How proteins trigger excitation energy transfer in the FMO complex of green sulfur bacteria

A simple electrostatic method for the calculation of optical transition energies of pigments in protein environments is presented and applied to the Fenna-Matthews-Olson (FMO) complex of Prosthecochloris aestuarii and Chlorobium tepidum. The method, for the first time, allows us to reach agreement between experimental optical spectra and calculations based on transition energies of pigments that are calculated in large part independently, rather than fitted to the spectra. In this way it becomes possible to understand the molecular mechanism allowing the protein to trigger excitation energy transfer reactions. The relative shift in excitation energies of the seven bacteriochlorophyll-a pigments of the FMO complex of P. aestuarii and C. tepidum are obtained from calculations of electrochromic shifts due to charged amino acids, assuming a standard protonation pattern of the protein, and by taking into account the three different ligand types of the pigments. The calculations provide an explanation of some of the earlier results for the transition energies obtained from fits of optical spectra. In addition, those earlier fits are verified here by using a more advanced theory of optical spectra, a genetic algorithm, and excitonic couplings obtained from electrostatic calculations that take into account the influence of the dielectric protein environment. The two independent calculations of site energies strongly favor one of the two possible orientations of the FMO trimer relative to the photosynthetic membrane, which were identified by electron microscopic studies and linear dichroism experiments. Efficient transfer of excitation energy to the reaction center requires bacteriochlorophylls 3 and 4 to be the linker pigments. The temporal and spatial transfer of excitation energy through the FMO complex is calculated to proceed along two branches, with transfer times that differ by an order of magnitude.     

Electro-optical properties of carboxymethylcellulose. I. Concentration and ionic strength dependence

The experimental conditions for studying the electro-optical properties of a natural, modified polyelectrolyte, carboxymethylcellulose (DS 1.3; DP 180) were determined. The transient Kerr effect was found to be a function of CMC concentration, field strength, and ionic strength, I. If the concentration and I were low enough (c < 20 mg.l^?1), saturation was obtained for field strengths of approximately 15 kV.cm^?1. The optical anisotropy was shown to be independent of I; the electrical anisotropy decreased sharply when I increased. These results are discussed in connection with polarization theories of polyelectrolytes. The molecular dimensions of carboxymethylcellulose, calculated from the birefringence kinetics, suggest that the molecule is a rigid rod.     

Theory of optical spectra of photosystem II reaction centers: location of the triplet state and the identity of the primary electron donor

Based on the structural analysis of photosystem II of Thermosynechococcus elongatus, a detailed calculation of optical properties of reaction-center (D1-D2) complexes is presented applying a theory developed previously. The calculations of absorption, linear dichroism, circular dichroism, fluorescence spectra, all at 6 K, and the temperature-dependence of the absorption spectrum are used to extract the local optical transition energies of the reaction-center pigments, the so-called site energies, from experimental data. The site energies are verified by calculations and comparison with seven additional independent experiments. Exciton relaxation and primary electron transfer in the reaction center are studied using the site energies. The calculations are used to interpret transient optical data. Evidence is provided for the accessory chlorophyll of the D1-branch as being the primary electron donor and the location of the triplet state at low temperatures.     

Ab initio calculations of the pyrophosphate hydrolysis reaction.

Ab initio quantum mechanical calculations were used to study the hydrolysis reaction H4P2O7 + H2O in equilibrium with 2H3PO4, as well as some molecular properties of the reactants and products. SCF calculations with several basis sets ranging from minimal to extended with polarization functions were used to look at the basis dependency of the reaction enthalpies and optimized geometries. Although the minimal basis sets yield erratic predictions of the enthalpy, when a more extended basis (3-21G*) was used for the geometry optimization, and the total energies of the reactants and products were computed with this and larger basis sets, we obtained more consistent predictions of the structural properties of the P-O-P bridge and of the heat of the hydrolysis reaction (delta E = -7.39 kcal/mol at the SCF/6-31G** level). A comparison is made with previous estimates performed with smaller basis sets and without taking into account the electron correlation effects, which are calculated in the present work. The inclusion of the zero point energy calculated using the harmonic approximation, and of the electronic correlation energy determined at the MBPT(2) level, raised the computed heat of the reaction to -3.83 kcal/mol, and when an estimate for the thermal energy was added, the value obtained was of -3.38 kcal/mol. In conclusion, we found that the hydrolysis of pyrophosphate should be exothermic in the gas phase. The implications of this result in relation to some recent theories about enzyme catalysis are discussed.     

Calculating proton uptake/release and binding free energy taking into account ionization and conformation changes induced by protein-inhibitor association: application to plasmepsin, cathepsin D and endothiapepsin-pepstatin complexes

The protein-inhibitor binding energies of enzymes are often pH dependent, and binding induces either proton uptake or proton release. The proton uptake/release and the binding energy for three complexes with available experimental data were numerically studied: pepstatin-cathepsin D, pepstatin-plasmepsin II and pepstatin-endothiapepsin. Very good agreement with the experimental data was achieved when conformational changes were taken into account. The role of the desolvation energy and the conformational changes was revealed by modeling the complex, the separated molecules in the complex conformation and the free molecules. It was shown that the conformational changes induced by the complex formation are as important for the proton transfer as the loss of solvation energy caused by the burial of interface residues. The residues responsible for the proton transfer were identified and their contribution to the proton uptake/release calculated. These residues were found to be scattered along the whole protein rather than being localized only at the active site. In the case of cathepsin D, these residues were found to be highly conserved among the cathepsin D sequences of other species. It was shown that conformation and ionization changes induced by the complex formation are critical for the correct calculation of the binding energy. Taking into account the electrostatics and the van der Waals (vdW) energies within the Boltzmann distribution of energies and allowing ionization and conformation changes to occur makes the calculated binding energy more realistic and closer to the experimental value. The interplay between electrostatic and vdW forces makes the pH dependence of the binding energy smoother, because the vdW force acts in reaction to the changes of the electrostatic energy. It was found that a small fraction of the ionizable groups remain uncharged in both the free and complexed molecules. The sequence and structural position of these groups aligns well within the three proteases, suggesting that these may have specific role.     

Orientation and spectral properties of two stilbazolium merocyanine dyes in stretched and unstretched polyvinyl alcohol films

Spectral properties (anisotropy coefficients calculated for absorption, emission and fluorescence decay time) of two stilbazolium merocyanine dyes have been determined to evaluate the applicability of these dyes as sensitizers in photodynamic therapy. The dyes were embedded in an anisotropic polymer matrix. Analysis of the emission decay components measured in polarized light provides information on the interactions of the dye molecules with the polymer matrix being a model of an anisotropic biological system. Different values of the emission anisotropies obtained from various polarized components of fluorescence decays have shown that the orientations of the dye molecules influence their interactions with the polymer. This means that differently oriented dye molecules located in biological systems should exhibit different interactions with membranes. The chain length and type of side groups attached as well as the salt form of the dye molecule were shown to influence the dye-polymer interactions and should be taken into account before the application of merocyanine dyes in medicine. These dyes seem to be promising optical sensors with spectral properties, including the calculated anisotropy coefficients, sensitive to the molecular environment, useful to study orientation and interaction with neighbouring molecules in biological membranes.     

Dependence of some conformational properties of polyglycine on composition and sequence of secondary structure

The values of four conformational properties, unperturbed dimensions 0, dipole moment , mean squared optical anisotropy and molar Kerr constant have been calculated for polyglycine chains of x = 100 repeat units with varying composition of alpha-helix, beta-sheet and random coil conformations. The influence of the conformational sequence on these properties has been investigated by calculating the four above-mentioned properties together with the end-to-end vector for several polyglycine oligomers.     

Influence of the solvent on the conformational-dependent properties of random-coil polypeptides. I. The mean-square of the end-to-end distance and of the dipole moment

Conformational energies for the N-acetyl-N'-methylamides of the 20 natural amino acids were calculated, including the solvent effects, as functions of the angles phi and psi for rotation of the main chain and for six positions chi 1 of the C alpha-C beta bond in the side chain (fixed values for chi 2, chi 3, ...). The computed energies were used to evaluate the mean-square end-to-end distance and mean-square dipole moment of homopolypeptides of the 20 natural amino acids. Ten proteins and three enzymes of current interest were also studied. Slight differences in both properties are found on taking the effects of solvent into consideration. Comparison with other computational and experimental results is made.     

Theoretical and experimental study of the Norrish I photodissociation of aromatic ketones.

A set of selected acetophenone derivatives was investigated using absorption and emission spectroscopy, laser flash photolysis and DFT calculations. The triplet state lifetimes and the activation energy of the cleavage reaction were measured. Computed triplet-triplet absorption spectra were found in very good agreement with the experimental ones. Bond dissociation energies, activation energies, partial charges, ground state geometries were calculated. The transition state theory TST was successfully used to calculate the cleavage rate constants: a very good correlation was found between the experimental and the calculated values. It is found that the entropy change influences the preexponential factor. This study also points out the role of the partial charges in the transition state, although this effect alone does not account for the reaction rate constants.     

Partitioning of tryptophan side-chain analogs between water and cyclohexane.

We have measured the partitioning of the tryptophan side-chain analogs 3-methylindole and N-methylindole between water and cyclohexane over the temperature range 8-55 degrees C to investigate the relative contribution of the imine-NH- to the free energy of transfer. We take advantage of the fact that the indole imine nitrogen is blocked by a methyl group in N-methylindole. Unlike previous studies, we take into account the water present in the cyclohexane phase. Free energies of partitioning were calculated using mole-fraction, volume-fraction, and Flory-Huggins-corrected volume-fraction partition coefficients [De Young, L. R., & Dill, K. A. (1990) J. Phys. Chem. 94, 801-809; Sharp, K. A., Nicholls, A., Friedman, R., & Honig, B. (1991) Biochemistry 30, 9686-9697]. These approaches account for configurational entropy changes in different ways and thus lead to different values for the calculated free energies of transfer. There is a 2-3-fold difference in the free energies calculated from our measurements, using the different units. Independent of units, the partitioning of both compounds involves identical entropy changes. However, 3-methylindole has an additional unfavorable enthalpic contribution to partitioning into cyclohexane of +1.6 kcal/mol (independent of units) which is presumably the cost of removing the indole -NH- group from water and transferring it to cyclohexane. In cyclohexane, 3-methylindole forms hydrogen bonds with water that cause water to copartition into cyclohexane with the solute. A method is described which allows the partitioning process to be examined independent of subsequent interactions with water in the solvent.     

Theoretical investigation of the effect of sugar substitution on the antioxidant properties of flavonoids

Natural flavonoids are secondary phenolic plant metabolites known for their bioactivity as antioxidants. The evaluation of this property is generally done by the estimation of their direct free radical-scavenging activity as hydrogen or electron donating compounds. This paper reviews experimental results available in the literature for a selection of flavonoids and compares them with calculated quantities characteristic of the hydrogen or electron donation. For that purpose, bond dissociation energies, ionization potentials and electron transfer enthalpies are computed by using DFT methods and the ONIOM procedure implemented in the ab initio program Gaussian. This process has been chosen because it can be extended to the study of large molecules. When acid dissociation and interaction with the solvent are taken into account, the results present very good concordance with experimental results, enlightening the complexity of the processes involved in the classical assays which measure the ability of compounds to scavenge the (2,2'-azinobis-(3-ethylbenzthiazoline-6-sulfonic acid) diammonium salt) radical cation (ABTS (+)) or the 2,2-diphenyl-1-picryl-hydrazyl radical (DPPH(·)). This study demonstrates the good accuracy of theoretical calculations in obtaining the relative energies involved in free radical scavenging abilities and its capacity for predictive behaviour. It also highlights the necessity to take into account the pK(a) of the compounds and the solvent interaction. The ability of the method to calculate the antioxidant properties of larger molecules are tested on glycosylated flavonoids and the effects of sugar substitution on the antioxidant properties of flavonoids are investigated, pointing out the importance of the charges on the oxygen atoms.     

Dielectric properties of the polar head group region of zwitterionic lipid bilayers.

A theoretical model describing the dielectric properties of the lipid membrane-water interface region was developed. The rotating polar head groups (e.g. phosphatidylcholine) were simulated as a collection of interacting dipoles imbedded in a nonhomogeneous dielectric. The interactions between the nearest neighborhood were explicitly taken into account, while the other interactions were evaluated by means of the continuum theories. The values of the dielectric constant, its anisotropy and the spontaneous polarization of the interface were evaluated. As an application, we calculated the energy of interaction between an ion and the membrane polar head group region. The results indicate a small spontaneous polarization of the interface (1-1.7 Debyes per lipid molecule) due to the tilting angle of the choline residue with respect to the membrane surface. This dipolar field partially compensates that of opposite orientation originating from the ester group region, giving calculated overall dipolar potentials in better agreement with the experimental data. Our model suggests also a very strong dielectric anisotropy of the interface region, the component of the dielectric constant perpendicular to the membrane plane being much smaller than the parallel component.     

Parameterization and optimization of the menthol force field for molecular dynamics simulations

Menthol’s various biological properties render it a useful component for medical and cosmetological applications, while its three centers of asymmetry mean that it can be used in a range of organic reactions. Menthol-substituted ionic liquids (ILs) have been found to exhibit promising antimicrobial and antielectrostatic properties, as well as being useful in organic catalysis and biochemical studies. However, so far, a force field designed and validated specifically for the menthol molecule has not been constructed. In the present work, the validation and optimization of force field parameters with regard to the ability to reproduce the macroscopic properties of menthol is presented. The set of optimized potentials for liquid simulations all atom (OPLS-AA) compatible parameters was tested and carefully tuned. The refinement of parameters included fitting of partial atomic charges, optimization of Lennard-Jones parameters, and recalculation of the dihedral angle parameters needed to reproduce quantum energy profiles. To validate the force field, a variety of physicochemical properties were calculated for liquid menthol. Both thermodynamic and kinetic properties were taken into account, including density, surface tension, enthalpy of vaporization, and shear viscosity. The obtained force field was proven to accurately reproduce the properties of the investigated compound while being fully compatible with the OPLS-AA force field.

     

On the characterization of energy networks of proteins

The construction of a realistic theoretical model of proteins is determinant for improving the computational simulations of their structural and functional aspects. Modeling proteins as a network of non-covalent connections between the atoms of amino acid residues has shown valuable insights into these macromolecules. The energy-related properties of protein structures are known to be very important in molecular dynamics. However, these same properties have been neglected when the protein structures are modeled as networks of atoms and amino acid residues. A new approach for the construction of protein models based on a network of atoms is presented. This method, based on interatomic interaction, takes into account the energy and geometric aspects of the protein structures that were not employed before, such as atomic occlusion inside the protein, the use of solvation, protein modeling and analysis, and the use of energy potentials to estimate the energies of interatomic non-covalent contacts. As a result, we achieved a more realistic network model of proteins. This model has the virtue of being more robust in face of different unknown variables that usually are arbitrarily estimated. We were able to determine the most connected residues of all the proteins studied, so that we are now in a better condition to study their structural role.     

Experimentally derived nearest-neighbor parameters for the stability of RNA three- and four-way multibranch loops.

Algorithms for predicting RNA secondary structure require approximations for the free energies of multibranch loops, also called junctions. The stabilities of 62 RNA duplexes with three- and four-way multibranch loops were determined by optical melting. To account for the observed sequence dependence, a revised loop free-energy approximation is proposed that accounts for the strain in three-way junctions with fewer than two unpaired nucleotides, penalizes asymmetry in the distribution of unpaired nucleotides, and gives a bonus for four-way loops relative to three-way loops. Parameters for this equation were determined by linear regression.     

Equilibrium constants of several reactions involved in the fermentation of glutamate

The equilibrium constants of the reactions catalysed by (S)-citramalate lyase and (R)-2-hydroxyglutarate dehydrogenase were determined using the purified enzymes from Clostridium tetanomorphum and Acidaminococcus fermentans, respectively. The former constant had to be determined at high ionic strength (I). Therefore it was corrected to I = 0.1 M by applying single-ion activity coefficients estimated from literature data. The result (Kapp = 4.31 +/- 0.07 M-1; direction of citramalate formation) agreed very well with the constant of the (2R,3S)-2,3-dimethylmalate lyase equilibrium when all optical isomers were taken into account. From these and other data values for the free energies of formation (delta Gzerof) of (2S,3S)-3-methylaspartate, mesaconate and (S)-citramalate were calculated. The constant of the (R)-2-hydroxyglutarate dehydrogenase equilibrium [Kapp = (1.47 +/- 0.12)10(-12) M, direction of 2-oxoglutarate formation, I = 0.1 M] was shown to lie between those for malate and lactate dehydrogenases as expected.     

Organization of visual axes in the compound eye of the flyMusca domestica L. and behavioural consequences

Summary The previously derived optical demands for the neural superposition eye are experimentally tested in the compound eye ofMusca domestica L. The optical requirements are fulfilled except in the marginal regions.Taking into account the gradient in spatial packing density of ommatidial axes in a horizontal direction the expected torque response of the fly is calculated and compared with results obtained by Reichardt (1973). The similarity of the curves suggests that existing gradients in the part of the neural network serving this orientation behaviour may be negligible with respect to the studied geometrical gradient.     

Computation of the dipole moments of proteins.

A simple and computationally feasible procedure for the calculation of net charges and dipole moments of proteins at arbitrary pH and salt conditions is described. The method is intended to provide data that may be compared to the results of transient electric dichroism experiments on protein solutions. The procedure consists of three major steps: (i) calculation of self energies and interaction energies for ionizable groups in the protein by using the finite-difference Poisson-Boltzmann method, (ii) determination of the position of the center of diffusion (to which the calculated dipole moment refers) and the extinction coefficient tensor for the protein, and (iii) generation of the equilibrium distribution of protonation states of the protein by a Monte Carlo procedure, from which mean and root-mean-square dipole moments and optical anisotropies are calculated. The procedure is applied to 12 proteins. It is shown that it gives hydrodynamic and electrical parameters for proteins in good agreement with experimental data.     

Theoretical investigation of the effect of sugar substitution on the antioxidant properties of flavonoids

Natural flavonoids are secondary phenolic plant metabolites known for their bioactivity as antioxidants. The evaluation of this property is generally done by the estimation of their direct free radical-scavenging activity as hydrogen or electron donating compounds. This paper reviews experimental results available in the literature for a selection of flavonoids and compares them with calculated quantities characteristic of the hydrogen or electron donation. For that purpose, bond dissociation energies, ionization potentials and electron transfer enthalpies are computed by using DFT methods and the ONIOM procedure implemented in the ab initio program Gaussian. This process has been chosen because it can be extended to the study of large molecules. When acid dissociation and interaction with the solvent are taken into account, the results present very good concordance with experimental results, enlightening the complexity of the processes involved in the classical assays which measure the ability of compounds to scavenge the (2,2′-azinobis-(3-ethylbenzthiazoline-6-sulfonic acid) diammonium salt) radical cation (ABTS ⁺) or the 2,2-diphenyl-1-picryl-hydrazyl radical (DPPH^·). This study demonstrates the good accuracy of theoretical calculations in obtaining the relative energies involved in free radical scavenging abilities and its capacity for predictive behaviour. It also highlights the necessity to take into account the pK_a of the compounds and the solvent interaction. The ability of the method to calculate the antioxidant properties of larger molecules are tested on glycosylated flavonoids and the effects of sugar substitution on the antioxidant properties of flavonoids are investigated, pointing out the importance of the charges on the oxygen atoms.     

Fluorescent derivatives of the GFP chromophore give a new insight into the GFP fluorescence process

The photophysical properties of synthetic compounds derived from the imidazolidinone chromophore of the green fluorescent protein were determined. Various electron-withdrawing or electron-donating substituents were introduced to mimic the effect of the chromophore surroundings in the protein. The absorption and emission spectra as well as the fluorescence quantum yields in dioxane and glycerol were shown to be highly dependent on the electronic properties of the substituents. We propose a kinetic scheme that takes into account the temperature-dependent twisting of the excited molecule. If the activation energy is low, the molecule most often undergoes an excited-state intramolecular twisting that leads it to the ground state through an avoided crossing between the S(1) and S(0) energy surfaces. For a high activation energy, the torsional motion within the compounds is limited and the ground-state recovery will occur preferentially by fluorescence emission. The excellent correlation between the fluorescence quantum yields and the calculated activation energies to torsion points to the above-mentioned avoided crossing as the main nonradiative deactivation channel in these compounds. Finally, our results are discussed with regard to the chromophore in green fluorescent protein and some of its mutants.