Differences in hydrocarbon chain tilt between hydrated phosphatidylethanolamine and phosphatidylcholine bilayers. A molecular packing model.

Both wide-angle and lamellar x-ray diffraction data are interpreted in terms of a difference in hydrocarbon chain tilt between fully hydrated dipalmitoyl phosphatidylcholine (DPPC) and dipalmitoyl phosphatidylethanolamine (DPPE). Although the hydrocarbon chains of multilayers of DPPC tilt ty approximately 30 degrees relative to the normal to the plane of the bilayer, as previously reported by others, the hydrocarbon chains of DPPE appear to be oriented approximately normal to the plane of the bilayer. It is found that the chain tilt in DPPC bilayers can be reduced by either: (a) adding an n-alkane to the bilayer interiors or (b) adding lanthanum ions to the fluid layers between bilayers. A molecular packing model is presented which accounts for these data. According to this model, DPPC chains tilt because of the size and conformation of the PC polar head group.     

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.     

Interactions between poly(Gly-Pro-Pro) triple helices: a model for molecular packing in collagen

Potential-energy calculations are reported on the interaction between two collagenlike triple-stranded poly(Gly-L-Pro-L-Pro) helices. Short helices can pack in a variety of orientations, but there is a unique parallel packing arrangement of the two helices for longer polypeptide chains.     

A stereochemical model for DNA-Na+ (H20) complex]

By computer calculation with the use of atom-atom potentials a stereochemical model of the DNA-hydrate Na+ complex was obtained according to which the Na+(H2O)6 octahedrons are localized in the narrow groove of DNA with formation of a great number of van der vaals contacts and hydrogen bonds. The model explains why the C-form of DNA is stabilized in the Na-DNA complex which is formed in the presence of 80% methanol (v/v). A possibility of the existence of such complexes in vivo at the DNA regions surrounded with media of diminished water activity (the DNA-membrane complex, chromosomes, phage heads) is discussed.     

The stereochemical configuration of lysosomal phosphatidylcholine and phosphatidylethanolamine: comparison with lysobisphosphatidic acid.

Lysosomal phosphatidylcholine and phosphatidylethanolamine were isolated from liver of rats treated with Triton WR 1339 and from cultured BHK-cells. Stereochemical analysis proved that these lipids, in contrast to the lysosomal lysobisphosphatidic acid, were derivatives of sn-glycero-3-phosphate.     

Stereochemical model for phospholipids. III: Molecular conformation and molecular packing of l-O-phosphatidylserine (PS)

In analogy with part II of this study an empirical energy calculation was carried out to evaluate the conformational state of $\text{l}\text{-O-}\text{phosphatidylserine}$ (PS), which constitutes the polar head of a class of phospholipid molecules.A set of conformers which differ in the orientation of the carboxyl and ammonium groups with respect to the phosphate group was identified.An energy packing calculation was carried out by considering each derived conformer located in a hexagonal lattice, with a calculation procedure identical to that previously applied.Molecular aggregates with different degrees of reticulation arose in relation to the conformational state and the orientation of the molecule in the eulerian space.The stability and the physical significance of each derived geometry is discussed.     

Endogenous phospholipids of swine liver: effect of fat deprivation on molecular species of phosphatidylcholine and phosphatidylethanolamine

Three 1-yr-old swine and two 2.5-wk-old swine were fed a fat-free diet for 1 month and 5 months, respectively. The hepatic phosphatidylcholine and phosphatidylethanolamine were fractionated by silver ion thin-layer chromatography. A distinctive feature of the chromatographic procedure was the development of the chromatograms at low temperatures: -10 degrees C for phosphatidylcholine and 4 degrees C for phosphatidylethanolamine. The chromatographic fractions were hydrolyzed with phospholipase A(2), and the fatty acids were characterized. Significant concentrations of odd-chain saturated and unsaturated fatty acids were found in the swine deprived of fat for 5 months. The major molecular species of phosphatidylcholine in both groups contained monoenoic fatty acids: 16:0/18:1(n - 9), 18:0/18:1(n - 9), and 18:1(n - 9)/18:1(n - 9). Their concentrations changed only slightly with the diet. The molecular species of phosphatidylethanolamine were more sensitive to dietary changes. In the swine deprived of fat for 1 month, about 50% of the molecular species of phosphatidylethanolamine contained tetraenoic fatty acids: 16:0/20:4(n - 6), 18:0/20:4(n - 6), and 18:1(n - 9)/20:4(n - 6). The phosphatidylethanolamine of animals deprived of fat for 5 months contained only 3% molecular species with tetraenoic acids, 18:0/20:4(n - 6), but 36% molecular species with trienoic acids: 18:0/20:3(n - 9), 18:1(n - 9)/20:3(n - 9), 18:0/19:3(n - 8), 16:0/20:3(n - 9), and 17:0/20:3(n - 9). Doubly unsaturated species, such as 18:1(n - 9)/18:1(n - 9), 18:1(n - 9)/20:3(n - 9), and 18:1(n - 9)/20:4(n - 6), were found in both groups of swine, although their total concentrations were higher in the group deprived of fat for a longer period.     

Conformational analysis of levanbiose by molecular mechanics.

A relaxed conformational energy map for levanbiose, O-beta-D-fructofuranosyl-(2----6)-beta-D-fructofuranoside, was computed with the molecular mechanics program MM2(87). All torsion angles of the three linkage bonds were driven by 30 degrees increments while two primary alcohol groups were held at three staggered forms. The steric energy of all other parameters was optimized. The side groups were retained at the same relative positions on the two rings in this first part of the study so our results are directly applicable to the study of polymeric levan with identical repeating units. The low-energy dimers did not lead to viable polymers. The interresidue linkage torsion angles defined by C-6-O-2'-C-2'-C-1' (phi) and O-5-C-5-C-6-O-2' (omega) have minima at +60 degrees and -60 degrees, respectively, with accessible minima at other staggered forms. As observed in inulobiose, the preferred torsion angle at central linkage bond defined by C-5-C-6-O-2'-C-2' (psi) was antiperiplanar. An analysis of all conformations of staggered side groups showed that the C-1 and C-1' groups had little effect but the C-6' group showed a preference for chi-6'(O-5'-C-5'-C-6'-O-6') = -60 degrees. The fructofuranose rings were started at the low-energy 4(3)T conformation (angle of pseudorotation, phi 2 = 265 degrees) that was retained except when the linkage conformations created severe inter-residue conflict.     

Composition and structure of phospholipids in hydrocarbon yeasts. I. Phosphatidylcholine and phosphatidylethanolamine

From fooder yeast grown on purified liquid n-parafins two fractions--phosphatydylcholin and phosphatydyletanolamin--have been isolated. Structure, composition and properties of these compounds have been studied. It is established that double bonds in fatty acids ends are located near their polar group.     

Skip residues and charge interactions in myosin II coiled-coils: implications for molecular packing

Molecular packing of myosin II coiled-coil rods into myosin filaments and the role of skip residues in the heptad sequence have been investigated. Sequence comparison of rods from skeletal, smooth and non-muscle myosin II shows that different myosin II subtypes have significantly different charge distributions. Analysis of the ionic interactions between adjacent rods with changing molecular overlap relates the different patterns of charge to the different structures of skeletal and smooth muscle myosin II filaments. It is shown in the case of skeletal muscle myosin II that the skip residues have a critical role in keeping these unique patterns of charge in perfect phase. Only one of the previously suggested packing models for myosin II filaments, with a slight modification, is supported, since it satisfies all the sequence-predicted axial shifts between adjacent rods. Such analysis significantly advances understanding of myosin filament assembly properties and will help to provide a basis for the proper understanding of myosin-associated diseases.     

Conformational and hydrational properties during the L(beta)- to L(alpha)- and L(alpha)- to H(II)-phase transition in phosphatidylethanolamine

Differential scanning calorimetry (DSC) measurements have been carried out simultaneously with small- and wide-angle X-ray scattering recordings on liposomal dispersions of stearoyl-oleoyl-phosphatidylethanolamine (PE) in a temperature range from 20 to 80 degrees C. The main transition temperature, T(m), was determined at 30.9 degrees C with an enthalpy of 28.5 kJ/mol and the lamellar-to-inverse hexagonal phase transition temperature, T(hex), at 61.6 degrees C with an enthalpy of 3.8 kJ/mol. Additionally highly resolved small angle X-ray diffraction experiments performed at equilibrium conditions allowed a reliable decomposition of the lattice spacings into hydrophobic and hydrophilic structure elements as well as the determination of the lipid interface area of the lamellar gel-phase (L(beta)), the fluid lamellar phase (L(alpha)) and of the inverse hexagonal phase (H(II)). The rearrangement of the lipid matrix and the coincident change of free water per lipid is illustrated for both transitions. Last, possible transition mechanisms are discussed on a molecular level.     

Conformational analysis of octa- and tetrabromo tetraphenylporphyrins and their Ni(II) and Tb(III) complexes

Molecular mechanics (MM) calculations were used to analyze the puckering of metalloporphyrins as a function of metal ion size and the position of substituents on the porphyrin periphery, on a three series of octa- and tetrabromo tetraphenylporphyrins: without metal, and with Ni(II), and Tb(III) as representative small and large metal ions, respectively. Molecular energy optimization calculations were carried out using the Consistent Force Field (CFF) program, with the parameters developed previously and new parameters for bromine atom. Normal-coordinate structural decomposition (NSD) analysis was performed on the equilibrium structures obtained by MM calculations. The conformers are also stereochemically characterized, compared with available X-ray structures and with the conformers obtained in our previous MM study using chloro instead of bromo beta-pyrrole substituents.     

Conformational analysis of genotoxic benzo[a]pyrene-7,8-dione-duplex DNA adducts using a molecular dynamics method (II)

The conformations of the benzo[a]pyrene-7,8-quinone (BPQ) modified oligonucleotide were investigated using molecular dynamic simulation. In the initial structures, the central guanine base was modified with BPQ resulting in the formation of four structurally distinguishable 10-(N2-deoxyguanosyl)-9,10-dihydro-9-hydroxy benzo[a]pyrene-7,8-dione adducts (BPQ-G3,4). Each of the oligonucleotide adduct consisted of two conformers, namely syn and anti conformations, depending on the rotation around the glycosidic bond between BPQ and the guanine base. The results revealed that the BPQ moiety was located in the major groove for all four syn conformers. The relative energies of these conformers were high, and the backbone largely deviated from the B-form. On the other hand, BPQ was located in the minor groove with relatively low energies, and backbone was retained in all of the anti conformer cases. The most conceivable BPQ-modified double stranded oligonucleotide structure was proposed from the energy calculation and the structural analysis.     

Biosynthesis of 1-alkenes in higher plants: stereochemical implications. A model study with Carthamus tinctorius (Asteraceae)

Odd numbered 1-alkenes, such as 1-pentadecene or 1,8,11,14-heptadecatetraene are formed from palmitic or linolenic acid by fragmentative decarboxylation. Incubation studies with germinating safflower (Carthamus tinctorius) and (2R,3R)-12-phenyl[2,3-2H2]dodecanoic acid, (2S,3S)-12-phenyl[2,3-2H2]dodecanoic acid, (2R)-12-phenyl[2-2H]dodecanoic acid and (2S)-12-phenyl[2-2H]dodecanoic acid instead of the natural alpha-linolenic acid precursor revealed the fragmentation to be an overall anti elimination of the 3-pro(S) hydrogen and the carboxyl group (anti-periplanar transition state geometry). Externally offered 3-hydroxy acids are not fragmented to 1-alkenes. The most probable mechanistic alternatives are in agreement with abstraction of the 3-pro(S) hydrogen as a radical followed by electron transfer and fragmentation, or transient insertion of oxygen into the 3-pro(S) C-H bond and subsequent fragmentation into an 1-alkene and CO2 after appropriate activation. The mechanism seems to be of general importance for the biosynthesis of vinylic substructures of natural products from oxygenated precursors.     

Conformational analysis of endomorphin-1 by molecular dynamics methods.

Endomorphin-1 (EM1, H-Tyr-Pro-Trp-Phe-NH2) is a highly potent and selective agonist for the mu-opioid receptor. A conformational analysis of this tetrapeptide was carried out by simulated annealing and molecular dynamics methods. EM1 was modeled in the neutral (NH2-) and cationic (NH-) forms of the N-terminal amino group. The results of NMR measurements were utilized to perform simulations with restrained cis and trans Tyr1-Pro2 peptide bonds. Preferred conformational regions in the Phi 2-Psi 2, Phi 3-Psi 3 and Phi 4-Psi 4 Ramachandran plots were identified. The g(+), g(-) and trans rotamer populations of the side-chains of the Tyr1, Trp3 and Phe4 residues were determined in chi 1 space. The distances between the N-terminal N atom and the other backbone N and O atoms, and the distances between the centers of the aromatic side-chain rings and the Pro2 ring were measured. The preferred secondary structures were determined as different types of beta-turns and gamma-turns. In the conformers of trans-EM1, an inverse gamma-turn can be formed in the N-terminal region, but in the conformers of cis-EM1 the N-terminal inverse gamma-turn is absent. Regular and inverse gamma-turns were observed in the C-terminal region in both isomers. These beta- and gamma-turns were stabilized by intramolecular H-bonds and bifurcated H-bonds.     

A family of double helices of alternating poly(gamma-benzyl-D-L-glutamate), a stereochemical model for gramicidin A.

Poly(γ-benzyl-d-l-glutamate) with strict alternation of l and d residues is found to exist, in addition to the α_DL and π_DL^4.4 helical structures already described (Heitz et al., 1975a), in four more helical structures. Models based on double helices made of antiparallel strands are proposed for all four structures, based on infrared, X-ray and electron diffraction data. These double helices are, like the single-stranded π_DL helices, specific to polypeptides with a strict stereosequence of alternating l and d residues. The diameter of the helical core of three of these helices appears to depend on the dimensions of the solvent molecules. Conformational angles (located in the β regions) and atomic co-ordinates determined by conformational energy analysis are given for the four structures. Experimental conditions used to obtain these helices, and to induce transconformations between the various helical structures of PBd-lG are described. The present investigations on PBd-lG help to make more precise the structure and geometry of models proposed (Veatch et al., 1974) for the antibiotic gramicidin A.     

Conformational analysis and molecular dynamics simulations of maltose

Constrained conformational energy minimizations have been used to calculate an adiabatic (Φ, ψ) potential energy surface for the disaccharide β-maltose. The inclusion of molecular flexibility in the conformational energy analysis of the disaccharide was found to significantly lower the barriers to conformational transitions, as has been observed previously for other systems. Several low energy wells were identified on the adiabatic surface which differ in energy by small amounts and with low absolute barriers separating them, indicating the possibility of a non-negligible equilibrium population distribution in each well. If such a distribution of conformations existed in the physical system, the conformation observed by NMR NOE measurements would thus be a “virtual” conformation. Molecular dynamics simulations of the motions of this molecule in vacuum were also conducted and indicate that the rate of relaxation of the molecule to the adiabatic surface may be slower than the typical timescale of conformational fluctuations. This effect is apparently due to an unphysical persistence of hydrogen bond patterns in vacuum which does not occur in aqueous solution. Trajectories undergoing transitions between wells were calculated and the effects of such conformational transitions upon the ensemble mean structure, such as might be observed in an NMR experiment, were demonstrated.     

A computer model for hydrodynamic shearing of DNA (Gibb's phenomenon): Part II.

This paper presents an extension of the distribution proposed during hydrodynamic shearing of DNA. In the Fourier least square approximation of uniform random distribution or a square wave, Gibb's phenomena occur at the boundaries. The same behavior occurs at the boundaries of the DNA strands undergoing hydrodynamic shearing of DNA. This hypothesis is corroborated by results from a computer simulation of hydrodynamic shearing of DNA. The evidence helps confirm the kinetic experiments of Britten and Kohne [4]. Furthermore the results predict that sequence very near the end (0.2 LAMBDA) should be the most intact.     

Conformational changes following Mn(II) binding to demetalized concanavalin A

A temperature-dependent conformational change occurs following the binding of only one Mn(II) to a concanavalin A monomer. This change is independent of Ca(II) near pH 7 and is characterized by an activation energy of 22.3 kcal mol^?1, a value similar to that attributed to a cis-trans peptide isomerization. Two conformations have been detected in magnetic resonance experiments on solvent water protons where spin lattice relaxation times are influenced by bound Mn(II). Both conformations possess saccharide binding activity and Ca(II) stoichiometrically enhances the rate of conversion to the final, more stable conformation.