The conformational phase space of the photoprotective switch in the major light harvesting complex II

Daskalakis, Vangelis; Papadatos, Sotiris; Stergiannakos, Taxiarchis

doi:10.1039/d0cc04486e

Cited by 25 publications

(42 citation statements)

References 53 publications

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“…To this end, we follow refs. 46 , 64 , 65 where it was proposed that an alteration of the inter-helical crossing angle between helices A and B (the torsion defined by the nodes A2–A1–B1–B2 in Fig. 5 a) could account for NPQ in LHCII monomers.…”

Section: Resultsmentioning

confidence: 99%

A different perspective for nonphotochemical quenching in plant antenna complexes

et al. 2021

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Light-harvesting complexes of plants exert a dual function of light-harvesting (LH) and photoprotection through processes collectively called nonphotochemical quenching (NPQ). While LH processes are relatively well characterized, those involved in NPQ are less understood. Here, we characterize the quenching mechanisms of CP29, a minor LHC of plants, through the integration of two complementary enhanced-sampling techniques, dimensionality reduction schemes, electronic calculations and the analysis of cryo-EM data in the light of the predicted conformational ensemble. Our study reveals that the switch between LH and quenching state is more complex than previously thought. Several conformations of the lumenal side of the protein occur and differently affect the pigments’ relative geometries and interactions. Moreover, we show that a quenching mechanism localized on a single chlorophyll-carotenoid pair is not sufficient but many chlorophylls are simultaneously involved. In such a diffuse mechanism, short-range interactions between each carotenoid and different chlorophylls combined with a protein-mediated tuning of the carotenoid excitation energies have to be considered in addition to the commonly suggested Coulomb interactions.

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Section: Resultsmentioning

confidence: 99%

A different perspective for nonphotochemical quenching in plant antenna complexes

et al. 2021

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“…[28][29][30][31][32][33] Furthermore, additional models were created taking into account the lumenal pH gradient and the presence of PsbS proteins trying to realistically mimic the NPQ process. [34][35][36][37][38] In these models, either the population transfer of excitons 39,40 or the associated rates were determined. 33,34 The major input parameters that are required in such calculations are the excitation energies of the individual pigments, also known as site energies, the excitonic couplings between the pigments and the so-called spectral densities.…”

Section: Introductionmentioning

confidence: 99%

Time-dependent atomistic simulations of the CP29 light-harvesting complex

Maity

Sarngadharan

Daskalakis

et al. 2021

The Journal of Chemical Physics

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Light harvesting as the first step in photosynthesis is of prime importance for life on earth. For a theoretical description of photochemical processes during light harvesting, spectral densities are key quantities. They serve as input functions for modeling the excitation energy transfer dynamics and spectroscopic properties. Herein, a recently developed procedure is applied to determine the spectral densities of the pigments in the minor antenna complex CP29 of photosystem II, which has recently gained attention because of its active role in non-photochemical quenching processes in higher plants. To this end, the density functional-based tight binding (DFTB) method has been employed to enable simulation of the ground state dynamics in a quantum-mechanics/molecular mechanics (QM/MM) scheme for each chlorophyll pigment. Subsequently, the time-dependent extension of the long-range corrected DFTB approach has been used to obtain the excitation energy fluctuations along the ground-state trajectories also in a QM/MM setting. From these results, the spectral densities have been determined and compared for different force fields and to spectral densities from other light-harvesting complexes. In addition, time-dependent and timeindependent excitonic Hamiltonians of the system have been constructed and applied to the determination of absorption spectra as well as exciton dynamics.

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“…The chemical space of natural products, and especially that of polyphenols, has provided valuable candidate lead molecules in a number of diseases, including COVID-19 [ 5 , 11 , 12 ]. All-atom molecular dynamics (MD) simulations, along with enhanced sampling techniques and elaborate methods of analysis, have allowed unprecedented insight into complex phenomena in biology at extreme efficiency and accuracy, especially for the conformational changes of proteins [ 13 , 14 , 15 ]. A comprehensive review on antiviral agents and simulation approaches employed for SARS-CoV-2 proteins can be found in [ 3 ].…”

Section: Introductionmentioning

confidence: 99%

Natural Polyphenols Inhibit the Dimerization of the SARS-CoV-2 Main Protease: The Case of Fortunellin and Its Structural Analogs

Panagiotopoulos

Karakasiliotis

et al. 2021

Molecules

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3CL-Pro is the SARS-CoV-2 main protease (MPro). It acts as a homodimer to cleave the large polyprotein 1ab transcript into proteins that are necessary for viral growth and replication. 3CL-Pro has been one of the most studied SARS-CoV-2 proteins and a main target of therapeutics. A number of drug candidates have been reported, including natural products. Here, we employ elaborate computational methods to explore the dimerization of the 3CL-Pro protein, and we formulate a computational context to identify potential inhibitors of this process. We report that fortunellin (acacetin 7-O-neohesperidoside), a natural flavonoid O-glycoside, and its structural analogs are potent inhibitors of 3CL-Pro dimerization, inhibiting viral plaque formation in vitro. We thus propose a novel basis for the search of pharmaceuticals as well as dietary supplements in the fight against SARS-CoV-2 and COVID-19.

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The conformational phase space of the photoprotective switch in the major light harvesting complex II

Abstract: Transitions between protein states are triggered by external stimuli. This knowledge leads to the control of protein function. Herein, we report a large scale (90μs) study on the conformational space...

Cited by 25 publications

References 53 publications

A different perspective for nonphotochemical quenching in plant antenna complexes

A different perspective for nonphotochemical quenching in plant antenna complexes

Time-dependent atomistic simulations of the CP29 light-harvesting complex

Natural Polyphenols Inhibit the Dimerization of the SARS-CoV-2 Main Protease: The Case of Fortunellin and Its Structural Analogs

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