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ASCT2 is an obligate exchanger of neutral amino acids, contributing to cellular amino acid homeostasis. ASCT2 belongs to the same family (SLC1) as Excitatory Amino Acid Transporters (EAATs) that concentrate glutamate in the cytosol. The mechanism that makes ASCT2 an exchanger rather than a concentrator remains enigmatic. Here, we employ cryo-electron microscopy and molecular dynamics simulations to elucidate the structural basis of the exchange mechanism of ASCT2. We establish that ASCT2 binds three Na + ions per transported substrate and visits a state that likely acts as checkpoint in preventing Na + ion leakage, both features shared with EAATs. However, in contrast to EAATs, ASCT2 retains one Na + ion even under Na + -depleted conditions. We demonstrate that ASCT2 cannot undergo the structural transition in TM7 that is essential for the concentrative transport cycle of EAATs. This structural rigidity and the high-affinity Na + binding site effectively confine ASCT2 to an exchange mode., (© 2024. The Author(s).)

As a critical step in advancing the simulation of photosynthetic complexes, we present the Martini 3 coarse-grained (CG) models of key cofactors associated with light harvesting (LHCII) proteins and the photosystem II (PSII) core complex. Our work focuses on the parametrization of beta-carotene, plastoquinone/quinol, violaxanthin, lutein, neoxanthin, chlorophyll A, chlorophyll B, and heme. We derived the CG parameters to match the all-atom reference simulations, while structural and thermodynamic properties of the cofactors were compared to experimental values when available. To further assess the reliability of the parameterization, we tested the behavior of these cofactors within their physiological environments, specifically in a lipid bilayer and bound to photosynthetic complexes. The results demonstrate that our CG models maintain the essential features required for realistic simulations. This work lays the groundwork for detailed simulations of the PSII-LHCII super-complex, providing a robust parameter set for future studies.

The photosystem II PsbS protein triggers the photoprotective mechanism of plants by sensing the acidification of the thylakoid lumen. Despite the mechanism of action of PsbS would require a pH-dependent monomerization of the dimeric form, a clear connection between the pH-induced structural changes and the dimer stability is missing. Here, by applying constant pH coarse-grained and all-atom molecular dynamics simulations, we investigate the pH-dependent structural response of the PsbS dimer. We find that the pH variation leads to structural changes in the lumen-exposed helices, located at the dimeric interface, providing an effective switch between PsbS inactive and active form. Moreover, the monomerization free energies reveal that in the neutral pH conformation, where the network of H-bond interactions at the dimeric interface is destroyed, the protein-protein interaction is weaker. Our results show how the pH-dependent conformations of PsbS affect their dimerization propensity, which is at the basis of the photoprotective mechanism.

The excited state proton transfer (ESPT) reaction from the photoacid 8-hydroxypyrene-1,3,6-trisulfonic acid (HPTS or pyranine) to an acetate molecule has been investigated in explicit aqueous solution via excited state ab initio molecular dynamics simulations based on hybrid quantum/molecular mechanics (QM/MM) potentials. In all the trajectories, the direct proton transfer has been observed in the excited state within 1 ps. We find that the initial structural configuration extracted from the ground state distribution strongly affects the ESPT kinetics. Indeed, the relative orientation of the proton donor-acceptor pair and the presence of a water molecule hydrogen bonded to the phenolic acid group of the pyranine are the key factors to facilitate the ESPT. Furthermore, we analyze the vibrational fingerprints of the ESPT reaction, reproducing the blue shift of the acetate CO stretching ( CO ac ), from 1666 to 1763 cm -1 testifying the transformation of acetate to acetic acid. Finally, our findings suggest that the acetate CC stretching ( CC ac ) is also sensitive to the progress of the ESPT reaction. The CC ac stretching is indeed ruled by the two vibrational modes (928 and 1426 cm -1 ), that in the excited state are alternately activated when the proton is shared or bound to the donor/acceptor, respectively.

The CLC family of anion channels and transporters includes Cl - /H + exchangers (blocked by F - ) and F - /H + exchangers (or CLC F s). CLC F s contain a glutamate (E318) in the central anion-binding site that is absent in CLC Cl - /H + exchangers. The X-ray structure of the protein from Enterococcus casseliflavus (CLC F -eca) shows that E318 tightly binds to F - when the gating glutamate (E118; highly conserved in the CLC family) faces the extracellular medium. Here, we use classical and DFT-based QM/MM metadynamics simulations to investigate proton transfer and release by CLC F -eca. After up to down movement of protonated E118, both glutamates combine with F - to form a triad, from which protons and F - anions are released as HF. Our results illustrate how glutamate insertion into the central anion-binding site of CLC F -eca permits the release of H + to the cytosol as HF, thus enabling a net 1:1 F - /H + stoichiometry.

In this work, we simulate the excited state proton transfer (ESPT) reaction involving the pyranine photoacid and an acetate molecule as proton acceptor, connected by a bridge water molecule. We employ ab initio molecular dynamics combined with an hybrid quantum/molecular mechanics (QM/MM) framework. Furthermore, a time-resolved vibrational analysis based on the wavelet-transform allows one to identify two low frequency vibrational modes that are fingerprints of the ESPT event: a ring wagging and ring breathing. Their composition suggests their key role in optimizing the structure of the proton donor-acceptor couple and promoting the ESPT event. We find that the choice of the QM/MM partition dramatically affects the photoinduced reactivity of the system. The QM subspace was gradually extended including the water molecules directly interacting with the pyranine-water-acetate system. Indeed, the ESPT reaction takes place when the hydrogen bond network around the reactive system is taken into account at full QM level.

We present electronic structure methods to unveil the non-radiative pathways of photoinduced charge transfer (CT) reactions that play a main role in photophysics and light harvesting technologies. A prototypical π-stacked molecular complex consisting of an electron donor (1-chloronaphthalene, 1ClN) and an electron acceptor (tetracyanoethylene, TCNE) was investigated in dichloromethane solution for this purpose. The characterization of TCNE:π:1ClN in both its equilibrium ground and photoinduced low-lying CT electronic states was performed by using a reliable and accurate theoretical-computational methodology exploiting ab initio molecular dynamics simulations. The structural and vibrational time evolution of key vibrational modes is found to be in excellent agreement with femtosecond stimulated Raman spectroscopy experiments [R. A. Mathies et al. , J. Phys. Chem. A , 2018, 122 , 14, 3594], unveiling a correlation between vibrational fingerprints and electronic properties. The evaluation of nonadiabatic coupling matrix elements along generalized normal modes has made possible the interpretation on the molecular scale of the activation of nonradiative relaxation pathways towards the ground electronic state. In particular, two low frequency vibrational modes such as the out of plane bending and dimer breathing and the TCNE central C[double bond, length as m-dash]C stretching play a prominent role in relaxation phenomena from the electronic CT state to the ground state one., Competing Interests: There are no conflicts of interest to declare., (This journal is © The Royal Society of Chemistry.)

The rapid growth of time-resolved spectroscopies and the theoretical advances in ab initio molecular dynamics (AIMD) pave the way to look at the real-time molecular motion following the electronic excitation. Here, we exploited the capabilities of AIMD combined with a hybrid implicit/explicit model of solvation to investigate the ultrafast excited-state proton transfer (ESPT) reaction of a super photoacid, known as QCy9, in water solution. QCy9 transfers a proton to a water solvent molecule within 100 fs upon the electronic excitation in aqueous solution, and it is the strongest photoacid reported in the literature so far. Because of the ultrafast kinetics, it has been experimentally hypothesized that the ESPT escapes the solvent dynamics control (Huppert et al., J. Photochem. Photobiol. A 2014, 277, 90). The sampling of the solvent configuration space on the ground electronic state is the first key step toward the simulation of the ESPT event. Therefore, several configurations in the Franck-Condon region, describing an average solvation, were chosen as starting points for the excited-state dynamics. In all cases, the excited-state evolution spontaneously leads to the proton transfer event, whose rate is strongly dependent on the hydrogen bond network around the proton acceptor solvent molecule. Our study revealed that the explicit representation at least of three solvation shells around the proton acceptor molecule is necessary to stabilize the excess proton. Furthermore, the analysis of the solvent molecule motions in proximity of the reaction site suggested that even in the case of the strongest photoacid, the ESPT is actually assisted by the solvation dynamics of the first and second solvation shells of the water accepting molecule.

We present a novel time-resolved vibrational analysis for studying photoinduced nuclear relaxation. Generalized modes velocities are defined from ab initio molecular dynamics and wavelet transformed, providing the time localization of vibrational signals in the electronic excited state. The photoexcited pyranine in aqueous solution is presented as a case study. The transient and sequential activation of the simulated vibrational signals is in good agreement with vibrational dynamics obtained from femtosecond stimulated Raman spectroscopy data.

Electrons and protons are the main actors in play in proton coupled electron transfer (PCET) reactions, which are fundamental in many biological (i.e., photosynthesis and enzymatic reactions) and electrochemical processes. The mechanism, energetics and kinetics of PCET reactions are strongly controlled by the coupling between the transferred electrons and protons. Concerted PCET reactions are classified according to the electronical adiabaticity degree of the process. To discriminate among different mechanisms, we propose a new analysis based on the use of electron density based indexes. We choose, as test case, the 3-Methylphenoxyl/phenol system in two different conformations to show how the proposed analysis is a suitable tool to discriminate between the different degree of adiabaticity of PCET processes. The very low computational cost of this procedure is extremely promising to analyze and provide evidences of PCET mechanisms ruling the reactivity of many biological and catalytic systems., (© 2020 Wiley Periodicals, Inc.)

CLC channels and transporters conduct or transport various kinds of anions, with the exception of fluoride, which acts as an effective inhibitor. Here, we performed sub-nanosecond DFT-based QM/MM simulations of the E. coli anion/proton exchanger ClC-ec1 and observed that fluoride binds incoming protons within the selectivity filter, with excess protons shared with the gating glutamate E148. Depending on E148 conformation, the competition for the proton can involve either a direct F - /E148 interaction or the modulation of water molecules bridging the two anions. The direct interaction locks E148 in a conformation that does not allow for proton transport, and thus inhibits protein function.

In this work, excited state ab initio molecular dynamics together with a time resolved vibrational analysis is employed to shed light on the vibrational photoinduced dynamics of a well-known diarylethene molecule experiencing a ring opening reaction upon electronic excitation. The photoreactivity of diarylethenes is recognized to be controlled by a non-adiabatic intersection point between the ground and the first excited state surfaces. The computation of an energy scan, along a suitable reaction coordinate, allows us to identify the region of potential energy surfaces in which the ground (S0) and the first excited (S1) state are well separated. The adiabatic sampling of that region in S1 shows that in the first 3 picoseconds, the central CC bond, which is subject to break, oscillates in an antiphase with respect to the energy gap ΔE(S1 - S0). A multiresolution analysis based on the wavelet transform was then applied to the structural parameters extracted from the excited state dynamics. The wavelet maps show characteristic oscillations of the frequencies, mainly CC stretching and CCC bending localized on the central 4-ring moiety. Moreover, we have identified the main frequency (methyl wagging motion) involved in the modulation of these oscillations. The anharmonic coupling within a group of vibrational modes was therefore highlighted, in good agreement with experimental evidence. For the first time, a quantitative analysis of time resolved signals from a wavelet transform/ab initio molecular dynamics approach was performed.

Fe(III)-Mimochrome VI (MC6) is a recently reported artificial heme-peptide conjugate system with a high peroxidase-like activity. By design, its structure features a five-coordinated Fe(III)-deuteroporphyrin active site, embedded in a compact α-helix-heme-α-helix "sandwich" motif. Up to now, no detailed MC6 structural characterization is available. In this work we propose a theoretical investigation based on molecular dynamics (MD) simulations and hybrid quantum mechanics/molecular mechanics (QM/MM) optimizations, aimed to shed light on several Fe(III)-MC6 structural features and to validate the de novo designed fold. Key structural elements were analyzed to achieve indirect insight relevant to understand Fe(III)-MC6 catalytic performances in solution. Extensive MD simulations showed a partial stability of the "sandwich" fold in water solution. The smaller peptide chain bonded to the heme revealed a high conformational freedom, which promoted the exposition of the heme distal side to the solvent. Regarding the accessibility of water molecules, even in Fe(III)-MC6 "closed" structure the heme cavity appeared hydrated, suggesting an easy accessibility by exogenous ligands. Fe(III)-MC6 structure in both high and low spin states was then further characterized through hybrid QM/MM optimizations. In particular, an accurate description of the active site structure was obtained, allowing a direct comparison of Fe(III)-MC6 coordination environment with that observed in the Horseradish Peroxidase crystal structures. Our results suggest a structural similarity between Fe(III)-MC6 and the natural enzyme. This study supports the interpretation of data from experimental Fe(III)-MC6 structural and functional characterization and the rational design of new artificial mimics with improved catalytic performances., (© 2018 Wiley Periodicals, Inc.)

Advances in time-resolved vibrational spectroscopy techniques provided a new stimulus for understanding the transient molecular dynamics triggered by the electronic excitation. The detailed interpretation of such time-dependent spectroscopic signals is a challenging task from both experimental and theoretical points of view. We simulated and analyzed the transient photorelaxation of the pyranine photoacid in aqueous solution, with special focus on structural parameters and low frequency skeleton modes that are possibly preparatory for the photoreaction occurring at later time, as suggested by experimental spectroscopic studies. To this aim, we adopted an accurate computational protocol that combines excited state ab initio molecular dynamics within an hybrid quantum mechanical/molecular mechanics framework and a time-resolved vibrational analysis based on the Wavelet transform. According to our results, the main nuclear relaxation on the excited potential energy surface is completed in about 500 fs, in agreement with experimental data. The rearrangement of C-C bonds occurs according to a complex vibrational dynamics, showing oscillatory patterns that are out of phase and modulated by modes below 200 cm -1 . We also analyzed in both the ground and the excited state the evolution of some structural parameters involved in excited state proton transfer reaction, namely, those involving the pyranine and the water molecule hydrogen bonded to the phenolic O-H group. Both the hydrogen bond distance and the intermolecular orientation are optimized in the excited state, resulting in a tighter proton donor-acceptor couple. Indeed, we found evidence that collective low frequency skeleton modes, such as the out of plane wagging at 108 cm -1 and the deformation at 280 cm -1 , are photoactivated by the ultrafast part of the relaxation and modulate the pyranine-water molecule rearrangement, favoring the preparatory step for the photoreactivity.