Intermolecular Conformation Research Articles

Oxidative Stability of Marine Phospholipids in the Liposomal Form and Their Applications

Marine phospholipids (MPL) have attracted a great deal of attention recently as they are considered to have a better bioavailability, a better resistance towards oxidation and a higher content of eicosapentaenoic (EPA) and docosahexaenoic acids (DHA) than oily triglycerides (fish oil) from the same source. Due to their tight intermolecular packing conformation at the sn-2 position and their synergism with α-tocopherol present in MPL extracts, they can form stable liposomes which are attractive ingredients for food or feed applications. However, MPL are still susceptible to oxidation as they contain large amounts polyunsaturated fatty acids and application of MPL in food and aquaculture industries is therefore a great challenge for researchers. Hence, knowledge on the oxidative stability of MPL and the behavior of MPL in food and feed systems is an important issue. For this reason, this review was undertaken to provide the industry and academia with an overview of (1) the stability of MPL in different forms and their potential as liposomal material, and (2) the current applications and future prospects of MPL in both food and aquaculture industries with special emphasis on MPL in the liposomal form.

Flexibility of the Cu,Zn superoxide dismutase structure investigated at 0.57 GPa

The 2 A resolution crystal structure of bovine erythrocyte Cu,Zn superoxide dismutase (CuZnSOD) has been determined by X-ray diffraction at high pressure (0.57 GPa) and room temperature. At 0.57 GPa the secondary, tertiary and quaternary structures are similar to other previously determined bovine erythrocyte CuZnSOD structures. Nevertheless, pressure has a localized impact on the atomic coordinates of C(alpha) atoms and on side chains. The compression of the crystal and of the protein backbone is anisotropic. This anisotropy is discussed, taking into account intermolecular contacts and protein conformation. Pressure perturbation highlights the more flexible zones in the protein such as the electrostatic loop. At 0.57 GPa, a global shift of the dimetallic sites in both subunits and changes in the oxidation state of Cu were observed. The flexibility of the electrostatic loop may be useful for the interaction of different metal carriers in the copper-uptake process, whereas the flexibility of the metal sites involved in the activity of the protein could contribute to explaining the ubiquitous character of CuZnSODs, which are found in organisms living in very different conditions, including the deep-sea environment. This work illustrates the potential of combining X-ray crystallography with high pressure to promote and stabilize higher energy conformational substates.

Effects of immobilization onto aluminum hydroxide particles on the thermally induced conformational behavior of three model proteins

Although the thermal unfolding/aggregation behavior of proteins in solution has been extensively studied, little is known about proteins immobilized on the surface of nanoparticles and other solid-phase materials. In this study we carefully monitor and analyze the thermal denaturation process of three model proteins adsorbed onto aluminum hydroxide as a function of temperature by FT-IR spectroscopy. The results reveal that the proteins immobilized onto aluminum hydroxide retain their native conformation at lower temperatures (<45 °C). Upon thermal denaturation, the structural transition between the native and denatured states is very similar, in terms of disappearance of the major native secondary structural elements, between the proteins adsorbed onto aluminum hydroxide adjuvant and in solution. This result suggests that the thermal stability of proteins is not significantly affected, or marginally affected at most, by the adsorption onto aluminum hydroxide adjuvant, considering a 5 °C temperature interval used for data collection. However, the adsorption rate and crowding of proteins on aluminum hydroxide particles have a profound effect on the aggregation behavior of the proteins, hydrogen bonding strength of intermolecular β-sheet aggregates and conformation of intermediate states.

Intermolecular interaction-directed conformations of bridged bis(1,4-piperazine-2,5-diones)

Intermolecular interaction-directed conformations of bridged bis(1,4-piperazine-2,5-diones)

Switch from Intra- to Intermolecular H-Bonds by Ultrasound: Induced Gelation and Distinct Nanoscale Morphologies

During cooling of the ( R)-N-Fmoc-Octylglycine (Fmoc-OG)/cyclohexane solution, gelation is observed exclusively when ultrasound is used as an external stimulus, while deposit is obtained without sonication. The xerogel consists of entangled fibrous network made by interconnected nanofibers, while the deposit comprises large numbers of unbranched nanowires. It is found that the Fmoc-OG molecules form bilayer structures in both the deposit and the gel. However, the ratio ( R) between the Fmoc-OG molecules in a stable intramolecular H-bonding conformation and those in a metastable intermolecular H-bonding conformation can be tuned by the ultrasound, R (deposit) > R (gel). The increased population of the intermolecular H-bonding Fmoc-OG molecules induced by the ultrasonication facilitates to the interconnection of nanofibers for the formation of the fibrous network, and therefore gelation. The alteration in the morphologies and properties of the obtained nanomaterials induced by the ultrasound wave demonstrates a potential method for smart controlling of the functions of nanomaterials from the molecular level.

Effect of acceptor on efficiencies of exciplex-type organic light emitting diodes

The relationship between the electroluminescent (EL) efficiencies of interfacial exciplex emission and the lowest unoccupied molecular orbital (LUMO) of the acceptors systematically investigated. A nearly linear relationship was observed between LUMOs of acceptors and exciplex efficiency for a fixed donor of 4,4′,4″-tris[3-methyl-phenyl(phenyl)amino]-triphenylamine in exciplex-type devices. This result indicates that the lower the LUMO of the acceptor is, the higher the EL efficiency of the exciplex is. The effect of acceptor on the efficiencies of exciplex-type devices is attributable to the interactions between the donor and acceptor molecules, which were closely related to the matched LUMOs and intermolecular conformations overlap between donor and acceptor molecules.

Energy level alignment and morphology of interfaces between molecular and polymeric organic semiconductors

Ultraviolet photoelectron spectroscopy (UPS) was used to determine the energy level alignment at organic–organic conductor–semiconductor and semiconductor–semiconductor hetero-interfaces that are relevant for organic optoelectronic devices. Such interfaces were formed by in situ vacuum sublimation of small molecular materials [C 60 and pentacene (PEN)] and ex situ spin-coating of poly(3-hexylthiophene) (P3HT), all on the common substrate poly(3,4-ethylenedioxythiophene)/poly(styrenesulfonate) (PEDOT:PSS). We found that the deposition sequence had a significant impact on the interface energetics. The hole injection barrier (HIB) of C 60 on PEDOT:PSS could be changed from 1.0 eV (moderate hole injection) to 1.7 eV (good electron injection) by introducing a layer of P3HT. The HIB of P3HT/PEDOT:PSS was increased by 0.35 eV due to an interfacial PEN layer. However, PEN deposited on PEDOT:PSS and P3HT/PEDOT:PSS exhibited the same value. These observations are explained by material-dependent dipoles at the interfaces towards PEDOT:PSS and substrate dependent inter-molecular conformation.

Lithium Ethylene Dicarbonate Identified as the Primary Product of Chemical and Electrochemical Reduction of EC in 1.2 M LiPF6/EC:EMC Electrolyte

Lithium ethylene dicarbonate ((CH2OCO2Li)2) was chemically synthesized and its Fourier transform infrared (FTIR) spectrum was obtained and compared with that of surface films formed on Ni after cyclic voltammetry (CV) in 1.2 M lithium hexafluorophosphate (LiPF6)/ethylene carbonate (EC):ethyl methyl carbonate (EMC) (3:7, w/w) electrolyte and on metallic lithium cleaved in-situ in the same electrolyte. By comparison of IR experimental spectra with that of the synthesized compound, we established that the title compound is the predominant surface species in both instances. Detailed analysis of the IR spectrum utilizing quantum chemical (Hartree-Fock) calculations indicates that intermolecular association through O...Li...O interactions is very important in this compound. It is likely that the title compound in the passivation layer has a highly associated structure, but the exact intermolecular conformation could not be established on the basis of analysis of the IR spectrum.

A pyrimidine thiolate Rh(i) complex: structure, bonding and one-dimensional interactions in solid and in solution

The reaction of [Rh(micro-Cl)(COD)]2 with 4,6-dimethyl-pyrimidinethiolate (Me2-pymt) and subsequent substitution of COD by CO yields [Rh(Me2-pymt)(CO)2]. The stacking pattern found in this compound is in contradiction with previously studied comparable square-planar complexes of type d8-[M(chelate)(monodentate)2] in which each ligand has different pi-acidic character. A theoretical study of the intermolecular interactions and conformation of the title compound has been carried out, combining semi-empirical band calculations on the real chains and ab initio(MP2 level) calculations on a model dimer. The combination of electronic and steric effects determines the rotation of the successive monomers and the deviation from linearity of the one-dimensional stacks. Its behaviour in solution is also special, developing a blue colour and forming micelles, when adding water to acetone solutions.

Role of Surface Intramolecular Dynamics in the Efficiency of Energy Transfer in Ne Atom Collisions with a n-Hexylthiolate Self-Assembled Monolayer

The energy-transfer dynamics associated with Ne atom collisions with a n-hexylthiolate self-assembled monolayer (SAM) surface at 20 kcal/mol collision energy are studied in chemical dynamics simulations by using both harmonic/separable and anharmonic/coupled surface models and by considering a SAM in both its classical potential energy minimum and containing a 293 K energy distribution. For the anharmonic surface, excitation of higher-energy potential energy minima arising from different intermolecular conformations of the alkyl chains and intramolecular vibrational energy redistribution (IVR) between the surface modes during the collision enhance the energy transfer from Ne atom translation to the surface. IVR is efficient for the alkyl chain's torsional modes and intramolecular chain-bending modes and occurs on the time scale of the Ne atom collisions. It does not occur during the collisions for other modes, such as the higher-frequency intrachain CCC bends. This IVR between surface modes, during the co...

Biophysical Characterization of Triacyl Monosaccharide Lipid A Partial Structures in Relation to Bioactivity

Synthetic triacyl glucosamine monosaccharide lipid A part structures corresponding to the non-reducing moiety of enterobacterial lipid A with an acyloxyacyl chain linked to position 3 of the glucosamine and an unbranched chain linked to position 2 (group 1) and vice versa (group 2) were analyzed biophysically: Fourier-transform infrared spectroscopy was performed to characterize the gel-to-liquid crystalline phase transition, the phosphate band contour, and the orientation of the glucosamine with respect to the membrane surface. Small-angle x-ray diffraction was applied for the elucidation of the supramolecular aggregate structure and, with that, of the molecular shape. With fluorescence resonance energy transfer the lipopolysaccharide-binding protein (LBP)-mediated intercalation of the lipid A partial structures into phospholipid liposomes was monitored. The physical data clearly exhibit a classification of the synthetic compounds into two groups: group 1 compounds have sharp phase transitions, indicating dense acyl chain packing and an inclination of the glucosamine backbone with respect to the membrane surface of 30° with the phosphate buried in the membrane. Group 2 compounds have a very broad phase transition, indicating poorly packed acyl chains, and an inclination of −30° with the phosphate group sticking outward. For the first group unilamellar phases are observed superimposed by a non-lamellar structure, and for the second one only multilamellar aggregate structures. The cytokine-inducing capacity in human mononuclear cells is relatively high for the first group and low or absent for the second group. Based on these data a model of the intra and intermolecular conformations is proposed which also extends the concept of “endotoxic conformation.”

Measuring the elastic properties of protein crystals by brillouin scattering

We report preliminary measurements of the elastic properties of tetragonal lysozyme crystals using Brillouin scattering. This microscopic, non-contact technique is ideally suited for study of fragile, optically transparent macromolecular crystals. Brillouin scattering should allow much more complete characterization of crystal elasticity, and provide a novel probe of intermolecular interactions, conformation changes, and defect formation.

Structural analysis of G-DNA in solution: A combination of polarized and depolarized dynamic light scattering with hydrodynamic model calculations.

Specific intra- and intermolecular quadruplex conformations of model G-DNA oligonucleotides have been identified from their translational and rotational diffusion coefficients in aqueous solution. The transport properties were determined by polarized and depolarized dynamic light scattering. A comparison with hydrodynamic model calculations provides detailed information about the size and shape of the molecules and allows one to distinguish between alternative intra- and intermolecular association. The potential of this combination of methods to elucidate biomolecular structures in solution, to characterize conformational changes, and follow intermolecular interaction processes due to a response to external stimuli has been discussed.

Conformational studies of synthetic lipid A analogues and partial structures by infrared spectroscopy

Synthetic lipid A analogues and partial structures were analyzed and compared with natural hexaacyl lipid A from E. coli applying Fourier transform infrared spectroscopy. The investigations comprised (i) the measurement of the β ⇔ α phase transition of the acyl chains via monitoring of the symmetric stretching vibration of the methylene groups, (ii) an estimation of the supramolecular aggregate structures evaluating vibrations from the interface like ester carbonyl and applying theoretical calculations (iii) a determination of the inter- and intramolecular conformations monitoring functional groups from the interface and the diglucosamine backbone (ester carbonyl, phosphate). The phase transition temperature T c was found to be nearly a linear function of the number of acyl chains for most bisphosphoryl compounds indicating comparable packing density, whereas the deviating behaviour of some samples indicated a higher packing density. From the determination of the supramolecular aggregate structures (cubic, H II) of natural hexaacyl lipid A by X-ray small-angle diffraction, the existence of the same aggregate structures also for the synthetic hexaacyl lipid A was deduced from the nearly identical thermotropism of the ester carbonyl band. From this, a good approximation of the supramolecular structures of all synthetic samples was possible on the basis of the theory of Israelachvili. The analysis of the main phosphate band, together with that of the T c data and former colorimetric results, allowed the establishment of a model of the intermolecular conformations of neighbouring lipid A/LPS molecules. The biological relevance of the findings is discussed in terms of the strongly varying biological activity (between high and no activity) of the samples.

Synthetic putative transmembrane region of minimal potassium channel protein (minK) adopts an alpha-helical conformation in phospholipid membranes.

Minimal potassium channel protein (minK) is a potassium channel protein consisting of 130 amino acids, possessing just one putative transmembrane domain. In this study we have synthesized a peptide with the amino acid sequence RDDSKLEALYILMVLGFFGFFTLGIMLSYI, containing the putative transmembrane region of minK, and analysed its secondary structure by using Fourier-transform IR and CD spectroscopy. The peptide was virtually insoluble in aqueous buffer, forming intermolecular beta-sheet aggregates. On attempted incorporation of the peptide into phospholipid membranes with a method involving dialysis, the peptide adopted a predominantly intermolecular beta-sheet conformation identical with that of the peptide in aqueous buffer, in agreement with a previous report [Horvàth, Heimburg, Kovachev, Findlay, Hideg and Marsh, (1995) Biochemistry 34, 3893-3898]. However, by using an alternative method of incorporating the peptide into phospholipid membranes we found that the peptide adopted a predominantly alpha-helical conformation, a finding consistent with various proposed structural models. These observed differences in secondary structure are due to artifacts of aggregation of the peptide before incorporation into lipid.

Protein supramolecular systems for molecular information processing

Several protein supramolecular systems have been assembled for processing molecular information through intramolecular transfer of conformational change on the model of the biomolecular information network in biological systems. Intermolecular conformation transfer systems consist of calmodulin and phosphodiesterase. Calmodulin selectively binds calcium ions with a resulting change in its conformation that causes phosphodiesterase to change its conformation on being activated. Intermolecular transfer of conformational change has been successfully performed in response to the calcium ion by three different supramolecular systems: (1) calmodulin covalently conjugated with phosphodiesterase and immobilized on solid matrix; (2) lipid-conjugated calmodulin of monolayer on the water surface and coupled with phosphodiesterase in solution and (3) genetically engineered calmodulin self-assembled on a solid matrix and coupled with phosphodiesterase in solution. These supramolecular systems were found to be responsive to such environmental conditions as calcium ion concentration in the reversible alteration of enzyme activity.

The XIIth Seminar on Intermolecular Interaction and Conformations of Molecules

Symposia and seminars on intermolecular interaction and conformations of molecules constitute one of the most efficient directions of activity of the Crystal Chemistry Section of the Scientific Council on Chemical Kinetics and Structure of the RAS. They were initiated in 1971. Since then, eight symposia attended by up to 300 participants each (over a period from 1972 to 1990) and twelve seminars were held. Initially, these were Moscow seminars (up to 1979), and then they took on the status of All-Union seminars. The XIIth Seminar was held in Kharkov on October 3--8, 1994. About 100 scientists from 55 scientific centers (mostly of Russia and Ukraine) participated in it. The main attention was focused on the theoretical calculation studies as well as the most significant experimental works that contain fundamentally new information or point to new ingenious ways for the development of this branch of science. Investigations dealing with computer simulation; comprehensive studies of structure-dependent properties of chemical compounds carried out using modern physical methods; a series of works considering partially ordered specific objects (such as Langmuir--Blodgett films); biochemical and biophysical works dealing with studies of the dependence of biological activity or biological functions on the atomic and molecular structures of systems and interatomic or intermolecular forces were presented at the Seminar. In recent years, the reports presented at these Seminars have been published as collective thematic selections (Zhurnal Fizicheskoi Khimii [Russian Journal of Physical Chemistry (Engl. Transl.)], No. 1 and 2 in 1992, No. 2 in 1993, No. 6 in 1994, No. 1 in 1995). The materials of the XIIth Seminar will be published in Zhurnal Fizicheskoi Khimii [Russian Journal of Physical Chemistry (Engl. Transl.)[, Zhurnal Strukturnoi Khimii [Journal of Structural Chemistry (Engl. Transl)], and Izvestiya Akademii Nauk, Seriya Khimicheskaya [Russian Chemical Bulletin (Engl. Transl.), see the "Physical Chemistry" and "Chemistry of Natural Compounds and Bioorganic Chemistry" sections[.

A Study by Infrared Spectroscopy of the Conformations of Gluten Proteins Differing in their Gliadin and Glutenin Compositions

The conformations of gluten proteins extracted from three near-isogenic lines of the wheat cultivar Sicco, which differed in their high Mr glutenin subunit compositions, were studied by infrared spectroscopy. Whole gluten and gluten fractions prepared by sequential extraction were analysed in solution and in the doughy hydrated state by transmission and attenuated total reflectance spectroscopy, respectively. In the hydrated viscoelastic state, the β-sheet content, especially that of intermolecular β-sheet conformation, of gluten proteins was higher than that in solution. In viscoelastic gluten fractions, the proportion of intermolecular β-sheet increased as the glutenin content increased. In addition, the α-helix content was lowest and the intermolecular β-sheet content highest when disulphide bonds were reduced in the hydrated state because interactions between gluten polypeptides can be maximised under these conditions. These results suggest that the interactions between subunits in glutenin polymers and aggregates involve intermolecular β-sheets located in their repetitive domains or in the region of chain entanglements that are responsible for the viscoelastic properties of gluten proteins.

The Influence of Inter- and Intramolecular Hydrogen Bonding upon the Structure and Photochemistry of 3-(2-Pyridyl)propenamides

The molecular structures and photochemical behavior of (E)- and (Z)-N-methyl-3-(2-pyridyl)-propenamide have been investigated in the solid state and in solution. While the molecular conformation of the thermodynamically more stable E isomer is independent of phase or solvent, the conformation of the Zisomer is dependent upon its environment, adopting an s-trans intramolecular hydrogen-bonded conformation in chlorocarbon solvents, an s-cis conformation in methyl sulfoxide solution, and an orthogonal intermolecular hydrogen-bonded conformation in the solid state. The electronic structure of these molecules has been investigated using the semiemperical INDO/S-SCF-CI (ZINDO) algorithm

Solution conformations and aggregational properties of synthetic amyloid β-peptides of Alzheimer's disease: Analysis of circular dichroism spectra

The A4 or β-peptide (39 to 43 amino acid residues) is the principal proteinaceous component of amyloid deposits in Alzheimer's disease. Using circular dichroism (c.d.), we have studied the secondary structures and aggregational properties in solution of 4 synthetic amyloid β-peptides: β-(1–28), β-(1–39), β-(1–42) and β-(29–42). The natural components of cerebrovascular deposits and extracellular amyloid plaques are β-(1–39) and β-(1–42), while β-(1–28) and β-(29–42) are unnatural fragments. The β-(1–28), β-(1–39) and β-(1–42) peptides adopt mixtures of β-sheet, α-helix and random coil structures, with the relative proportions of each secondary structure being strongly dependent upon the solution conditions. In aqueous solution, β-sheet structure is favored for the β-(1–39) and β-(1–42) peptides, while in aqueous solution containing trifluoroethanol (TFE) or hexafluoroisopropanol (HFIP), α-helical structure is favored for all 3 peptides. The α-helical structure unfolds with increasing temperature and is favored at pH 1 to 4 and pH 7 to 10; the β-sheet conformation is temperature insensitive and is favored at pH 4 to 7. Peptide concentration studies showed that the β-sheet conformation is oligomeric (intermolecular), whereas the α-helical conformation is monomeric (intramolecular). The rate of aggregation to the oligomeric β-sheet structure (α-helix → random coil → β-sheet) is also dependent upon the solution conditions such as the pH and peptide concentration; maximum β-sheet formation occurs at pH 5.4. These results suggest that β-peptide is not an intrinsically insoluble peptide. Thus, solution abnormalities, together with localized high peptide concentrations, which may occur in Alzheimer's disease, may contribute to the formation of amyloid plaques. The hydrophobic β-(29–42) peptide adopts exclusively an intermolecular β-sheet conformation in aqueous solution despite changes in temperature or pH. Therefore, this segment may be the first region of the β-peptide to aggregate and may direct the folding of the complete β-peptide to produce the β-pleated sheet structure found in amyloid deposits. Differences between the solution conformations of the β-(1–39) and β-(1–42) peptides suggests that the last 3 C-terminal amino acids are crucial to amyloid deposition.