Triplet state energy transfer in several proteins.

Energy transfer between excited triplet states of aromatic amino acid residues was observed at 1.4 degrees K. The distance necessary for energy transfer between monomeric tyrosine and tryptophan residues was determined to be roughly 63 A. Total phosphorescence decay rate constants for several proteins were determined while emission corresponding to tyrosine and tryptophan residues was monitored. The observed decay rate constants are interpreted in terms of intramolecular interactions of the polypeptide residues.     

2,3-diphenyl-1,4-naphthoquinone: a potential chemotherapeutic agent against Trypanosoma cruzi

Chagas disease, caused by Trypanosoma cruzi, is a widespread infection in Latin America. Currently, only 2 partially effective and highly toxic drugs, i.e., benznidazole and nifurtimox, are available for the treatment of this disease, and several efforts are underway in the search for better chemotherapeutic agents. Here, we have determined the trypanocidal activity of 2,3-diphenyl-1 ,4-naphthoquinone (DPNQ), a novel quinone derivative. In vitro, DPNQ was highly cytotoxic at a low, micromolar concentration (LD50 = 2.5 microM) against epimastigote, cell-derived trypomastigote, and intracellular amastigote forms of T. cruzi, but not against mammalian cells (LD50 = 130 microM). In vivo studies on the murine model of Chagas disease revealed that DPNQ-treated animals (3 doses of 10 mg/kg/day) showed a significant delay in parasitemia peak and higher (up to 60%) survival rate 70 days post-infection, when compared with the control group (infected, untreated). We also observed a 2-fold decrease in parasitemia between the control group (infected, untreated) and the treated group (infected, treated). No apparent drug toxicity effects were noticed in the control group (uninfected, treated). In addition, we determined that DPNQ is the first competitive inhibitor of T. cruzi lipoamide dehydrogenase (TcLipDH) thus far described. Our results indicate that DPNQ is a promising chemotherapeutic agent against T. cruzi.     

Photoreactions of cisoid 1,4-diphenyl-1,3-butadienes. Direct irradiation in solution and in low temperature organic glass.

The photoreactions of 1,4-diphenyl-1,3-butadienes (DPB) fused with a bicyclo[2.2.1]heptano ring under direct irradiation were examined in solution at room temperature and in organic glass at liquid nitrogen temperature. Photocyclization yielding a phenylnaphthalene compound was shown to be preceded by facile E,E to E,Z photoisomerization. The reverse E,Z to E,E isomerization took place with equal ease in low temperature organic glass and in solution at room temperature. The pattern of reaction at low temperature is consistent with the involvement of the Hula-twist mechanism. However, complexity in conformational population, suggested by ab initio calculated data, made the experimental evidence less clear-cut than in previously reported examples of HT.     

Mapping folding energy landscapes with theory and experiment

The detailed characterization of the overall free energy landscape associated with the folding process of a protein is the ultimate goal in protein folding studies. Modern experimental techniques and all-atom simulations provide a way to obtain accurate thermodynamic and kinetic measurements, but they are oftentimes restricted to probe limited regions of a protein landscape. Although simplified protein models can access larger regions of the landscape, they are built on assumptions and approximations that can affect the accuracy of the results. We review here recent promising approaches that allow to combine the complementary strengths of theory and experiment for a more complete characterization of a protein folding landscape at multiple resolutions. Recent results and possible applications are discussed.     

Gas-phase molecular structures of substituted 1,3-bisketenes: A challenge for theory and experiment

Molecular structures of dimethylbis(trimethylsilylketyl)silane (Me₂Si[C(SiMe₃)CO]₂), dimethylbis(trimethylgermylketyl)silane (Me₂Si[C(GeMe₃)CO]₂), and dimethylbis(trimethylstannylketyl)germane (Me₂Ge[C(SnMe₃)CO]₂) have been studied in the gas phase by electron diffraction accompanied by high level ab initio and DFT calculations. Extensive theoretical conformational analyses of the molecules in the vapour predicted a possibility of existence of two types of conformers with small energy differences. The first type had gauche-gauche arrangements of the ketenyl groups in the central C(CO)XC(CO) fragments directed away from each other. The second type had nearly syn-gauche arrangements of the ketenyl groups. In addition, the energy differences were found to depend on the level of computations used. The experimental analysis, in turn, was unable to distinguish between different conformers due to the large number of similar overlapping distances. The experimental data were fitted by an averaged single-conformer model, which nevertheless allowed reliable determination of bonds and bonded angles in the molecules. Main experimental (r_h1) structural parameters for Me₂Si[C(SiMe₃)CO]₂, Me₂Si[C(GeMe₃)CO]₂, and Me₂Ge[C(SnMe₃)CO]₂, i.e. Me₂X[C(YMe₃)CO]₂ (X,Y = Si, Ge, Sn), are (X-C)_mean 187.7(1) pm, 194.6(2) pm, 216.1(3) pm; (Y-C)_mean, 187.7(1) pm, 188.8(8) pm, 194.6(4) pm; (CC)_mean, 135.3(5) pm, 131.6(5) pm, 131.5(13) pm; (CO)_mean, 117.0(7) pm, 117.4(7) pm, 119.0(11) pm; (C-H)_mean, 110.6(7) pm, 110.0(4) pm, 109.1(13) pm; (X(Y)-CC)_mean, 114.4(2)°, 115.6(1)°, 115.6(2)°; (C-X(Y)-C_Me)_mean, 108.3(3)°, 108.4(3)°, 108.9(13)°; C(2)-C(1)-Y(4)-C(10), −19(6)°, 5(4)°, −9(10)°; C(7)-C(6)-Y(9)-C(38),−22(7)°, −32(3)°, −9(10)°; C(2)-C(1)-X(5)-C(6), 128(4)°, 142(1)°, 108(9)°; C(7)-C(6)-X(5)-C(1), 92(6)°, 115(2)°, 108(9)°, respectively.     

Understanding protein folding via free-energy surfaces from theory and experiment

The ability of protein molecules to fold into their highly structured functional states is one of the most remarkable evolutionary achievements of biology. In recent years, our understanding of the way in which this complex self-assembly process takes place has increased dramatically. Much of the reason for this advance has been the development of energy surfaces (landscapes), which allow the folding reaction to be described and visualized in a meaningful manner. Analysis of these surfaces, derived from the constructive interplay between theory and experiment, has led to the development of a unified mechanism for folding and a recognition of the underlying factors that control the rates and products of the folding process.     

Exposure and risk assessment of 1,3-butadiene in Japan

1,3-Butadiene is on the list of Substances Requiring Priority Action published by the Central Environmental Council of Japan in 1996. Emission of 1,3-butadiene has been controlled by a voluntary reduction program since 1997. Although the industrial emission of 1,3-butadiene in Japan has decreased in recent years, primarily due to a voluntary industrial emissions reduction program, the risks of exposure to it remain largely unknown. We assessed the risks and consequences of exposure to 1,3-butadiene on human health. A remarkable advantage of our risk assessment approach is the detailed assessment of exposure. Previously, we developed two different models that can be applied for the assessment of exposure: the first, the AIST-ADMER model estimates regional concentration distributions, whereas the second, the METI-LIS model estimates concentration distributions in the vicinity of factories. Both models were used for the assessment of exposure to 1,3-butadiene. Using exposure concentration and carcinogenic potency determined and reported by Environment Canada and Health Canada, we evaluated the excess lifetime cancer risk for persons exposed to 1,3-butadiene over the course of a lifetime. The results suggested that the majority of the population in Japan has an excess lifetime cancer risk of less than 10(-5), whereas a small number of people living close to industrial sources had a risk of greater than 10(-5). The results of the present assessment also showed that 1,3-butadiene in the general environment originates primarily from automobile emissions, such that a countermeasure of reducing emissions from cars is expected to be effective at reducing the total cancer risk among Japanese. On the other hand, individual risks among a population living in the vicinity of certain industrial sources were found to be significantly higher than those of the population living elsewhere, such that a reduction in emissions from a small number of specific industrial sources should be realized in order to reduce the high level of individual risk. Based on the results of our assessment, the Industrial Structure Council of the Ministry of Economy, Trade and Industry (METI) in Japan decided to announce that the voluntary reduction program had been successful, and that emissions reductions should no longer be targeted across all industries in general, but instead that such reductions should be carried out in a small number of selected factories that emit excessively large amounts of emissions.     

Triplet state magnetic resonance and fluorescence spectroscopy of metal-substituted hemoglobins.

Fluorescence detected magnetic resonance (FDMR) spectra detected at 596 nm of zinc-substituted hemoglobins at 4.2 K show a split D-E transition, which is not observed for zinc protoporphyrins ligated by methylimidazole in glasses. Incorporation of the zinc heme into the globin pocket is also accompanied by a blue shift of the fluorescence of 20 nm at 4.2 K. FDMR spectra recorded at 576 nm do not show the D-E splitting. The D-E splitting and the huge blue shift are not observed for the magnesium-substituted hemoglobins. Fluorescence measurements at 4.2 K and 77 K, and EPR measurements at 110 K, were carried out to obtain information about the ligation states of the zinc and magnesium protoporphyrins in glasses and in hemoglobin. The results are explained by considering ligation effects and distortion of the porphyrin plane.     

Protein folding: matching theory and experiment.

The impact of folding funnels and folding simulations on the way experimentalists interpret results is examined. The image of the transition state has changed from a unique species that has a strained configuration, with a correspondingly high free energy, to a more ordinary folding intermediate, whose balance between limited conformational entropy and stabilizing contacts places it at the top of the free energy barrier. Evidence for a broad transition barrier comes from studies showing that mutations can change the position of the barrier. The main controversial issue now is whether populated folding intermediates are productive on-pathway intermediates or dead-end traps. Direct experimental evidence is needed. Theories suggesting that populated intermediates are trapped in a glasslike state are usually based on mechanisms which imply that trapping would only be extremely short-lived (e.g., nanoseconds) in water at 25 degrees C. There seems to be little experimental evidence for long-lived trapping in monomers, if folding aggregates are excluded. On the other hand, there is good evidence for kinetic trapping in dimers. alpha-Helix formation is currently the fastest known process in protein folding, and incipient helices are present at the start of folding. Fast helix formation has the effect of narrowing drastically the choice of folding routes. Thus helix formation can direct folding. It changes the folding metaphor from pouring liquid down a folding funnel to a train leaving a switchyard with only a few choices of exit tracks.     

MM3 potential energy surfaces of trisaccharides. II. Carrageenan models containing 3,6-anhydro-D-galactose

The adiabatic potential energy surfaces (PES) of six trisaccharides-namely 3,6-An-alpha-D-Galp-(1-->3)-beta-D-Galp-(1-->4)-3,6-An-alpha-D-Galp, beta-D-Galp-(1-->4)-3,6-An-alpha-D-Galp-(1-->3)-beta-D-Galp, and their derivatives sulfated on positions 2 and 4 of the beta-galactose unit-were obtained using the MM3 force field. Each PES was described by a single contour map for which the energy is plotted against the two psi glycosidic angles, given the small variations of the phi glycosidic torsional angle in the low-energy regions of disaccharide maps. In five of the six examples, the surfaces are those expected from the maps of the disaccharidic repeating units of carrageenans, with less important factors altering the additive effect of both linkages. However, when a sulfate group is present on C2 of a beta-galactose reducing end, a new low-energy minimum in a different region is produced, originated in a hydrogen bond between the first and third monosaccharidic moieties of the trisaccharide. The flexibility of the beta-linkages is nearly identical to that in their disaccharide counterparts, while that of the alpha-linkages is slightly reduced, independent of their presence closer or further away from the reducing end. A fair agreement is observed between the x-ray fiber diffraction analysis for a kappa-carrageenan double helix and the surfaces obtained for the trisaccharide analogs of that polymer.     

Effect of electric field induced transmembrane potential on spheroidal cells: theory and experiment

The transmembrane potential on a cell exposed to an electric field is a critical parameter for successful cell permeabilization. In this study, the effect of cell shape and orientation on the induced transmembrane potential was analyzed. The transmembrane potential was calculated on prolate and oblate spheroidal cells for various orientations with respect to the electric field direction, both numerically and analytically. Changing the orientation of the cells decreases the induced transmembrane potential from its maximum value when the longest axis of the cell is parallel to the electric field, to its minimum value when the longest axis of the cell is perpendicular to the electric field. The dependency on orientation is more pronounced for elongated cells while it is negligible for spherical cells. The part of the cell membrane where a threshold transmembrane potential is exceeded represents the area of electropermeabilization, i.e. the membrane area through which the transport of molecules is established. Therefore the surface exposed to the transmembrane potential above the threshold value was calculated. The biological relevance of these theoretical results was confirmed with experimental results of the electropermeabilization of plated Chinese hamster ovary cells, which are elongated. Theoretical and experimental results show that permeabilization is not only a function of electric field intensity and cell size but also of cell shape and orientation.     

Ion-electron recombination on silica gel surfaces: experiment and modelling.

Kinetics on silica gel and other solid, porous surfaces are often complex. In this paper we have studied the decay kinetics of radical cations produced following multiphoton ionisation on silica gel, and have characterised these using an empirical model. Trends in kinetics have been observed both as a function of concentration and of temperature. Concentration dependent studies suggest heterogeneity of surface adsorption, both in terms of the nature of adsorption sites and aggregation effects. Temperature dependent studies show that the activation energies for surface diffusion correlate with the size of the radical cation, suggesting that its movement rather than that of the electron dominates the observed kinetics. Monte Carlo simulations have been shown to give useful qualitative insights into the interpretation of the extracted parameters, in particular into how apparent distributions of rate constants can arise as a result of low surface dimensionality.     

A stability boundary based method for finding saddle points on potential energy surfaces.

The task of finding saddle points on potential energy surfaces plays a crucial role in understanding the dynamics of a micromolecule as well as in studying the folding pathways of macromolecules like proteins. The problem of finding the saddle points on a high dimensional potential energy surface is transformed into the problem of finding decomposition points of its corresponding nonlinear dynamical system. This paper introduces a new method based on TRUST-TECH (TRansformation Under STability reTained Equilibria CHaracterization) to compute saddle points on potential energy surfaces using stability boundaries. Our method explores the dynamic and geometric characteristics of stability boundaries of a nonlinear dynamical system. A novel trajectory adjustment procedure is used to trace the stability boundary. Our method was successful in finding the saddle points on different potential energy surfaces of various dimensions. A simplified version of the algorithm has also been used to find the saddle points of symmetric systems with the help of some analytical knowledge. The main advantages and effectiveness of the method are clearly illustrated with some examples. Promising results of our method are shown on various problems with varied degrees of freedom.     

Highly trans-1,4 selective polymerization of 1,3-butadiene initiated by iron(III) bis(imino)pyridyl complexes

A series of 2,6-bis(imino)pyridyl iron(III) complexes of the general formula [2,6-(ArNCMe)₂C₅H₃N]FeCl₃ (Ar = -C₆H₅, 3a; 2-MeC₆H₄, 3b; 2-EtC₆H₄, 3c; 2-ⁱPrC₆H₄, 3d; cyclohexyl, 3e; 4-MeC₆H₄, 3f; 4-ⁱPrC₆H₄, 3g; 4-FC₆H₄, 3h and 4-CF₃C₆H₄, 3i), activated by alkylaluminum, MAO or MMAO, have been investigated in 1,3-butadiene polymerization. Iron(III) complex (3a), with the least steric hindrance around the metal center, gives polymer up to 99% in yield in 4 h (butadiene to iron ratio = 1000), and trans-1,4 selectivity about 94.7% at room temperature in toluene, while those (3b-3d) bearing alkyl substituents at the 2-position of each N-aryl ring exhibit much lower catalytic activity and tunable trans-1,4 selectivity. Introduction of an alkyl group at the 4-position (para-position, 3f and 3g) exerts a slightly beneficial effect on the trans-1,4 selectivity, while electronegative groups at the same position (3h and 3i) affect negatively on the activity. The effects of temperature, types of cocatalyst and Al/Fe molar ratio on the polymerization behavior are investigated. More importantly, a mechanism for forming trans-1,4 structure is also proposed.     

Lednev's model: theory and experiment

The results of theoretical and experimental investigations of V.V. Lednev on interactions of weak and extremely weak magnetic fields with biosystems have been reviewed. The period since 1989, when the first version of the interference model has been suggested, until now has been considered. Some mathematical expressions, are presented, which have been published earlier in the papers that are now bibliographic rarity. The results of experimental investigations are also summarized that have been performed in this period under the supervision of V.V. Lednev in the laboratory of biophysics of intracellular regulation in the Institute of Theoretical and Experimental Biophysics of the Russian Academy of Sciences.     

Models for mRNA translation: theory versus experiment.

Three models for mRNA translation are discussed in the light of available experimental data. It is concluded that the elongation rates vary along a messenger, possibly as a result of a coupling between ribosome movement and mRNA secondary structure. Some promising areas of further experimentation are indicated.     

Triplet state spectra and dynamics of geometric isomers of carotenoids

The observation of preferential binding of cis-carotenoids in purple bacterial photosynthetic reaction centers versus trans-isomers in antenna pigment protein complexes has led to the hypothesis that the natural selection of stereoisomers has physiological significance. In order to test this hypothesis, we have undertaken a systematic series of investigations comparing the optical spectroscopic properties and excited state dynamics of cis and trans isomers of carotenoids. The present work compares the triplet state spectra, lifetimes, and energy transfer rates of all-trans-spheroidene and 13,14-locked-cis-spheroidene, the latter of which is incapable of isomerizing to the all-trans configuration, and therefore provides a unique opportunity to examine the triplet state properties of a structurally stable cis molecule. The data reveal only small differences in spectra, decay dynamics, and transfer times and suggest there is little intrinsic advantage in either triplet energy transfer or triplet state decay arising from the inherently different isomeric forms of cis compared to trans carotenoids.