Energy transfer in photosynthesis

A theoretical model is presented to account for the physical mechanism of energy transfer from antenna molecules to the reaction centers in photosynthesis. The energy transfer is described by a generalized transport equation or “master equation”. The solution of this equation for the proposed model gives a relationship between the antennae interaction energy and the transfer rate. The results are shown to be in agreement with inter-antenna transfer rates calculated from experimental fluorescence lifetimes. Previous theories were based either on the Förster mechanism, which is valid for very small interaction energies, or an exciton model valid for very large interactions, but experimental results seemed to indicate that the actual situation was intermediate between these two. The Förster theory and the exciton model are limiting cases of the master equation.     

Physical association between MHC class I and class II molecules detected on the cell surface by flow cytometric energy transfer

The physical association of HLA class I and class II Ag in the membranes of PGF and JY lymphoblastoid cell lines was studied using flow cytometric energy transfer. This technique measures the proximity of cell surface molecules in the nm range and provides a distribution histogram of the average proximity of molecules on each cell of a population. HLA Ag were labeled with mAb conjugated to fluorescein, serving as donor, or tetramethylrhodamine, serving as acceptor molecules. Significant fluorescence energy transfer was detected between various combinations of class I and class II molecules indicating that these molecules are within 10 nanometers of each other. Specifically, energy transfer was observed between class I molecules and DR, DQ, or DP class II HLA molecules. In addition, energy transfer between all combinations of DR, DQ, and DP molecules was observed. No transfer was observed among class I molecules or among DR or among DP molecules. Among DQ molecules, subpopulations transferred fluorescence energy to each other. The close contact measured between class I and class II Ag correlates with previous reports of cocapping and may reflect an immunologically significant interaction or the reported tendency of class I Ag to associate with other cell surface receptors, including growth factor receptors. The energy transfer between fluorescent antibodies to class II Ag suggests the existence of heterodimers formed from the different locus products, as well as possible quaternary surface interactions between alpha/beta complexes from separate loci.     

Reliable computational design of biological-inorganic materials to the large nanometer scale using Interface-FF

Abstract

The function of nanomaterials and biomaterials greatly depends on understanding nanoscale recognition mechanisms, crystal growth and surface reactions. The Interface Force Field (IFF) and surface model database are the first collection of transferable parameters for inorganic and organic compounds that can be universally applied to all materials. IFF uses common energy expressions and achieves best accuracy among classical force fields due to rigorous validation of structural and energetic properties of all compounds in comparison to perpetually valid experimental data. This paper summarises key aspects of parameterisation, including atomic charges and transferability of parameters and current coverage. Examples of biomolecular recognition at metal and mineral interfaces, surface reactions of alloys, as well as new models for graphitic materials and pi-conjugated molecules are described. For several metal–organic interfaces, a match in accuracy of computed binding energies between of IFF and DFT results is demonstrated at ten million times lower computational cost. Predictive simulations of biomolecular recognition of peptides on phosphate and silicate surfaces are described as a function of pH. The use of IFF for reactive molecular dynamics is illustrated for the oxidation of Mo₃Si alloys at high temperature, showing the development of specific porous silica protective layers. The introduction of virtual pi electrons in graphite and pi-conjugated molecules enables improvements in property predictions by orders of magnitude. The inclusion of such molecule-internal polarity in IFF can reproduce cation–pi interactions, pi-stacking in graphite, DNA bases, organic semiconductors and the dynamics of aqueous and biological interfaces for the first time.     

Many-body energies during proton transfer in an aqueous system

The energetics of the mechanism of proton transfer from a hydronium ion to one of the water molecules in its first solvation shell are studied using density functional theory and the Møller–Plesset perturbation (MP2) method. The potential energy surface of the proton transfer mechanism is obtained at the B3LYP and MP2 levels with the 6-311++G** basis set. Many-body analysis is applied to the proton transfer mechanism to obtain the change in relaxation energy, two-body, three-body and four-body energies when proton transfer occurs from the hydronium ion to one of the water molecules in its first solvation shell. It is observed that the binding energy (BE) of the complex decreases during the proton transfer process at both levels of theory. During the proton transfer process, the % contribution of the total two-body energy to the binding energy of the complex increases from 62.9 to 68.09% (39.9 to 45.95%), and that of the total three-body increases from 25.9 to 27.09% (24.16 to 26.17%) at the B3LYP/6-311++G** (MP2/ 6-311++G**) level. There is almost no change in the water–water–water three-body interaction energy during the proton transfer process at both levels of theory. The contribution of the relaxation energy and the total four-body energy to the binding energy of the complex is greater at the MP2 level than at the B3LYP level. Significant differences are found between the relaxation energies, the hydronium–water interaction energies and the four-body interaction energies at the B3LYP and MP2 levels.     

Anisotropic excitation transfer to acceptors randomly distributed on surfaces.

We presented exact expressions for the ensemble averaged decay of the excitation of a donor molecule due to the energy transfer via anisotropic dipolar interactions to acceptors distributed randomly on a surface. The disorder extended both over the positions of the acceptors and over the orientations of their transition dipoles with respect to that of the donor molecule. Several cases were considered explicitly (a) random orientations of the acceptors in space, with the donor being (a1) perpendicular to the plane, (a2) in the plane, (a3) randomly oriented in space; (b) random orientations of both donor and acceptors in the plane; (c) parallel orientations of donor and acceptors (no orientational disorder). For all these cases we evaluated the analytic, Förster-like expressions, valid for long times and low acceptor densities, and obtained their domains of validity by comparison with the exact, numerically calculated decay laws.     

A possible new mechanism of temperature dependence of electron transfer in photosynthetic systems

A new theory for the electron transfer by the non-adiabatic process is formulated taking into account the origin shift and the frequency change of the vibration. The resultant formulas are quite similar to those of Jortner (Jortner, J. (1976) J. Chem. Phys. 64, 4860–4867) except that the free energy gap ΔG is used instead of the energy gap ΔE. By applying this theory to the photosynthetic electron transfer, the role of the remarkable temperature dependence of the electron transfer from cytochrome to P⁺ in Chromatium vinosum and the experimental data were reproduced very well using a small value of the coupling strength in contrast with the previous theory. This implies that proteins play a role to exclude many of the solvent molecules from the region of the electron transfer reaction between the donor and acceptor molecules. The negative activation process in the back electron transfer from Q^?_A to P⁺, the very slow back electron transfer from I^? to P⁺ and the solvent isotope effect on the cytochrome oxidation are also successfully explained by this new theory. It is shown that even a qualitative conclusion as to the molecular parameters obtained from the temperature dependence of the electron transfer is different between the present theory and that of Jortner.     

Fluorescent probe study of the spatial structure of membranes and lipoproteins

A review is devoted to principles of studies in spatial structure of the model and biological membranes and lipoproteins on the basis of measuring radiationless energy transfer between fluorescent probes and from proteins to the probes. Recently the theory has been developed for energy transfer in membranes of various geometry and in lipoproteins of different size and structure. Special fluorescent probes are designed and made. The measurement procedure was tested in simulated systems and used to study a series of membranes as well as blood plasma lipoproteins of main classes. Everything above-mentioned resulted in obtaining data on the size of protein molecules in membranes and lipoproteins, proteins location relative to the lipid phase, on the surface area of the membranes (isolated and directly in a cell), association of protein molecules, state of near-protein lipid layer, membrane asymmetry, spreading of proteins on the lipoprotein surface, on the cholesterol effect on the lipid bilayer size etc.     

Enhanced Intermolecular Energy Transfer in the Vicinity of a Plasmonic Nanorice

The problem of radiationless Förster energy transfer between a donor and an acceptor molecule is studied in the vicinity of a metallic nanorice. Using a recently formulated effective medium theory, the modified dipole–dipole interaction between the molecules in the vicinity of a spheroidal metallic nanoshell can be easily formulated, from which huge enhancement of the energy transfer rate is obtained due to the resonant excitation of the bonding and the antibonding plasmonic modes of the nanoshell. Effects due to the different locations and orientations of the molecules are also studied. The results show that the plasmonic resonances depend mainly on the nanorice geometry and much less on the configuration of the molecules, whereas the enhancement is more sensitive to the relative orientations and locations of the molecules.     

带电磷脂膜泡的内、外表面电荷密度和表面电位

本文按Gouy-Chapman理论,推导了稳定条件下磷脂膜泡膜内、外表面电荷密度/表面电位关系和表面电位分布以及带电磷脂在膜泡内外两侧的不对称分布的近似表达式.并对这些表示式的极限情况和可能的应用进行了讨论,同时对带电磷脂在膜泡膜内、外两侧的不对称分布也作了讨论.     

Direct numerical simulation of expiratory crackles: Relationship between airway closure dynamics and acoustic fluctuations

This paper investigates the relationship between airway closure dynamics and acoustic fluctuations in expiratory crackles using direct numerical simulation. A unified mathematical model is proposed to deal with flow in an airway, elastic deformation of the airway wall, surface tension driven motion of the liquid film that lines the airway, and their acoustic fluctuations because of material compressibility. Airway closure is induced by increasing the surrounding pressure, then the source of the pressure fluctuations is measured over time. Our results show that the airway closure occurs suddenly because of a bridge formation of the liquid film, and high energy transfer occurs between the kinetic energy, the surface energy of the liquid interface, and the elastic energy of the airway wall, invoking a large acoustic fluctuation that causes the expiratory crackles. Nonlinear behavior is observed in terms of the airway wall stiffness; the dynamic motion of the airway closure becomes moderate and both the energy transfer and acoustic fluctuations are dramatically reduced with an increase in airway wall stiffness.     

Detection of receptor clustering by flow cytometric fluorescence anisotropy measurements

BACKGROUND: Perrin equation suggests an alternative way for the accurate energy transfer determination on a cell-by-cell basis by measuring polarized donor intensities in a conventional flow cytometer. METHODS: The relationship between energy transfer and fluorescence anisotropy of the donor was investigated by flow cytometric generation of Perrin-lifetime plots of fluorescent antibody-labeled MHC class I and class II molecules on the surface of living cells. The energy transfer reduced the fluorescence lifetime of the donor. RESULTS: Perrin plots have proven to be sensitive to the segmental mobility of the labeling dye and that of antibodies of different isotypes, and homo-transfer due to the multiple labeling of antibodies. A method demonstrating the feasibility of energy transfer determination by measuring anisotropy enhancement of the donor is presented. Flow cytometric histograms of the donor anisotropy and of the deduced energy transfer efficiency are shown, indicating clustering of MHC class I and class II molecules on the surface of human T lymphoblasts. In the Appendix, a method for the simultaneous determination of both energy transfer efficiency and donor fluorescence anisotropy, without need for G-factor measurement, is also presented. CONCLUSIONS: We demonstrate that energy transfer efficiency, i.e., proximity, between suitably selected donor and acceptor, and the rotational relaxation of the donor, i.e., donor mobility, can be simultaneously measured in a flow cytometer.     

Localization of adriamycin in model and natural membranes. Influence of lipid molecular packing

The interaction of adriamycin with lipids was studied in model (monolayers, small unilamellar vesicles, large multilamellar vesicles) and natural (chinese hamster ovary cell) membranes by measurement of fluorescence energy transfer and fluorescence quenching. 2-APam, 7-ASte, 12-ASte and anthracene-phosphatidylcholine were used as fluorescent probes in which the anthracene group is well located at graded depths in the membrane. Egg-yolk phosphatidylcholine and a 1/1 mixture of it with bovine brain phosphatidylserine were used in model membrane systems. Large fluorescence energy transfer was observed between these molecules as donors and the drug as acceptor. With liposomes, at pH 7.4 and over an adriamycin concentration range of 0-100 microM, the efficiency of energy transfer was 12-ASte greater than 7-ASte greater than 2-APam, with 100% energy transfer for 12-ASte above a drug concentration of 30 microM. At pH 5, where the fatty acids are buried deeper (0.45 nm) in the lipid bilayer due to protonation of the carboxyl group, the order of energy transfer 7-ASTe greater than 12-ASte = 2-APam was observed. Measurements of fluorescence quenching using the non-permeant Cu2+ ion as quencher and spectrophotometric assays indicated that around 40% of the adriamycin molecules were deeply embedded in the lipid bilayer. Adriamycin molecules thus appear to penetrate the lipid bilayer, with the aminoglycosyl group interacting with the lipid phosphate groups and the dihydroanthraquinone residue in contact with the lipid fatty acid chains. In contrast, fluorescence energy transfer and quenching studies on CHO cells showed that adriamycin penetrated the plasma membrane of these cells to a much more limited extent than in the model membrane systems. This can be related to the squeezing out of the drug from a film of phosphatidylcholine which was observed in monolayers by means of surface pressure, potential and fluorescence experiments. These observations indicated that the penetration of adriamycin into lipid bilayers strongly depends on the molecular packing of the lipid.     

Kinetics of conditioning layer formation on stainless steel immersed in seawater

Adhesion of microorganisms to surfaces in marine environments leads to biofouling. The deleterious effects of biofilm growth in the marine environment are numerous and include energy losses due to increased fluid frictional resistance or to increased heat transfer resistance, the risk of corrosion induced by microorganisms, loss of optical properties, and quality control and safety problems. Antifouling agents are generally used to protect surfaces from such a biofilm. These agents are toxic and can be persistent, causing harmful environmental and ecological effects. Moreover, the use of biocides and regular cleaning considerably increase the maintenance costs of marine industries. An improved knowledge of bio‐film adhesion mechanisms is needed for the development of an alternative approach to the currently used antifouling agents. The aim of this study is to characterise the chemical composition of the molecules first interacting with stainless steel during the period immediately following immersion in natural seawater and to elucidate the kinetics of the adsorbtion process. Proteins are shown to adhere very rapidly, closely followed by carbohydrates. The distribution on the surface of organic molecules is also examined. The ad‐sorbate on the surface is not a continuous film but a heterogeneous deposit, whose average thickness varies widely. The cleaning procedures used affect the adsorption kinetics. In particular, cleaning with hexane results in slower adsorption of nitrogen‐containing species than does cleaning in acetone.     

van der Waals forces influencing adhesion of cells

Adhesion molecules, often thought to be acting by a ‘lock and key’ mechanism, have been thought to control the adhesion of cells. While there is no doubt that a coating of adhesion molecules such as fibronectin on a surface affects cell adhesion, this paper aims to show that such surface contamination is only one factor in the equation. Starting from the baseline idea that van der Waals force is a ubiquitous attraction between all molecules, and thereby must contribute to cell adhesion, it is clear that effects from geometry, elasticity and surface molecules must all add on to the basic cell attractive force. These effects of geometry, elasticity and surface molecules are analysed. The adhesion force measured between macroscopic polymer spheres was found to be strongest when the surfaces were absolutely smooth and clean, with no projecting protruberances. Values of the measured surface energy were then about 35 mJ m⁻², as expected for van der Waals attractions between the non-polar molecules. Surface projections such as abrasion roughness or dust reduced the molecular adhesion substantially. Water cut the measured surface energy to 3.4 mJ m⁻². Surface active molecules lowered the adhesion still further to less than 0.3 mJ m⁻². These observations do not support the lock and key concept.     

Distribution of a Glycosylphosphatidylinositol-anchored Protein at the Apical Surface of MDCK Cells Examined at a Resolution of <100 Å Using Imaging Fluorescence Resonance Energy Transfer

Membrane microdomains (“lipid rafts”) enriched in glycosylphosphatidylinositol (GPI)-anchored proteins, glycosphingolipids, and cholesterol have been implicated in events ranging from membrane trafficking to signal transduction. Although there is biochemical evidence for such membrane microdomains, they have not been visualized by light or electron microscopy. To probe for microdomains enriched in GPI- anchored proteins in intact cell membranes, we used a novel form of digital microscopy, imaging fluorescence resonance energy transfer (FRET), which extends the resolution of fluorescence microscopy to the molecular level (<100 Å). We detected significant energy transfer between donor- and acceptor-labeled antibodies against the GPI-anchored protein 5′ nucleotidase (5′ NT) at the apical membrane of MDCK cells. The efficiency of energy transfer correlated strongly with the surface density of the acceptor-labeled antibody. The FRET data conformed to theoretical predictions for two-dimensional FRET between randomly distributed molecules and were inconsistent with a model in which 5′ NT is constitutively clustered. Though we cannot completely exclude the possibility that some 5′ NT is in clusters, the data imply that most 5′ NT molecules are randomly distributed across the apical surface of MDCK cells. These findings constrain current models for lipid rafts and the membrane organization of GPI-anchored proteins.     

Statistical thermodynamic analysis of peptide and protein insertion into lipid membranes.

A statistical thermodynamic approach is used to analyze the various contributions to the free energy change associated with the insertion of proteins and protein fragments into lipid bilayers. The partition coefficient that determines the equilibrium distribution of proteins between the membrane and the solution is expressed as the ratio between the partition functions of the protein in the two phases. It is shown that when all of the relevant degrees of freedom (i.e., those that change their character upon insertion into the membrane) can be treated classically, the partition coefficient is fully determined by the ratio of the configurational integrals and thus does not involve any mass-dependent factors, a conclusion that is also valid for related processes such as protein adsorption on a membrane surface or substrate binding to proteins. The partition coefficient, and hence the transfer free energy, depend only on the potential energy of the protein in the membrane. Expressing this potential as a sum of a "static" term, corresponding to the equilibrium (minimal free energy) configuration of the protein in the membrane, and a "dynamical" term representing fluctuations around the equilibrium configuration, we show that the static term contains the "solvation" and "lipid perturbation" contributions to the transfer free energy. The dynamical term is responsible for the "immobilization" free energy, reflecting the loss of translational and rotational entropy of the protein upon incorporation into the membrane. Based on a recent molecular theory of lipid-protein interactions, the lipid perturbation and immobilization contributions are then expressed in terms of the elastic deformation free energy resulting from the perturbation of the lipid environment by the foreign (protein) inclusion. The model is formulated for cylindrically shaped proteins, and numerical estimates are given for the insertion of an alpha-helical peptide into a lipid bilayer. The immobilization free energy is shown to be considerably smaller than in previous estimates of this quantity, and the origin of the difference is discussed in detail.     

Enzyme electrokinetics: using protein film voltammetry to investigate redox enzymes and their mechanisms

Protein film voltammetry is a relatively new approach to studying redox enzymes, the concept being that a sample of a redox protein is configured as a film on an electrode and probed by a variety of electrochemical techniques. The enzyme molecules are bound at the electrode surface in such a way that there is fast electron transfer and complete retention of the chemistry of the active site that is observed in more conventional experiments. Modulations of the electrode potential or catalytic turnover result in the movement of electrons to, from, and within the enzyme; this is detected as a current that varies in characteristic ways with time and potential. Henceforth, the potential dimension is introduced into enzyme kinetics. The presence of additional intrinsic redox centers for providing fast intramolecular electron transfer between a buried active site and the protein surface is an important factor. Centers which carry out cooperative two-electron transfer, most obviously flavins, produce a particularly sharp signal that allows them to be observed, even as transient states, when spectroscopic methods are not useful. High catalytic activity produces a large amplification of the current, and useful information can be obtained even if the coverage on the electrode is low. Certain enzymes display optimum activity at a particular potential, and this can be both mechanistically informative and physiologically relevant. This paper outlines the principles of protein film voltammetry by discussing some recent results from this laboratory.