Search

Ultrafast transient infrared (TRIR) spectroscopy is widely used to measure the excitation-induced structural changes of protein-bound chromophores. Here, we design a novel and general strategy to compute TRIR spectra of photoreceptors by combining μs-long MM molecular dynamics with ps-long QM/AMOEBA Born–Oppenheimer molecular dynamics (BOMD) trajectories for both ground and excited electronic states. As a proof of concept, the strategy is here applied to AppA, a blue-light-utilizing flavin (BLUF) protein, found in bacteria. We first analyzed the short-time evolution of the embedded flavin upon excitation revealing that its dynamic Stokes shift is ultrafast and mainly driven by the internal reorganization of the chromophore. A different normal-mode representation was needed to describe ground- and excited-state IR spectra. In this way, we could assign all of the bands observed in the measured transient spectrum. In particular, we could characterize the flavin isoalloxazine-ring region of the spectrum, for which a full and clear description was missing.

Nowadays, hybrid QM/MM approaches are widely used to study (supra)molecular systems embedded in complex biological matrices. However, in their common formulation, mutual interactions between the quantum and classical parts are neglected. To go beyond such a picture, a polarizable embedding can be used. In this perspective, we focus on the induced point dipole formulation of polarizable QM/MM approaches and we show how efficient and linear scaling implementations have allowed their application to the modeling of complex biosystems. In particular, we discuss their use in the prediction of spectroscopies and in molecular dynamics simulations, including Born–Oppenheimer dynamics, enhanced sampling techniques and nonadiabatic descriptions. We finally suggest the theoretical and computational developments that still need to be achieved to overcome the limitations which have prevented so far larger diffusion of these methods.

We present a fully atomistic simulation of linear optical spectra (absorption, fluorescence and circular dichroism) of the Light Harvesting Complex II (LHCII) trimer using a hybrid approach, which couples a quantum chemical description of the chlorophylls with a classical model for the protein and the external environment (membrane and water). The classical model uses a polarizable Molecular Mechanics force field, thus allowing mutual polarization effects in the calculations of the excitonic properties. The investigation is performed both on the crystal structure and on structures generated by a μs long classical molecular dynamics simulation of the complex within a solvated membrane. The results show that this integrated approach not only provides a good description of the excitonic properties and optical spectra without the need for additional refinements of the excitonic parameters, but it also allows an atomistic investigation of the relative importance of electronic, structural and environment effects in determining the optical spectra.

Phytochromes are red-light sensing proteins, with important light-regulatory roles in different organisms, which are capturing an increasing interest in bioimaging and optogenetics. Upon absorption of light by the embedded bilin chromophore, they undergo structural changes that extend from the chromophore to the protein and finally drive the biological function. Up to now, the underlying mechanism still has to be characterized fully. Here we investigate the Pfr activated form of a bacterial phytochrome, by combining extensive molecular dynamics simulations with a polarizable QM/MM description of the spectroscopic properties, revealing a large structure relaxation in solution, compared to the crystal structure, both in the chromophore-binding pocket and in the overall structure of the phytochrome. Our results indicate that the final opening of the dimeric structure is preceded by an important internal reorganization of the phytochrome specific (PHY) domain involving a bend of the helical spine connecting the PHY domain with the chromophore-binding domain, opening the way to a new understanding of the activation pathway., A combination of MD simulations and a polarizable QM/MM description of a bacteriophytochrome in solution reveals the changes in the chromophore-binding pocket and in the overall structure of the phytochrome involved in the signaling mechanism.

The function of light-harvesting complexes is determined by a complex network of dynamic interactions among all the different components: the aggregate of pigments, the protein, and the surrounding environment. Complete and reliable predictions on these types of composite systems can be only achieved with an atomistic description. In the last few decades, there have been important advances in the atomistic modeling of light-harvesting complexes. These advances have involved both the completeness of the physical models and the accuracy and effectiveness of the computational protocols. In this Perspective, we present an overview of the main theoretical and computational breakthroughs attained so far in the field, with particular focus on the important role played by the protein and its dynamics. We then discuss the open problems in their accurate modeling that still need to be addressed. To illustrate an effective computational workflow for the modeling of light harvesting complexes, we take as an example the plant antenna complex CP29 and its H111N mutant.

We present the first comprehensive multiscale computational investigation of Resonance Raman (RR), absorption and Circular Dichroism (CD) spectra of the resting state of the dimeric phy- tochrome ofDeinococcus radiodurans. The spectra are simulated in all their components, namely the energy position and the lineshapes of both the far-red and the blue bands. To achieve such a goal, we have combined a 4.5μsMD simulation of the solvated dimeric phytochrome with a hybrid quantum mechanics/molecular mechanics (QM/MM) model, which accounts for both electrostatic and mutual polarization effects between the QM and the MM subsystems. From simulations, we find a transient H-bond network within the binding pocket of the chromophore that, unexpect- edly, do not significantly affect the absorption and CD spectra. In parallel, we characterize the vibrations which are more strongly coupled to the excitation confirming the important role of the hydrogen-out-of-plane mode of the vinyl C-H in between C and D rings together with the expected C=C stretching of the double bond involved in the photoisomerization.

Recently, a method to calculate the absorption and circular dichroism (CD) spectra based on the exciton coupling has been developed. In this work, the method was utilized for the decomposition of the CD and circularly polarized luminescence (CPL) spectra of a multichromophoric system into chromophore contributions for recently developed through-space conjugated oligomers. The method which has been implemented using rotatory strength in the velocity form and therefore it is gauge-invariant, enables us to evaluate the contribution from each chromophoric unit and locally excited state to the CD and CPL spectra of the total system. The excitonic calculations suitably reproduce the full calculations of the system, as well as the experimental results. We demonstrate that the interactions between electric transition dipole moments of adjacent chromophoric units are crucial in the CD and CPL spectra of the multichromophoric systems, while the interactions between electric and magnetic transition dipole moments are not negligible. © 2018 Wiley Periodicals, Inc.

We present here a combined spectroscopic and theoretical analysis of the binding of N,N’-bis(2-(1-piperazino)ethyl)-3,4,9,10-perylenetetracarboxylic acid diimide dichloride (PZPERY) to different biosubstrates. Absorbance titrations and circular dichroism experiments, melting studies and isothermal calorimetry (ITC) titrations reveal a picture where the binding to natural double-stranded DNA is very different from that to double and triple-stranded RNAs (poly(A)∙poly(U) and poly(U)∙poly(A)⁎poly(U)). As confirmed also by the structural and energetic details clarified by density functional theory (DFT) calculations, intercalation occurs for DNA, with a process driven by the combination of aggregates disruption and monomers intercalation. Oppositely, for RNAs, no intercalation but groove binding with the formation of supramolecular aggregates is observed. Among all the tested biosubstrates, the affinity of PZPERY towards DNA G-quadruplexes (G4) is the greatest one with a preference for human telomeric G4s. Focusing on hybrid G4 forms, either sitting-atop (“tetrad-parallel”) or lateral (“groove-parallel”) binding modes were considered in the discussion of the experimental results and molecular dynamics (MD) simulations. Both turned out to be possible concurrently, in agreement also with the experimental binding stoichiometries higher than 2:1., “la Caixa” Foundation (LCF/PR/PR12/11070003), Ministerio de Ciencia, Innovación y Universidades-FEDER (RTI2018-102040-B-100) and Junta de Castilla y León-FEDER (BU305P18). LC acknowledges funding by the European Research Council, under the grant ERC-AdG-786714 (LIFETimeS)

Due to the involvement of oxygen in many essential metabolic reactions, all living organisms have developed molecular systems that allow adaptive physiological and metabolic transitions depending on oxygen availability. In mammals, the expression of hypoxia-response genes is controlled by the heterodimeric Hypoxia-Inducible Factor. The activity of this transcriptional regulator is linked mainly to the oxygen-dependent hydroxylation of conserved proline residues in its α-subunit, carried out by prolyl-hydroxylases, and subsequent ubiquitination via the E3 ligase von Hippel-Lindau tumor suppressor, which targets Hypoxia-Inducible Factor-α to the proteasome. By exploiting bioengineered versions of this mammalian oxygen sensor, we designed and optimized a synthetic device that drives gene expression in an oxygen-dependent fashion in plants. Transient assays in Arabidopsis (Arabidopsis thaliana) mesophyll protoplasts indicated that a combination of the yeast Gal4/upstream activating sequence system and the mammalian oxygen sensor machinery can be used effectively to engineer a modular, oxygen-inducible transcriptional regulator. This synthetic device also was shown to be selectively controlled by oxygen in whole plants when its components were expressed stably in Arabidopsis seedlings. We envision the exploitation of our genetically encoded controllers to generate plants able to switch gene expression selectively depending on oxygen availability, thereby providing a proof of concept for the potential of synthetic biology to assist agricultural practices in environments with variable oxygen provision.

A donor acceptor dyad composed of a BF2-chelated dipyrromethene (BODIPY) and a C-60 fullerene has been newly synthesized and characterized. The two moieties are linked by direct addition of an azido substituted BODIPY on the C-60, producing an imino fullerene BODIPY adduct. The photoinduced charge transfer process in this system was studied by ultrafast transient absorption spectroscopy. Electron transfer toward the fullerene was found to occur selectively exciting both the BODIPY chromophore at 475 nm and the C-60 unit at 266 nm on a time scale of a few picoseconds, but the dynamics of charge separation was different in the two cases. Eletrochemical studies provided information on the redox potentials of the involved species and spectroelectrochemical measurements allowed to unambiguously assign the absorption band of the oxidized BODIPY moiety, which helped in the interpretation of the transient absorption spectra. The experimental studies were complemented by a theoretical analysis based on DFT computations of the excited state energies of the two components and their electronic couplings, which allowed identification of the charge transfer mechanism and rationalization of the different kinetic behavior observed by changing the excitation conditions.

Nonlinear electronic spectroscopies represent one of the most powerful techniques to study complex multichromophoric architectures. For these systems, in fact, linear spectra are too congested to be used to disentangle the many coupled vibroelectronic processes that are activated. By using a 2D approach, instead, a clear picture can be achieved, but only when the recorded spectra are combined with a proper interpretative model. So far, this has been almost always achieved through parametrized exciton Hamiltonians that necessarily introduce biases and/or arbitrary assumptions. In this study, a first-principles approach is presented that combines accurate quantum chemical descriptions with state-of-the-art models for the environment through the use of atomistic and polarizable embeddings. Slow and fast bath dynamics, along with exciton transport between the pigments, are included. This approach is applied to the 2DES spectroscopy of the Light-Harvesting 2 (LH2) complex of purple bacteria. Simulations are extended over the entire visible-near-infrared spectral region to cover both carotenoid and bacteriochlorophyll signals. Our results provide an accurate description of excitonic properties and relaxation pathways, and give an unprecedented insight into the interpretation of the spectral signatures of the measured 2D signals.