Three-chromophore FRET microscopy to analyze multiprotein interactions in living cells

Nearly every major process in a cell is carried out by assemblies of multiple dynamically interacting protein molecules. To study multi-protein interactions within such molecular machineries, we have developed a fluorescence microscopy method called three-chromophore fluorescence resonance energy transfer (3-FRET). This method allows analysis of three mutually dependent energy transfer processes between the fluorescent labels, such as cyan, yellow and monomeric red fluorescent proteins. Here, we describe both theoretical and experimental approaches that discriminate the parallel versus the sequential energy transfer processes in the 3-FRET system. These approaches were established in vitro and in cultured mammalian cells, using chimeric proteins consisting of two or three fluorescent proteins linked together. The 3-FRET microscopy was further applied to the analysis of three-protein interactions in the constitutive and activation-dependent complexes in single endosomal compartments. These data highlight the potential of 3-FRET microscopy in studies of spatial and temporal regulation of signaling processes in living cells.     

Fluorescence resonance energy transfer-based stoichiometry in living cells

Imaging of fluorescence resonance energy transfer (FRET) between fluorescently labeled molecules can measure the timing and location of intermolecular interactions inside living cells. Present microscopic methods measure FRET in arbitrary units, and cannot discriminate FRET efficiency and the fractions of donor and acceptor in complex. Here we describe a stoichiometric method that uses three microscopic fluorescence images to measure FRET efficiency, the relative concentrations of donor and acceptor, and the fractions of donor and acceptor in complex in living cells. FRET stoichiometry derives from the concept that specific donor-acceptor complexes will give rise to a characteristic FRET efficiency, which, if measured, can allow stoichiometric discrimination of interacting components. A first equation determines FRET efficiency and the fraction of acceptor molecules in complex with donor. A second equation determines the fraction of donor molecules in complex by estimating the donor fluorescence lost due to energy transfer. This eliminates the need for acceptor photobleaching to determine total donor concentrations and allows for repeated measurements from the same cell. A third equation obtains the ratio of total acceptor to total donor molecules. The theory and method were confirmed by microscopic measurements of fluorescence from cyan fluorescent protein (CFP), citrine, and linked CFP-Citrine fusion protein, in solutions and inside cells. Together, the methods derived from these equations allow sensitive, rapid, and repeatable detection of donor-, acceptor-, and donor-acceptor complex stoichiometry at each pixel in an image. By accurately imaging molecular interactions, FRET stoichiometry opens new areas for quantitative study of intracellular molecular networks.     

Calculations on crystal packing of a flexible molecule, Leu-enkephalin

Crystal packing calculations have been carried out on a substantial number of conformations of Leu-enkephalin; namely, those obtained both from crystal structures and from energy minimizations on isolated molecules, and with and without waters of crystallization. The known crystal structures represent the most energetically stable packings found. The conformations of the enkephalin molecules in the crystal are not the most stable for an isolated molecule; i.e. intermolecular interactions force the isolated molecule to change conformation in order to achieve a small packing volume and an optimal packing energy in the crystal. It is found that the packing energy of an enkephalin molecule is a reasonably smooth function of its molecular volume in the unit cell, if structures with intermolecular hydrogen bonding are excluded, and is substantially independent of other details of the molecular conformation or of the crystal packing. Hydrogen bonding provides additional stabilization of the crystal structure, and would likely permit crystallization of the system if it is sufficiently dense. Solvent molecules further stabilize the structure when they can also provide intermolecular hydrogen bonds.     

Macromolecular crowding at membrane interfaces: adsorption and alignment of membrane peptides

Association of proteins to cellular membranes is involved in various biological processes. Various theoretical models have been developed to describe this adsorption mechanism, commonly implying the concept of an ideal solution. However, due to the two-dimensional character of membrane surfaces intermolecular interactions between the adsorbed molecules become important. Therefore previously adsorbed molecules can influence the adsorption behavior of additional protein molecules and their membrane-associated structure. Using the model peptide LAH₄, which upon membrane-adsorption can adopt a transmembrane as well as an in-planar configuration, we carried out a systematic study of the correlation between the peptide concentration in the membrane and the topology of this membrane-associated polypeptide. We could describe the observed binding behavior by establishing a concept, which includes intermolecular interactions in terms of a scaled particle theory.High surface concentration of the peptide shifts the molecules from an in-planar into a transmembrane conformation, a process driven by the reduction of occupied surface area per molecule. In a cellular context, the crowding-dependent alignment might provide a molecular switch for a cell to sense and control its membrane occupancy. Furthermore, crowding might have pronounced effects on biological events, such as the cooperative behavior of antimicrobial peptides and the membrane triggered aggregation of amyloidogenic peptides.     

Molecular origin of biphasic response of main phase-transition temperature of phospholipid membranes to long-chain alcohols

A statistical mechanical theory is proposed which explains the molecular mechanism of the nonlinear response of the phase-transition temperature of phospholipid vesicle membranes to added 1-alkanols. By assuming that the free energy of transfer of 1-alkanols from the aqueous phase to the membrane and the interaction energy between 1-alkanol molecules are linear functions of alkanol alkyl chain-length, the nonlinear behavior is explained in the Bragg-Williams approximation. For dipalmitoylphosphatidylcholine vesicle membranes, the theory reveals a larger free energy of transfer of 1-alkanols from the aqueous phase to the solid-gel membrane than to the liquid-crystalline membrane when the number of carbon atoms of 1-alkanol exceeds 12. When the intermolecular interaction force between 1-alkanol molecules residing in the gel phase is stronger than the interaction force between those residing in the liquid-crystalline phase, the ligand effect is to tighten the lipid matrix structure, causing the transition temperature to rise. The interaction force is a quadratic function of 1-alkanol concentration; hence, the response of the transition temperature to the 1-alkanol concentration is nonlinear. At low concentrations of the long-chain 1-alkanols that predominantly elevate the transition temperature, this intermolecular interaction force is negligible. In this case, the entropic effect of the incorporated ligand molecules, which loosens the lipid matrix, predominates, and the transition temperature decreases. The biphasic action of long-chain 1-alkanols originates from the balance of these two opposing effects: entropy and intermolecular interaction.     

The bhopalator: a molecular model of the living cell based on the concepts of conformons and dissipative structures

A molecular model of the living cell has been formulated based on a new theory of enzymic catalysis which takes into account the complementary roles of free energy and genetic information. The elementary units of free energy and genetic information that are necessary and sufficient for effectuating molecular mechanisms responsible for the life of the cell are called conformons. Conformons are visualized as a collection of a small number of catalytic residues of enzymes or segments of nucleic acids that are arranged in space and time with appropriate force vectors so as to cause chemical transformations or physical changes of a substrate or a bound ligand. So defined, conformons provide a plausible molecular means to link the genetic information stored in DNA and its ultimate expression, namely networks of coupled intracellular biochemical reactions and physical processes maintained by a continuous dissipation of free energy--dissipative structures of Prigogine. The proposed model of the living cell appears to possess the potential for bridging the gap between molecular biology and the biology of multicellular systems.     

Special features of water structure formation in biosystems according to dielkometric data

Experimental data on dielectric function and dielectric loss tangent in living and non-living water-containing systems have been discussed from the viewpoint of our earlier concept on energy transfer in living systems and the role of water in this process. Estimates have been made of a mean length of fractal quasi-crystals, representing the form of biomolecules hydration in the living system; the expected lengths of these quasicrystals are of order of 1000 H₂O molecules. It is concluded that the peaks at the curve of frequency dependence of dielectric loss tangent in living systems is due to water sub-system, but not biomolecular vibrations.     

Stepwise molecular evolution of bacterial photosynthetic energy conversion

The concept of continuity in molecular evolution implies a stepwise formation of metabolic systems and processes. In this manner, chemical and biological evolution have given rise, step by step, to such complicated systems as the photosynthetic apparatus and thus, such elaborate processes as photosynthesis in the living cell. Among currently living organisms, the bacteria contain a much less complex photosynthetic system than the algae and higher plants, which uniquely are capable fo splitting H2O. But also the bacterial system is a very highly evolved and sophisticated, membrane-bound apparatus for the transformation of light energy to other biologically useful energy forms. The study of its molecular evolution is here undertaken by the method of attempting to break down the system into its main components and functions in order to elucidate how they had originated and evolved, and how, by divergent and convergent evolutionary steps, the stage was set for the arrival of bacterial photophosphorylation.     

Resonance energy transfer in cells: a new look at fixation effect and receptor aggregation on cell membrane

Fluorescence resonance energy transfer (FRET) measurements offer a reliable and noninvasive approach to studying protein and lipid colocalization in cells. We have considered systems in which FRET occurs as intramolecular and/or intermolecular process. The proposed dynamic FRET model shows that in the case of intermolecular process the degree of aggregation only slightly affects the energy transfer efficiency. The theory was tested on a set of donor-acceptor pairs in which energy transfer occurs intramolecularly, intermolecularly, or both. The obtained experimental results are in a good agreement with the proposed model. It is well known that the energy transfer efficiency depends both on the distance between the donor and acceptor molecules and the relative orientation of their respective transition dipole moments. This dual dependence often leads to ambiguity. In this article, we show how FRET efficiency can be significantly reduced even in highly coupled system through conformational restrictions in the donor-acceptor pair. Importantly, such restrictions can be imposed on the system by cell fixation, a procedure routinely used when conducting FRET measurements.     

Comparison of molecular mechanisms mediating cell contact phenomena in model developmental systems: an exploration of universality

Are there universal molecular mechanisms associated with cell contact phenomena during metazoan ontogenesis? Comparison of adhesion systems in disparate model systems indicates the existence of unifying principles. Requirements for multicellularity are (a) the construction of three‐dimensional structures involving a crucial balance between adhesiveness and motility; and (b) the establishment of integration at molecular, cellular, tissue, and organismal levels of organization. Mechanisms for (i) cell–cell and cell–substrate adhesion, (if) cell movement, (Hi) cell‐cell communication, (iv) cellular responses, (v) regulation of these processes, and (vi) their integration with patterning, growth, and other developmental processes are all crucial to metazoan development, and must have been present for the emergence and radiation of Metazoa. The principal unifying themes of this review are the dynamics and regulation of cell contact phenomena. Our knowledge of the dynamic molecular mechanisms underlying cell contact phenomena remains fragmentary. Here we examine the molecular bases of cell contact phenomena using extant model developmental systems (representing a wide range of phyla) including the simplest i.e. sponges, and the eukaryotic protist Dictyostelium discoideum, the more complex Drosophila melanogaster, and vertebrate systems. We discuss cell contact phenomena in a broad developmental context. The molecular language of cell contact phenomena is complex; it involves a plethora of structurally and functionally diverse molecules, and diverse modes of intermolecular interactions mediated by protein and/or carbohydrate moieties. Reasons for this are presumably the necessity for a high degree of specificity of inter‐molecular interactions, the requirement for a multitude of different signals, and the apparent requirement for an increasingly large repertoire of cell contact molecules in more complex developmental systems, such as the developing vertebrate nervous system. However, comparison of molecular models for dynamic adhesion in sponges and in vertebrates indicates that, in spite of significant differences in the details of the way specific cell–cell adhesion is mediated, similar principles are involved in the mechanisms employed by members of disparate phyla. Universal requirements are likely to include (a) rapidly reversible intermolecular interactions; (b) low‐affinity intermolecular interactions with fast on–off rates; (c) the compounding of multiple intermolecular interactions; (d) associated regulatory signalling systems. The apparent widespread employment of molecular mechanisms involving cadherin‐like cell adhesion molecules suggests the fundamental importance of cadherin function during development, particularly in epithelial morphogenesis, cell sorting, and segregation of cells.     

Electric Field Orientation for Gene Delivery Using High-Voltage and Low-Voltage Pulses

Electropermeabilization is a biological physical process in response to the presence of an applied electric field that is used for the transfer of hydrophilic molecules such as anticancer drugs or DNA across the plasma membranes of living cells. The molecular processes that support the transfer are poorly known. The aim of our study was to investigate the effect of high-voltage and low-voltage (HVLV) pulses in vitro with different orientations on cell permeabilization, viability and gene transfection. We monitored the permeabilization with unipolar and bipolar HVLV pulses with different train repetition pulses, showing that HVLV pulses increase cell permeabilization and cell viability. Gene transfer was also observed by measuring green fluorescent protein (GFP) expression. The expression was the same for HVLV pulses and electrogenotherapy pulses for in vitro experimentation. As the viability was better preserved for HVLV-pulsed cells, we managed to increase the number of GFP-expressing cells by up to 65?% under this condition. The use of bipolar HVLV train pulses increased gene expression to a higher extent, probably by affecting a larger part of the cell surface.     

Superweak effects of chemical compounds and physical factors on biological systems

The results of extensive investigations of the responses of living systems to superweak influences are summarized. The results of the effect of ultralow concentrations of various biologically active substances and ultraweak physical fields (primarily electromagnetic) on biological systems of different level of organization, from molecular to population, were considered. Several single-type regularities peculiar to all systems were revealed: polymodal dose dependences, the efficiency of influences at doses below the background level and its dependence on the state of the system, the modification of the sensitivity of a system to subsequent influences, etc. Several hypotheses of the mechanisms of superweak influences and the role of water as a universal intermediate in these processes are presented. Possible consequences of the phenomenon and its applications in practice are discussed.     

Characterization of one- and two-photon excitation fluorescence resonance energy transfer microscopy

Advances in molecular biology provide various methods to define the structure and function of the individual proteins that form the component parts of subcellular structures. The ability to see the dynamic behavior of a specific protein inside the living cell became possible through the application of advanced fluorescence resonance energy transfer (FRET) microscope techniques. The fluorophore molecule used for FRET imaging has a characteristic absorption and emission spectrum that should be considered for characterizing the FRET signal. In this article we describe the system development for the image acquisition for one- and two-photon excitation FRET microscopy. We also describe the precision FRET (PFRET) data analysis algorithm that we developed to remove spectral bleed-through and variation in the fluorophore expression level (or concentration) for the donor and acceptor molecules. The acquired images have been processed using a PFRET algorithm to calculate the energy transfer efficiency and the distance between donor and acceptor molecules. We implemented the software correction to study the organization of the apical endosome in epithelial polarized MDCK cells and dimerization of the CAATT/enhancer binding protein alpha (C/EBPalpha). For these proteins, the results revealed that the extent of correction affects the conventionally calculated energy transfer efficiency (E) and the distance (r) between donor and acceptor molecules by 38 and 9%, respectively.     

Intermolecular interaction studies of winter flounder antifreeze protein reveal the existence of thermally accessible binding state

The physical nature underlying intermolecular interactions between two rod-like winter flounder antifreeze protein (AFP) molecules and their implication for the mechanism of antifreeze function are examined in this work using molecular dynamics simulations, augmented with free energy calculations employing a continuum solvation model. The energetics for different modes of interactions of two AFP molecules is examined in both vacuum and aqueous phases along with the water distribution in the region encapsulated by two antiparallel AFP backbones. The results show that in a vacuum two AFP molecules intrinsically attract each other in the antiparallel fashion, where their complementary charge side chains face each other directly. In the aqueous environment, this attraction is counteracted by both screening and entropic effects. Therefore, two nearly energetically degenerate states, an aggregated state and a dissociated state, result as a new aspect of intermolecular interaction in the paradigm for the mechanism of action of AFP. The relevance of these findings to the mechanism of function of freezing inhibition in the context of our work on Antarctic cod antifreeze glycoprotein (Nguyen et al., Biophysical Journal, 2002, Vol. 82, pp. 2892-2905) is discussed.     

Molecular modelling of amphotericin B-ergosterol primary complex in water

The properties of amphotericin B-ergosterol primary complex have been studied with the use of the molecular dynamics simulation. Possible geometries of the complex were tested first in order to find the structures with the most favourable values of the intermolecular interactions energy. The molecules studied possessed a tendency to fit each other's shapes, which favours intermolecular van der Waals interactions. The main simulations were performed for the best structures found. Presence of hydrogen bonds between the sterol hydroxyl group and polar fragments of mycosamine (most frequently 2'OH) was coupled with a relatively high level of the intermolecular energy values. The structures obtained are hardly comparable to the hypothetical and 'computational' models of the antibiotic-sterol complex. The geometries found are not suitable to assemble the presupposed structure of the water channel, however, the existence of the complex in the shape anticipated is not in contradiction to the results of biophysical experiments on the complexation in water and in hydroalcoholic media.     

Quantitation of the förster energy transfer for two-dimensional systems: II. Protein distribution and aggregation state in biological membranes

Analytical solutions are presented of the average rate of the Förster energy transfer for several processes affecting intrinsic membrane proteins within a phospholipid bilayer. The physical phenomena considered here are lateral phase separation of the protein, i.e., formation of eutectic mixtures, changes in the aggregation state of the protein and non-random distribution of protein molecules. It is shown that the average rate of energy transfer among protein and phospholipid molecules labelled with donor and acceptor molecules, respectively, allows differentiation between them and also that the average rate of energy transfer can be used to quantitate these phenomena.     

Incorporation of lone pairs into the electrostatic term in the empirical intra- and intermolecular energy calculations

The method hitherto used for estimating the electrostatic term in empirical intramolecular calculations of stable conformations of biologically important molecules and macromolecules and intermolecular calculations of molecular associations or packing energy in molecular crystals had been analyzed. It has been shown that the contribution of atomic hybridization moments is omitted in the calculation of electrostatic interactions from net atomic charges localized on nuclei which have been determined by standard quantum-chemical methods. This contribution plays an important part in determining electrostatic interactions, mainly in molecules containing atoms with lone pairs. Simultaneously, a modified method for calculating the electrostatic term comprising the interaction of the lone pairs, which are represented by atomic hybridization moments, has been proposed. The relationship between the atomic hybridization moment and the bond angle has been expressed for some typical configurations occurring in biologically important molecules. Finally, this new approach is illustrated by results of the conformational analysis of some model compounds for biomolecules and compared with the approach used so far for the estimation of the electrostatic interaction in empirical methods of calculation of the intra- and intermolecular energy.     

Design and engineering of photosynthetic light-harvesting and electron transfer using length, time, and energy scales

Decades of research on the physical processes and chemical reaction-pathways in photosynthetic enzymes have resulted in an extensive database of kinetic information. Recently, this database has been augmented by a variety of high and medium resolution crystal structures of key photosynthetic enzymes that now include the two photosystems (PSI and PSII) of oxygenic photosynthetic organisms. Here, we examine the currently available structural and functional information from an engineer's point of view with the long-term goal of reproducing the key features of natural photosystems in de novo designed and custom-built molecular solar energy conversion devices. We find that the basic physics of the transfer processes, namely, the time constraints imposed by the rates of incoming photon flux and the various decay processes allow for a large degree of tolerance in the engineering parameters. Moreover, we find that the requirements to guarantee energy and electron transfer rates that yield high efficiency in natural photosystems are largely met by control of distance between chromophores and redox cofactors. Thus, for projected de novo designed constructions, the control of spatial organization of cofactor molecules within a dense array is initially given priority. Nevertheless, constructions accommodating dense arrays of different cofactors, some well within 1 nm from each other, still presents a significant challenge for protein design.     

Design and engineering of photosynthetic light-harvesting and electron transfer using length, time, and energy scales

Decades of research on the physical processes and chemical reaction-pathways in photosynthetic enzymes have resulted in an extensive database of kinetic information. Recently, this database has been augmented by a variety of high and medium resolution crystal structures of key photosynthetic enzymes that now include the two photosystems (PSI and PSII) of oxygenic photosynthetic organisms. Here, we examine the currently available structural and functional information from an engineer's point of view with the long-term goal of reproducing the key features of natural photosystems in de novo designed and custom-built molecular solar energy conversion devices. We find that the basic physics of the transfer processes, namely, the time constraints imposed by the rates of incoming photon flux and the various decay processes allow for a large degree of tolerance in the engineering parameters. Moreover, we find that the requirements to guarantee energy and electron transfer rates that yield high efficiency in natural photosystems are largely met by control of distance between chromophores and redox cofactors. Thus, for projected de novo designed constructions, the control of spatial organization of cofactor molecules within a dense array is initially given priority. Nevertheless, constructions accommodating dense arrays of different cofactors, some well within 1 nm from each other, still presents a significant challenge for protein design.     

Aspects of insect chemical ecology: exploitation of reception and detection as tools for deception of pests and beneficial insects

Empirical exploitation of insect reception and detection at the peripheral neurosensory level has been extremely valuable for identifying pheromones and other semiochemicals, mainly by electroantennogram or single cell preparations coupled with capillary gas chromatography. Differential sensitivity to semiochemicals at the single‐cell level has allowed the identification of some of the most active semiochemicals relating to host location and, more importantly, to the avoidance of nonhosts. However, in terms of molecular recognition, there is still a considerable gap in understanding the detection of particular molecules and their discrimination from closely‐related chemical structures. New approaches will be needed to understand the processes of molecular recognition more precisely. Nevertheless, from electrophysiological studies to the most advanced molecular techniques, it has been possible to identify semiochemicals for the deception of pests in their quest to find plant and animal hosts, as well as mates. Even the deception of insects antagonistic to pests, particularly parasitoids, can now be exploited for managing pests in more sustainable systems. Successes in exploiting insect semiochemicals in the interests of better agriculture and animal husbandry are exemplified, and potential new ways of learning more about reception and detection for deception are discussed. This takes the subject beyond the management of pest and beneficial insects to wider commercial and social opportunities.