Two-level heterogenous energy migration. Modeling and application to purple bacteria

The dynamics of migration of electronic excitations and the efficiency of their trapping in two-dimensional ensembles of molecules were analyzed. Molecules were characterized using the following parameters: the width of long-wavelength bands, the values of extinction and rate constant of deactivation of electronic excitations, critical distances of migration close to those of dye molecules, in particular, bacteriochlorophyll a and purple bacteria. A comparative analysis of two-dimensional models of energy migration made it possible to chose a model with an optimum light-harvesting on traps from the largest numbers of light-absorbing molecules. It was shown that in ensembles of molecules having different spectral characteristics (spectral shifts between the short- and long-wavelength fractions of the molecules are hear 800 cm-1) the efficiency of excitation trapping is approximately 90 and 80% for the number of light-harvesting molecules per one trap 210 and 580, respectively.     

Time-resolved detection of energy transfer: theory and application to immunoassays

Energy-transfer measurements based upon acceptor fluorophore emission are plagued with background fluorescence resulting from absorption of the excitation light by the acceptor fluorophore. The present work examines the use of a long-lifetime donor fluorophore and a short-lifetime acceptor fluorophore, combined with pulsed-laser excitation and electronic gating of detector signals, to separate the component of acceptor emission due to energy transfer from the component due to absorption of the excitation light. Theoretical equations describing the acceptor fluorescence and integrated acceptor fluorescence show that increasing the integration delay relative to the excitation pulse should greatly enhance detection of the energy-transfer component. The time-resolved detection of energy transfer was tested in a competitive immunoassay format in which antibodies to human immunoglobulin G (IgG) F(ab')2 fragments were covalently labeled with pyrenebutyrate (tau = 100 ns) and IgG Fab' fragments were covalently labeled with B-phycoerythrin (tau = 2.5 ns). Solutions containing these two conjugates exhibited energy transfer from the pyrenebutyrate to the B-phycoerythrin upon excitation with a nitrogen laser. Acceptor emission was measured with 0- and 20-ns integration delays and the ratios of the energy-transfer component to the laser-excited component were found to increase by 9- to 15-fold when the 20-ns delay was used in three series of immunoassays. Good agreement between the experimental data and theory was obtained following convolution of the theoretical fluorescence responses with the instrumental response of the fluorometer.     

Introduction to theory/modeling methods in photosynthesis

Photosynthesis Research - Theory and molecular modeling play an increasingly important role in complementing the experimental findings and supporting the interpretation of the data. Owing to the...     

On the proposed energy switch in photosynthesis

This paper analyzes the “energy switch” that has often been proposed to direct quanta absorbed by a given photosynthetic unit alternately to the site of one and then the other primary reaction. Such a device is essential to the Franck-Rosenberg theory, but not to the Duysens-Witt-Kok (DWK) model, which needs to assume only that the reactions occur in series. If there is no energy switch, an incident quantum absorbed at any time by any particular pigment molecule stands a chance of ending up in the reactive site of either primary reaction. The “separate packages” model is a special case of this general picture. Without an energy switch, a series model requires a storage device to insure that a quantum will not be wasted if it arrives at the site of one reaction while the photosynthetic unit is set up to perform the other. Such a storage device can be appended to the DWK model. Alternatively, this model can be augmented by an energy switch. This gives what is commonly known as the “spillover model,” a confusing name which we suggest be abandoned. As a clear-cut-though perhaps technically unfeasible-test of the energy switch hypothesis, we imagine a quantum injector, a hypothetical source of flashing light which delivers a single quantum to every photosynthetic unit with each flash. We aim this useful figment at an (equally hypothetical) photosynthetic system all of whose units are set up to perform the same primary reaction. If there is an energy switch, we can now prepare a “synchronous” photosynthetic apparatus in which each photosynthetic unit is undergoing the same reaction at the same time.     

To automate or not to automate: this is the question

New protocols and instrumentation significantly boost the outcome of structural biology, which has resulted in significant growth in the number of deposited Protein Data Bank structures. However, even an enormous increase of the productivity of a single step of the structure determination process may not significantly shorten the time between clone and deposition or publication. For example, in a medium size laboratory equipped with the LabDB and HKL-3000 systems, we show that automation of some (and integration of all) steps of the X-ray structure determination pathway is critical for laboratory productivity. Moreover, we show that the lag period after which the impact of a technology change is observed is longer than expected.     

The question of the intermediate state P+Chl-in bacterial photosynthesis

In bacterial photosynthesis it has been proposed that an electron is transferred from the excited singlet state (P1) of theprimary electron donor first to a bacteriochlorophyll (BChl) molecule, generating a P⁺Chl charge-transfer state, and that BChl^-subsequently (4–7 ps) transfers an electron to a bacteriopheophytin molecule. Here we review the evidence for and against the intermediacy of P⁺BChl^- and present picosecond transient absorption and kinetic data that bear on this point. We conclude that there is no convincing evidence that P⁺BChl is a kinetically or spectrally resolved intermediary state in the charge separation process.     

Energy migration and exciton trapping in green plant photosynthesis

The possible origins of the different fluorescence decay components in green plants are discussed in terms of a random walk and Butler's bipartite model. The interaction of the excitations with the photosystem II reaction centers and, specifically, the regeneration of theses excitations by charge recombination within the reaction centers, are considered. Based on comparisons between fluorescence decay profiles, time-dependent exciton annihilation and photoelectric phenomena, it appears that the fast 200 ps decay component corresponds to primary energy transport from the antenna to the reaction centers and is dominant in filling the photosystem II reaction centers.     

Structure-based modeling of energy transfer in photosynthesis

We provide a minimal model for a structure-based simulation of excitation energy transfer in pigment–protein complexes (PPCs). In our treatment, the PPC is assembled from its building blocks. The latter are defined such that electron exchange occurs only within, but not between these units. The variational principle is applied to investigate how the Coulomb interaction between building blocks changes the character of the electronic states of the PPC. In this way, the standard exciton Hamiltonian is obtained from first principles and a hierarchy of calculation schemes for the parameters of this Hamiltonian arises. Possible extensions of this approach are discussed concerning (i) the inclusion of dispersive site energy shifts and (ii) the inclusion of electron exchange between pigments. First results on electron exchange within the special pair of photosystem II of cyanobacteria and higher plants are presented and compared with earlier results on purple bacteria. In the last part of this mini-review, the coupling of electronic and nuclear degrees of freedom is considered. First, the standard exciton–vibrational Hamiltonian is parameterized with the help of a normal mode analysis of the PPC. Second, dynamical theories are discussed that exploit this Hamiltonian in the study of dissipative exciton motion.     

To die or not to die: that is the autophagic question

Macroautophagy (commonly referred to as autophagy) is the process by which intact organelles and/or large portions of the cytoplasm are engulfed within double-membraned autophagic vacuoles for degradation. Whereas basal levels of autophagy ensure the physiological turnover of old and damaged organelles, the massive accumulation of autophagic vacuoles may represent either an alternative pathway of cell death or an ultimate attempt for cells to survive by adapting to stress. The activation of the autophagic pathway beyond a certain threshold may promote cell death directly, by causing the collapse of cellular functions as a result of cellular atrophy (autophagic, or type II, cell death). Alternatively, autophagy can lead to the execution of apoptotic (type I) or necrotic (type III) cell death programs, presumably via common regulators such as proteins from the Bcl-2 family. On the other hand, limited self-eating can provide cells with metabolic substrates to meet their energetic demands under stressful conditions, such as nutrient deprivation, or favor the selective elimination of damaged (and potentially dangerous) organelles. In these instances, autophagy operates as a pro-survival mechanism. The coordinate regulation of these opposite effects of autophagy relies upon a complex network of signal transducers, most of which also participate in non-autophagic signaling cascades. Thus, autophagy occupies a crucial position within the cell's metabolism, and its modulation may represent an alternative therapeutic strategy in several pathological settings including cancer and neurodegeneration. Here, we present a general outline of autophagy followed by a detailed analysis of organelle-specific autophagic pathways and of their intimate connections with cell death.     

To B or not to B: PIP2 answers the question

In a recent issue of Molecular Cell, Papayannopoulos et al. (2005) show that N-WASP activation of actin-related protein2/3 (Arp2/3) is ultrasensitive to PI(4,5)P(2) concentration. We discuss how interactions between basic regions in proteins and negatively charged membranes can produce sharp on-off switches that may regulate biological activity.     

To sialylate,or not to sialylate: that is the question

Most oropharyngeal pathogens express sialic acid units on their surfaces, mimicking the sialyl-rich mucin layer coating epithelial cells and the glycoconjugates present on virtually all host cell surfaces and serum proteins. Unlike the host's cells, which synthesize sialic acids endogenously, several microbial pathogens use truncated sialylation pathways. How microorganisms regulate sialic acid metabolism to ensure an adequate supply of free sugar for surface remodeling is a new area of research interest to basic scientists and those focused on the clinical outcome of the host-pathogen interaction.