinear least-squares procedure, in order to obtain the best fit of the averaged simulated spectrum to the experimental one. In both solvents the three-dimensional structure of the analogues studied can be interpreted only in terms of an ensemble of multiple conformations. For [MeLeu8]Scyl, the C-terminal 6-10 fragment adopts more rigid structure than the N-terminal one. In the case of the analogue with the tetrazole ring in DMSO-d6 the three-dimensional structure is characterized by two dominant conformers with similar geometry of their backbones. They superimpose especially well (RMSD = 0.28 A) in the 6-9 fragments. All conformers calculated in both solvents superimpose in their C-terminal fragments much better than those of the first analogue. The results obtained indicate that the introduction of the tetrazole ring into the Scyl molecule rigidifies its structure significantly more than that of MeLeu.     

Bioactive conformational generation of small molecules: A comparative analysis between force-field and multiple empirical criteria based methods

Background  

Conformational sampling for small molecules plays an essential role in drug discovery research pipeline. Based on multi-objective evolution algorithm (MOEA), we have developed a conformational generation method called Cyndi in the previous study. In this work, in addition to Tripos force field in the previous version, Cyndi was updated by incorporation of MMFF94 force field to assess the conformational energy more rationally. With two force fields against a larger dataset of 742 bioactive conformations of small ligands extracted from PDB, a comparative analysis was performed between pure force field based method (FFBM) and multiple empirical criteria based method (MECBM) hybrided with different force fields.     

The structure-function organization of neurokinin A and neurokinin B molecules. II. Theoretical conformational analysis of neurokinin B

The spatial structure of a neurokinin B molecule was investigated by the method of theoretical conformational analysis. The conformational analysis of this molecule indicated that the possible structure of neurokinin B under polar conditions may be described by five families of low-energy conformations possessing a conformationally relatively rigid C-terminal heptapeptide and variable N-terminal fragments.     

Theoretical studies of the conformational behavior of chain molecules containing polar groups: simulations of a poly(vinylidene fluoride) model

Atomistic Monte Carlo simulations have been conducted to elucidate the conformational behavior of a single chain molecule containing polar functional groups. Here, we resort to an atomistic poly(vinylidene fluoride) (PVDF) chain model as a representative example. The model is modified in such a way that bond lengths and bond angles are fixed, aiming to manifest the role of dipolar interactions. For a given chain length, chain conformation is sensitive to two environmental parameters, temperature and dielectric constant. The mean chain size increases when temperature and/or dielectric constant are increased. The conformational behavior is further characterized by chain size distribution function, and our findings show that temperature induced conformational transition for a chain molecule can be discrete or continuous, depending on its chain length. Also, the dipolar interactions in PVDF are effectively attractive, and enhance chain contraction. As a result, when the strength of dipolar interactions is increased, the discrete conformational transition shifts toward longer chains; and for a given chain length, such a transition occurs at higher temperatures.Figure Variation of R² with temperature for different dielectric constants =1 and 8, denoted by dotted and solid lines, respectively, and for different chain lengths M=8 and 12, as marked. Lines are meant for eye guidance     

Behavior of beef-heart cytochrome c oxidase in reconstituted proteovesicles. A systemtic evaluation of the influence of phospholipid polar headgroup and fatty-acyl side chains

1. Phospholipid-depleted cytochrome c oxidase is incorporated in vesicles, built up of phospholipids of known polar headgroup and fatty-acyl side chains. 2. Maximal reactivation is obtained only when the fatty-acyl side chains provide a fluid environment. 3. Fluid zwitterionic phospholipids are found to be more efficient reactivators than fluid anionic ones. 4. Irrespective of the polar headgroup type, two narrow ranges of activation energies for the enzymatic reaction are calculated from the Arrhenius plots: 81--92 kJ/mol in solid and 51--61 kJ/mol in fluid conditions. 5. Cytochrome c oxidase is also incorporated in a series of vesicles, each built up of an equimolar amount of two phospholipids which differ in their polar headgroup type and/or their fatty-acyl side chain characteristics. From the localization of the enzyme activity profiles, obtained with these mixtures, tentative deductions are made about the preference of cytochrome c oxidase for different phospholipid molecules.