O.J.G. Somsen

Transduction of Intracellular and Intercellular Dynamics in Yeast Glycolytic Oscillations

Under certain well-defined conditions, a population of yeast cells exhibits glycolytic oscillations that synchronize through intercellular acetaldehyde. This implies that the dynamic phenomenon of the oscillation propagates within and between cells. We here develop a method to establish by which route dynamics propagate through a biological reaction network. Application of the method to yeast demonstrates how the oscillations and the synchronization signal can be transduced. That transduction is not so much through the backbone of glycolysis, as via the Gibbs energy and redox coenzyme couples (ATP/ADP, and NADH/NAD), and via both intra- and intercellular acetaldehyde.

Direct observation of sub-picosecond equilibration of excitation energy in the light-harvesting antenna of Rhodospirillum rubrum.

Excitation energy transfer in the light-harvesting antenna of Rhodospirillum rubrum was studied at room temperature using sub-picosecond transient absorption measurements. Upon excitation of Rs. rubrum membranes with a 200 fs, 600 nm laser flash in the Qx transition of the bacteriochlorophyll-a (BChl-a) absorption, the induced transient absorption changes in the Qy region were monitored. In Rs. rubrum membranes the observed delta OD spectrum exhibits ground state bleaching, excited state absorption and stimulated emission. Fast Qx --> Qy relaxation occurs in approximately 100-200 fs as reflected by the building up of stimulated emission. An important observation is that the zero-crossing of the transient difference absorption (delta OD) spectrum exhibits a dynamic redshift from 863 to 875 nm that can be described with by a single exponential with 325 fs time constant. The shape of the transient difference spectrum observed in a purified subunit of the core light-harvesting antenna, B820, consisting of only a single interacting pair of BChl-as, is similar to the spectrum observed in Rs. rubrum membranes and clearly different from the spectrum of BChl-a in a protein/detergent mixture. In the B820 and monomeric BChl-a preparations the 100-200 fs Qx --> Qy relaxation is still observed, but the dynamic redshift of the delta OD spectrum is absent. The spectral kinetics observed in the Rs. rubrum membranes are interpreted in terms of the dynamics of excitation equilibration among the antenna subunits that constitute the inhomogeneously broadened antenna. A simulation of this process using a set of reasonable physical parameters is consistent with an average hopping time in the core light harvesting of 220-270 fs, resulting in an average single-site excitation lifetime of 50-70 fs. The observed rate of this equilibration process is in reasonable agreement with earlier estimations for the hopping time from more indirect measurements. The implications of the findings for the process of excitation trapping by reaction centers will be discussed.

Glucose and the ATP paradox in yeast.

A sustained decrease in the intracellular ATP concentration has been observed when extra glucose was added to yeast cells growing aerobically under glucose limitation. Because glucose degradation is the main source of ATP-derived free energy, this is a counter-intuitive phenomenon, which cannot be attributed to transient ATP consumption in the initial steps of glycolysis. We present a core model for aerobic growth in which glucose supplies carbon, as well as free energy, for biosynthesis. With Metabolic Control Analysis and numerical simulations, we demonstrate that the decrease in the ATP concentration can be reproduced if the biosynthetic route is more strongly activated by carbon substrates than is the catabolic (ATP-producing) route.

A perturbed two-level model for exciton trapping in small photosynthetic systems.

The study of exciton trapping in photosynthetic systems provides significant information about migration kinetics within the light harvesting antenna (LHA) and the reaction center (RC). We discuss two random walk models for systems with weakly coupled pigments, with a focus on the application to small systems (10-40 pigments/RC). Details of the exciton transfer to and from the RC are taken into consideration, as well as migration within the LHA and quenching in the RC. The first model is obtained by adapting earlier local trap models for application to small systems. The exciton lifetime is approximated by the sum of three contributions related to migration in the LHA, trapping by the RC, and quenching within the RC. The second model is more suitable for small systems and regards the finite rate of migration within the LHA as a perturbation of the simplified model, where the LHA and the RC are each represented by a single pigment level. In this approximation, the exciton lifetime is the sum of a migration component and a single nonlinear expression for the trapping and quenching of the excitons. Numerical simulations demonstrate that both models provide accurate estimates of the exciton lifetime in the intermediate range of 20-50 sites/RC. In combination, they cover the entire range of very small to very large photosynthetic systems. Although initially intended for regular LHA lattices, the models can also be applied to less regular systems. This becomes essential as more details of the structure of these systems become available. Analysis with these models indicates that the excited state decay in LH1 is limited by the average rate at which excitons transfer to the RC from neighboring sites in the LHA. By comparing this to the average rate of transfer within the LHA, various structural models that have been proposed for the LH1 core antenna are discussed.

The Role of Resonant Vibrations in Electronic Energy Transfer.

Abstract Nuclear vibrations play a prominent role in the spectroscopy and dynamics of electronic systems. As recent experimental and theoretical studies suggest, this may be even more so when vibrational frequencies are resonant with transitions between the electronic states. Herein, a vibronic multilevel Redfield model is reported for excitonically coupled electronic two‐level systems with a few explicitly included vibrational modes and interacting with a phonon bath. With numerical simulations the effects of the quantized vibrations on the dynamics of energy transfer and coherence in a model dimer are illustrated. The resonance between the vibrational frequency and energy gap between the sites leads to a large delocalization of vibronic states, which then results in faster energy transfer and longer‐lived mixed coherences.

Metabolic Control From The Back Benches: Biochemistry Towards Biocomplexity

Much of biochemistry finds its roots in the study of metabolism. Substantial progress came when it was discovered that important metabolic processes, such as fermentation of glucose to lactate by erythrocytes or to ethanol by yeast, consisted of series of apparently independent chemical reactions. The independence of these reactions was established by purifying protein fractions that were each capable of uniquely catalysing one of the reactions. Likewise membrane-dependent biological free-energy transduction was reduced to the action of two proton pumps, i.e. one linked to the electron-transfer chain in the mitochondrial or bacterial inner membrane, the other coupled to ATP hydrolysis (Mitchell, 1979). Accordingly, biochemistry and molecular biology assimilated the paradigm that each of the physiological processes of the living cell could be understood in terms of a series of independent biochemical reactions (Fig. 1). Although some processes are reluctant to be reduced in this manner this is usually believed to be a matter of practice rather than of principle.

Reply to Comment on `Non-equilibrium thermodynamics of light absorption'

In response to the comments made by Dr Andrews, we explain why his arguments support rather than compromise the analysis published in our recent paper. Our thermodynamical description of the early steps of photosynthesis is consistent both with the established theory of quantum electrodynamics and with the known biophysics of the process. Moreover, it ties in with the non-equilibrium thermodynamics of chemical processes.