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Light-Induced Function: from Excitation to Signal through Time and Space

Periodic Reporting for period 1 - LIFETimeS (Light-Induced Function: from Excitation to Signal through Time and Space)

Reporting period: 2018-09-01 to 2020-02-29

Organisms of all domains of life are capable of sensing, using and responding to light. This is achieved through the use of specific proteins which contain a molecule or a molecular aggregate (the pigment(s)) able to absorb light in selected regions of the visible spectrum. The molecular mechanisms used are diverse, but the starting event is an electronic excitation localized on the pigment(s). This initial excitation rapidly “travels” across space to be converted in other forms of energy and finally used to complete the biological function.
Here, we propose to create a single theoretical and computational framework able to “follow” the action of light from the initial electronic excitation up to the final biological function.
Theoretically addressing this cascade of processes calls for new models and computational strategies able to reproduce the dynamics across multiple space and time scales. Such a goal is formidably challenging as the interactions and the dynamics involved at each scale follow completely different laws, from those of the quantum world to those of classical particles.
Through the novel point of observation that will be realized, it will be possible not only to reveal the ‘design principles’ used by Nature but also to give a “practical” instrument to test “in silico” new techniques for the control of cellular processes by manipulating protein functions through light.
In the first reporting period we have mostly focused on the accurate description of the first time and space scale, namely the electronic and structural changes induced by the light absorption. The strategy has been based on the formulation and implementation of a hybrid approach which combines quantum chemical and classical models in a fully and integration it into molecular dynamics simulations. This computational machinery has been applied to various systems, among which we quote the ones for which we have obtained the most important results.

1) In photosynthetic purple bacteria, the light-harvesting can be tuned in response to the light conditions during cell growth. One of the used strategies is to tune the energy of the excitons in the major fight- harvesting complex. By applying our novel approach, for the first time, we have revealed that the mechanisms that govern the exciton tuning use the different H-bonding environment around the bacteriochlorophyll pigments to dynamically control both internal and inter-pigment degrees of freedom.
2) The photosynthetic apparatus of higher plants can dissipate excess excitation energy during high light exposure, by deactivating excited chlorophylls through a mechanism called non- photochemical quenching. However, the precise molecular details of quenching and the mechanism regulating the quenching level are still not completely understood. We have shown that a charge transfer state involving a specific carotenoid pigment can efficiently quench chlorophyll excitation, and reduce the excitation lifetime of the major light-harvesting complex of Photosystem II. Through a combination of molecular dynamics simulations, multiscale quantum chemical calculations, and kinetic modeling, we have demonstrated that the quenching level can be finely tuned by the protein, by regulating the energy of the charge transfer state. Our results suggest that the protein scaffold can act as a molecular switch to activate or deactivate the quenching mechanism through small changes in its structural constraints and electric fields.
3) To adapt to different light conditions, photosynthetic cyanobacteria have developed photoregulatory mechanisms that allow them to modulate the amount of energy harvested and dissipate the excess in heat. These mechanisms are mediated by a protein, the so-called Orange Carotenoid Protein (OCP). Upon exposure to high light conditions, OCP opens up into two separated but linked domains allowing the embedded carotenoid to translocate in one domain becoming active as a quencher for the antenna complexes. After having successfully reproduced the experimental spectra of the two complexes, we have used the obtained results to formulate a new hypothesis for the photoactivation mechanism. According to this hypothesis, the constraints of the binding pocket and the unfavorable electrostatic fields acting on the carotenoid in the closed form are the driving force leading to the dissociation and separation of the two domains accompanied by carotenoid translocation.
4) In plants, bacteria and fungi, red-light-sensing proteins (phytochromes) control diverse cellular functions. In these systems, the protein binds a tetrapyrrole chromophore (a bilin) which, absorbing light, acts as a switch between resting and active states. However, how the photoactivated changes in the chromophore can induce a global rearrangement of the protein is still poorly understood. Applying our computational machinery to a bacteriophytochrome, for the first time, it has been possible to accurately simulate absorption, circular dichroism and Resonance Raman spectra and reveal the main chromophore-protein interactions. The completeness and accuracy achieved in this study show that the selected integrated approach which combines a long molecular dynamics simulation with an accurate QM/MM description, represents a valid strategy to describe photo-induced multiscale processes in complex biosystems. The natural following step, which is in progress at the moment, is the extension of the same approach to investigate the downstream cascade of photochemical and conformational processes determining the photobiological activity of the phytochrome.
When considering the many different photosensing proteins present in living organisms, an image of evolutionary flexibility emerges, with examples of fusion proteins from multiple types of photosensors and photosensitive domains shared among diverse arrays of proteins. However, large questions remain: what are the ‘design principles’ used by Nature? Are there common themes, or is each solution truly unique?
The importance of answering these questions lies not only in the possibility of achieving a better understanding of the molecular mechanisms at the basis of the biological photoresponse but also in that of controlling the activity of biosystems in vivo and being able to manipulate protein functions in a noninvasive way and with unprecedented spatiotemporal resolution using light.
Here, we propose to create a novel theoretical and computational framework that, for the first time, will be able to “follow” the action of light, from the initial ultrafast electronic process localized at the subnanoscale, up to the final biological function covering time scales of the order of milliseconds. This description will be possible only if a new conceptual machinery is designed and transformed into new computational algorithms and new tools for the analyses of the simulations.
The completeness and accuracy reached by the simulations based on such a new machinery will represent a breakthrough in our understanding of the mechanisms which govern the light-driven bioactivity. The resulting outcome will show not only that a new way of looking at life sciences is possible but that computational molecular modeling can play a primary role in making biology predictable and ‘engineer-able’.