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Conformation of bacteriochlorophyll molecules in photosynthetic proteins from purple bacteria.

Fourier transform near-infrared resonance Raman spectroscopy can be used to obtain information on the bacteriochlorophyll a (BChl a) molecules responsible for the redmost absorption band in photosynthetic complexes from purple bacteria. This technique is able to distinguish distortions of the bacteriochlorin macrocycle as small as 0.02 A, and a systematic analysis of those vibrational modes sensitive to BChl a macrocycle conformational changes was recently published [Näveke et al. (1997) J. Raman Spectrosc. 28, 599-604]. The conformation of the two BChl a molecules constituting the primary electron donor in bacterial reaction centers, and of the 850 and 880 nm-absorbing BChl a molecules in the light-harvesting LH2 and LH1 proteins, has been investigated using this technique. From this study it can be concluded that both BChl a molecules of the primary electron donor in the photochemical reaction center are in a conformation close to the relaxed conformation observed for pentacoordinate BChl a in diethyl ether. In contrast, the BChl a molecules responsible for the long-wavelength absorption transition in both LH1 and LH2 antenna complexes are considerably distorted, and furthermore there are noticeable differences between the conformations of the BChl molecules bound to the alpha- and beta-apoproteins. The molecular conformations of the pigments are very similar in all the antenna complexes investigated.

Bacterial Proteins↗

Mass spectrometric and quantum chemical studies of the thermodynamics and bonding of neutral and ionized LnCl, LnCl2, and LnCl3 species (Ln = Ce, Lu).

The mass spectral patterns of CeCl3(g) and LuCl3(g) and appearance energies for the identified ions were measured using a Nier-type mass spectrometer coupled with a Knudsen cell. The molecular ion CeCl3+ was found to be considerably less stable in comparison to LuCl3+. Partial pressures and sublimation enthalpies of LnCl3(s) to monomeric LnCl3(g) and dimeric Ln2Cl6(g) species were obtained in the ranges of 882-1028 (Ln = Ce) and 850-1004 K (Ln = Lu). The contribution of dimeric Ce2Cl6(g) species to equilibrium vapors of CeCl3(s) is considerably smaller than the Lu2Cl6(g) contribution in LuCl3(s) vapors. The measurements were supplemented by quantum chemical ab initio studies of structures, energetics, and vibrational frequencies of neutral and singly ionized LnCl, LnCl2, and LnCl3 species (Ln = Ce, Lu). The theoretical appearance energies of different ions, calculated from the energies of the gaseous species, are in good agreement with experimental data. The fragmentation energies of LnCl, LnCl2, and LnCl3 were also computed and compared with the mass spectral patterns of respective vapor species. The Mulliken and natural bond orbital electron population methods were applied for the systematic analysis of the bonding scheme in molecules and cations.

Journal Article↗

Thermodynamic Properties of the Rare Earth Element Vapor Complexes LnAl(3)Cl(12) from Ln = La to Ln = Lu.

Systematic analysis of rare earth element complexes has been carefully carried out in the liquid and solid states but not in the gaseous state because of the lack of a complete set of experimental data for any kind of vapor complexes of all rare earth elements. Here we present experimental quenching results which suggest that the LnAl(3)Cl(12) complexes are the predominant vapor complexes roughly in the temperature range 588-851 K and pressure range 0.01-0.22 MPa for all of the 14 rare earth elements Ln = La, Ce, Pr, Nd, Sm, Eu, Gd, Tb, Dy, Ho, Er, Tm, Yb, and Lu. For these elements, thermodynamic functions of the reactions LnCl(3)(s) + (3)/(2)Al(2)Cl(6)(g) = LnAl(3)Cl(12)(g) were calculated from the measurements. Those for the radioelement Pm were smoothly interpolated. The results show Gd divergences from the standard enthalpies and standard entropies from LaAl(3)Cl(12) to LuAl(3)Cl(12).

Journal Article↗

Structural properties of docosahexaenoyl phospholipid bilayers investigated by solid-state 2H NMR spectroscopy.

Polyunsaturated lipids in cellular membranes are known to play key roles in such diverse biological processes as vision, neuronal signaling, and apoptosis. One hypothesis is that polyunsaturated lipids are involved in second messenger functions in biological signaling. Another current hypothesis affirms that the functional role of polyunsaturated lipids relies on their ability to modulate physical properties of the lipid bilayer. The present research has employed solid-state 2H NMR spectroscopy to acquire knowledge of the molecular organization and material properties of polyunsaturated lipid bilayers. We report measurements for a homologous series of mixed-chain phosphatidylcholines containing a perdeuterated, saturated acyl chain (n:0) at the sn-1 position, adjacent to docosahexaenoic acid (DHA, 22:6omega3) at the sn-2 position. Measurements have been performed on fluid (L(alpha))-state multilamellar dispersions as a function of temperature for saturated acyl chain lengths of n = 12, 14, 16, and 18 carbons. The saturated sn-1 chains are therefore used as an intrinsic probe with site-specific resolution of the polyunsaturated bilayer structure. The 2H NMR order parameters as a function of acyl position (order profiles) have been analyzed using a mean-torque potential model for the chain segments, and the results are discussed in comparison with the homologous series of disaturated lipid bilayers. At a given absolute temperature, as the sn-1 acyl length adjacent to the sn-2 DHA chain is greater, the order of the initial chain segments increases, whereas that of the end segments decreases, in marked contrast with the corresponding disaturated series. For the latter, the order of the end segments is practically constant with acyl length, thus revealing a universal chain packing profile. We find that the DHA-containing series, while more complex, is still characterized by a universal chain packing profile, which is shifted relative to the homologous saturated series. Moreover, we show how introduction of DHA chains translates the order profile along the saturated chains, making more disordered states accessible within the bilayer central region. As a result, the area per lipid headgroup is increased as compared to disaturated bilayers. The systematic analysis of the 2H NMR data provides a basis for studies of lipid interactions with integral membrane proteins, for instance in relation to characteristic biological functions of highly unsaturated lipid membranes.

Deuterium↗

The elusive atomic rationale for DNA base pair stability.

A systematic analysis of the electrostatic interaction between 27 natural DNA base pairs was carried out, based on ab initio correlated wave functions and the topology of the electron density. Using high rank multipole moments we show that the atomic partitioning of the interaction energy contains many substantial contributions between distant atoms. Profiles of cumulative energy versus internuclear distance show large fluctuations and provide an electrostatic fingerprint of the partitioning of interaction energy in a complex. A quantified comparison between each pair of energy profiles, one for each base pair, makes clear that there is no correlation between the total base pair interaction energy and the shape of the profile. In other words, base pairs with similar interaction energy are not stable for the same reasons in terms of atomic partitioning. In summary, simple rules to rationalize the pattern of energetic stability of naturally occurring base pairs in terms of subsets of atoms are elusive. Our work cautions against inappropriate use of Jorgensen's secondary interaction hypothesis.

Base Pairing↗

Mediated electrochemistry of horseradish peroxidase. Catalysis and inhibition.

A precise determination of the complex mechanism of catalysis and inhibition involved in the reaction of HRP with H(2)O(2) as substrate and an outersphere single electron donor ([Os(bpy)(2)pyCl](+)) as cosubstrate is made possible by a systematic analysis of the cyclic voltammetric responses as a function of the scan rate and of the substrate and cosubstrate concentrations, complemented by spectrophotometric steady-state and stopped-flow experiments. The bell-shaped calibration curve relating the electrochemical response to the concentration of H(2)O(2) is qualitatively and quantitatively explained by taking into account the conversion of the catalytically active forms of the enzyme into the inactive oxyperoxidase in addition to the primary catalytic cycle. These characteristics should be kept in mind in biosensor applications of HRP. The ensuing analysis and data allow one to predict biosensor amperometric responses in all practical cases. From a mechanistic standpoint, conditions may, however, be defined which render inhibition insignificant, thus allowing an electrochemical characterization of the primary catalytic cycle. At very low concentrations of H(2)O(2), its diffusion tends to control the electrochemical response, resulting in proportionality with H(2)O(2) concentration instead of the square root dependence characteristic of the classical catalytic currents. Intriguing hysteresis and trace crossings behaviors are also quantitatively explained in the framework of the same mechanism. As a consequence of the precise dissection of the rather complex reaction mechanism into its various elementary steps, a strategy may be devised for gaining a better understanding of the mechanism and reactivity patterns of each elementary step.

Catalysis↗

Relationship between side chain structure and 14-helix stability of beta3-peptides in water.

Folded polymers are used in Nature for virtually every vital process. Nonnatural folded polymers, or foldamers, have the potential for similar versatility, and the design and refinement of such molecules is of considerable current interest. Here we report a complete and systematic analysis of the relationship between side chain structure and the 14-helicity of a well-studied class of foldamers, beta(3)-peptides, in water. Our experimental results (1) verify the importance of macrodipole stabilization for maintaining 14-helix structure, (2) provide comprehensive evidence that beta(3)-amino acids branched at the first side chain carbon are 14-helix-stabilizing, (3) suggest a novel role for side chain hydrogen bonding as an additional stabilizing force in beta(3)-peptides containing beta(3)-homoserine or beta(3)-homothreonine, and (4) demonstrate that diverse functionality can be incorporated into a stable 14-helix. Gas- and solution-phase calculations and Monte Carlo simulations recapitulate the experimental trends only in the context of oligomers, yielding insight into the mechanisms behind 14-helix folding. The 14-helix propensities of beta(3)-amino acids differ starkly from the alpha-helix propensities of analogous alpha-amino acids. This contrast informs current models for alpha-helix folding, and suggests that 14-helix folding is governed by different biophysical forces than is alpha-helix folding. The ability to modulate 14-helix structure through side chain choice will assist rational design of 14-helical beta-peptide ligands for macromolecular targets.

Amino Acids↗

A versatile toolbox for variable DNA functionalization at high density.

To broaden the applicability of chemically modified DNAs in nano- and biotechnology, material science, sensor development, and molecular recognition, strategies are required for introducing a large variety of different modifications into the same nucleic acid sequence at once. Here, we investigate the scope and limits for obtaining functionalized dsDNA by primer extension and PCR, using a broad variety of chemically modified deoxynucleotide triphosphates (dNTPs), DNA polymerases, and templates. All natural nucleobases in each strand were substituted with up to four different base-modified analogues. We studied the sequence dependence of enzymatic amplification to yield high-density functionalized DNA (fDNA) from modified dNTPs, and of fDNA templates, and found that GC-rich sequences are amplified with decreased efficiency as compared to AT-rich ones. There is also a strong dependence on the polymerase used. While family A polymerases generally performed poorly on "demanding" templates containing consecutive stretches of a particular base, family B polymerases were better suited for this purpose, in particular Pwo and Vent (exo-) DNA polymerase. A systematic analysis of fDNAs modified at increasing densities by CD spectroscopy revealed that single modified bases do not alter the overall B-type DNA structure, regardless of their chemical nature. A density of three modified bases induces conformational changes in the double helix, reflected by an inversion of the CD spectra. Our study provides a basis for establishing a generally applicable toolbox of enzymes, templates, and monomers for generating high-density functionalized DNAs for a broad range of applications.

Base Sequence↗

Sequence-dependent conformational energy of DNA derived from molecular dynamics simulations: toward understanding the indirect readout mechanism in protein-DNA recognition.

Sequence dependence of DNA conformation plays a crucial role in its recognition by proteins and ligands. To clarify the relationship between sequence and conformation, it is necessary to quantify the conformational energy and specificity of DNA. Here, we make a systematic analysis of dodecamer DNA structures including all the 136 unique tetranucleotide sequences at the center by molecular dynamics simulations. Using a simplified conformational model with six parameters to describe the geometry of adjacent base pairs and harmonic potentials along these coordinates, we estimated the equilibrium conformational parameters and the harmonic potentials of mean force for the central base-pair steps from many trajectories of the simulations. This enabled us to estimate the conformational energy and the specificity for any given DNA sequence and structure. We tested our method by using sequence-structure threading to estimate the conformational energy and the Z-score as a measure of specificity for many B-DNA and A-DNA crystal structures. The average Z-scores were negative for both kinds of structures, indicating that the potential of mean force from the simulation is capable of predicting sequence specificity for the crystal structures and that it may be used to study the sequence specificity of both types of DNA. We also estimated the positional distribution of conformational energy and Z-score within DNA and showed that they are strongly position dependent. This analysis enabled us to identify particular conformations responsible for the specificity. The presented results will provide an insight into the mechanisms of DNA sequence recognition by proteins and ligands.

Base Sequence↗

Intermolecular charge transfer between heterocyclic oligomers. Effects of heteroatom and molecular packing on hopping transport in organic semiconductors.

For electron or hole transfer between neighboring conducting polymer strands or oligomers, the intrinsic charge-transfer rate is dictated by the charge-resonance integral and by the reorganization energy due to geometric relaxation. To explain conduction anisotropy and other solid-state effects, a multivariate, systematic analysis of bandwidth as a function of intermolecular orientations is undertaken for a series of oligoheterocycles, using first-principles methods. While cofacial oligomers show the greatest bandwidths at a given intermolecular C-C contact distance, for a fixed center-to-center intermolecular distance, tilted pi-stacking increases pi-overlap (particularly for LUMO orbitals) and decreases electrostatic repulsion, yielding optimum tilt angles for packing of approximately 40-60 degrees at small intermolecular separations. The calculations also reveal that bandwidths and intrinsic mobilities of holes and electrons in conjugated oligoheterocycles can be quite comparable.

Journal Article↗

An antiparallel alpha-helical coiled-coil model system for rapid assessment of side-chain recognition at the hydrophobic interface.

Both parallel and antiparallel alpha-helical coiled-coil dimers are common among proteins; however, biophysical scrutiny has focused almost entirely on parallel dimers. We describe the development of a model system that enables efficient and systematic analysis of hydrophobic packing between antiparallel alpha-helices. Our findings reveal significant differences in packing preferences between parallel and antiparallel coiled-coils.

Amino Acid Sequence↗

Pentagonal dodecahedranes: polyfunctionalization and MS fragmentation.

With the use of four- to eight-fold functionalized dodecahedranes (1-3), opportunities to arrive at highly strained dodecahedranes with two to four pairs of vicinal, eclipsed bromine substituents through front-side substitution and addition reactions have been explored. In standard processes, the interception of beta-OCH(3) radical/cationic intermediates was not problematic (9-12, 37, 50). The interception of beta-CO(2)R radicals was possible for Cl(*) (18) but not for Br(*) (17). The interception of beta-chloro radicals was possible for Cl(*) (27) but not for Br(*) (26), and the interception of beta-Br cations ("bromonium ions") with Br(-) was modest (45) to highly inefficient (24, 26). Two X-ray structural analyses (dimethoxy dibromide 9 and tetramethoxy tetrabromide 53) indicated the structural consequences of the molecular strain introduced by the two (four) vicinal CH(3)O/Br pairs. A systematic analysis of the MS spectra confirms that, in virtually all cases studied, the elimination of the substituents occurs without significant carbon-cage disruption, leading ultimately to multiply unsaturated dodecahedral ions for dodecahedrahexa(C(20)H(8))enes, -hepta(C(20)H(6))enes, and -octa(C(20)H(4))enes.

Journal Article↗

Vibrational energy relaxation rates via the linearized semiclassical approximation: applications to neat diatomic liquids and atomic-diatomic liquid mixtures.

We report the results obtained from the application of our previously proposed linearized semiclassical method for computing vibrational energy relaxation (VER) rates (J. Phys. Chem. A 2003, 107, 9059, 9070) to neat liquid oxygen, neat liquid nitrogen, and liquid mixtures of oxygen and argon. Our calculations are based on a semiclassical approximation for the quantum-mechanical force-force correlation function, which puts it in terms of the Wigner transforms of the force and the product of the Boltzmann operator and the force. The calculation of the multidimensional Wigner integrals is made feasible by the introduction of a local harmonic approximation. A systematic analysis has been performed of the temperature and mole-fraction dependences of the VER rate constant, as well as the relative contributions of centrifugal and potential forces, and of different types of quantum effects. The results were found to be in very good quantitative agreement with experiment, and they suggest that this semiclassical approximation can capture the quantum enhancement, by many orders of magnitude, of the experimentally observed VER rate constants over the corresponding classical predictions.

Algorithms↗

Transfer of parahydrogen-induced hyperpolarization to 19F.

Homogeneous hydrogenations of unsaturated substrates with parahydrogen yield strong NMR signal enhancements of the transferred 1H nuclei if the symmetry of H2 is broken in the resulting hydrogenated products. This chemically induced hyperpolarization known as Parahydrogen-induced polarization (PHIP) is also transferred to other protons and heteronuclei (2H, 13C, 29Si, 31P) when the hydrogenation is initiated at low magnetic fields. Hydrogenating various fluorinated styrenes and phenylacetylenes, we show that PHIP-derived hyperpolarization is transferred to 19F not only in the Earth's magnetic field (ALTADENA condition) but also in a strong magnetic field, e.g., when carrying out the reaction in the NMR spectrometer (PASADENA condition). Upon conducting a systematic analysis of the observed PHIP transfer to 1H, 13C, and 19F in the hydrogenation products to elucidate the mechanisms that govern this parahydrogen-aided resonance transfer (PART), we conclude that high- and low-field PHIP transfer mechanisms differ in detail depending on either through-bond or through-space interactions. Substrates with high hydrogenation rates and long spin-lattice relaxation times (T1) yield the highest degree of heteronuclear hyperpolarization. Possible medical applications for hyperpolarized 19F-containing molecules as "active" contrast agents for magnetic resonance imaging (MRI) are outlined.

Fluorine Radioisotopes↗

Weak first-order tilting transition in monolayers of mono- and bipolar docosanol derivatives.

A systematic analysis of pressure-area isotherms and grazing incidence X-ray diffraction (GIXD) data of 22-methoxydocosan-1-ol (H3C-O-(CH2)22-OH, MDO), docosan-1-ol (H3C-(CH2)21-OH, DO), and docosyl methyl ether (H3C-(CH2)21-O-CH3, DME) monolayers on pure water between 10 and 35 degrees C is presented. All monolayers form fully condensed phases in the investigated temperature region. The GIXD data reveal that the monolayers exhibit the phase sequence -S at lower temperature and -LS at higher temperature. Phase diagrams have been established. Inserting a second hydrophilic group at the opposite end of the molecule (bipolar MDO) shifts the S/LS boundary to higher temperatures. All monolayers exhibit herringbone (HB) packing at lower temperatures. The "kink" in the isotherms observed at lower temperatures is replaced by a very small plateau region at higher temperatures. The entropy changes connected with this weak first-order tilting transition are much smaller compared with the first-order transition from liquid-expanded (LE) to condensed (LC). Additionally, this transition is endothermic in contrast to the LE/LC transition. The reason for the endothermic transition is the weaker positional correlation in the nontilted state compared with the tilted one. The appearance of the weak first-order endothermic transition can be connected with the changed phase sequence. X-ray photoelectron spectroscopy (XPS) measurements provide information about the polar group orientation. Considerations based on GIXD and XPS data as well as adhesion energy of the different terminal end groups lead to the conclusion that the hydroxyl group of the bipolar MDO is attached to the water surface while the methoxy group is in contact with air. The presented results show that the second hydrophilic group influences the monolayer properties in a mild way.

Fatty Alcohols↗

Flux enhancement effects of ionic surfactants upon passive and electroosmotic transdermal transport.

This study focused upon the enhancement effects of ionic surfactants upon passive and electroosmotic transdermal flux. The first phase of the study involved validating theories relating surface properties of a membrane to electroosmotic solvent flow under appropriate experimental conditions using a synthetic model membrane (stack of 50 Nuclepore membranes). Numerical solutions to the Poisson-Boltzmann equation and the equations of fluid motion served as the theoretical basis for the experimental studies. Important outcomes of the model membrane studies were that electroosmotic solvent flow velocity was enhanced by the addition of an anionic surfactant, sodium dodecyl sulfate, and reversed by the addition of a cationic surfactant, dodecyltrimethylammonium bromide. The effective membrane pore wall surface charge densities were determined under a variety of experimental conditions. Adsorption of dodecyl sulfate to the pore wall increased the net negative charge on the pore wall. A reversal of the net pore wall surface charge density resulted from the adsorption of dodecyltrimethylammonium. The interrelationship between electroosmosis, surfactant adsorption, and ionic strength was also evaluated. The second phase of the study was an investigation of the effects of sodium dodecyl sulfate upon the transport of neutral polar permeants through human epidermal membrane (HEM). Fluxes of [14C]urea and [3H]sucrose were simultaneously measured across HEM samples under passive and 250 mV conditions; flux measurements were made before, during, and after HEM exposure to sodium dodecyl sulfate. A systematic analysis of the experimental data made it possible to elucidate the specific contributions of sodium dodecyl sulfate and the applied electric potential to the overall flux enhancement. Sodium dodecyl sulfate enhanced the intrinsic passive permeability of the HEM, and it also enhanced the contribution of electroosmosis to the flux during iontophoresis.

Humans↗

Surface modification of an ethylene-acrylic acid copolymer film: grafting amine-terminated linear and branched architectures.

Polymer films can be tailored for a specific application by modifying their surface properties. In this study, linear and branched architectures were grafted to ethylene-acrylic acid (EAA) copolymer films using the so-called grafting from approach. Dicyclohexylcarbodiimide was used to activate the carboxylic acid functionality on the surface of the EAA copolymer film before reacting it with selected di- and tri-amine compounds. The carboxylic acid functionality was subsequently regenerated by reacting the amine-grafted film with succinic anhydride. These reaction steps were then repeated to create the linear and branched architectures on the EAA film surface. The film surface resulting from each reaction step was analyzed using attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy and contact angle measurements. A systematic analysis of the ATR-FTIR results was performed to estimate the average conversion of the reaction schemes and to explain the observed contact angle results. A significant reduction in water contact angle for the EAA film grafted with a branched architecture was observed. The EAA film grafted with a linear architecture showed a marginal reduction in water contact angle when ethanol was used as a solvent for ethylenediamine. When the solvent for ethylenediamine was changed to water, the contact angle decreased noticeably. However, analysis of control films showed that the reduction in the contact angles was due to the solvent treatment. In the case of branched architectures, such reduction in contact angle due to the solvent treatment was not observed. Several control experiments were performed to ensure that the reduction in the contact angles was in fact due to the grafted species and not due to exposure to various solvents used in the reaction scheme.

Journal Article↗

Sequence-independent helical wrapping of single-walled carbon nanotubes by long genomic DNA.

Because of their nanometer sizes and molecular recognition capabilities, biological systems have garnered much attention as vehicles for the directed assembly of nanoscale materials.(1-6) One of the greatest challenges of this research has been to successfully interface biological systems with electronic materials, such as semiconductors and metals. As a means to address some of these issues, Sarikaya, Belcher, and others have used a combinatorial technique called phage display(7-9) to discover new families of peptides that showed binding affinities to various substrates. More recently, Zheng and co-workers used combinatorial DNA libraries to isolate short DNA oligomers (30-90 bases) that could disperse single-walled carbon nanotubes (SWCNT) in water.(10) Through a systematic analysis, they found that short oligonucleotides having repeating sequences of gunanines and thymines (dGdT)(n) could wrap in a helical manner around a CNT with periodic pitch.(11) Although helix formation around SWCNTs having regular pitches is an effective method for dispersing and separating CNTs, the need for specific repeating sequences limits use to non-natural DNA that must be synthesized with optimal lengths of less than 150 bases. In contrast, we demonstrate here that long genomic single-stranded DNA (>>100 bases) of a completely random sequence of bases can be used to disperse CNTs efficiently through the single-stranded DNA's (ssDNA) ability to form tight helices around the CNTs with distinct periodic pitches. Although this process occurs irrespective of the DNA sequence, we show that this process is highly dependent on the removal of complementary strands. We also demonstrate that although the helix pitch-to-pitch distances remain constant down the length of a single CNT, the distances are variable from one DNA-CNT to another. Finally, we report initial work that shows that methods developed to align long dsDNA can be applied in a similar fashion to produce highly dense arrays of aligned ssDNA-CNT hybrids.

DNA, Single-Stranded↗