Carotenoid-Chlorophyll Interactions in a Photosynthetic Antenna Protein: A Supramolecular QM/MM Approach

Guberman‐Pfeffer, Matthew J.; Gascón, José A.

doi:10.3390/molecules23102589

Cited by 10 publications

(8 citation statements)

References 32 publications

(61 reference statements)

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“…In an analogous fashion, photosynthetic organisms pair highly conserved photosystems with habitat-specific light-harvesting antennas to occupy very different spectral and spatial niches. 90 Because cellular respiration depends on the flow of electrons through the "nanowires", it seems evolutionarily advantageous for the conductivity to be largely insensitive to mutational insults. 91 Mutagenesis, therefore, is not likely to be a very successful strategy for modulating the electrical conductivity of cytochrome "nanowires" over many orders of magnitude.…”

Section: Marcus Electron Transfer Rate (K Et )mentioning

confidence: 99%

Structural Determinants of Redox Conduction Favor Robustness over Tunability in Microbial Cytochrome Nanowires

Guberman‐Pfeffer

2023

J. Phys. Chem. B

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Structural determinants of a 103-fold variation in electrical conductivity for helical homopolymers of tetra-, hexa-, and octa-heme cytochromes (named Omc- E, S, and Z, respectively) from Geobacter sulfurreducens are investigated with the Pathways model for electron tunneling, classical molecular dynamics, and hybrid quantum/classical molecular mechanics. Thermally averaged electronic couplings for through-space heme-to-heme electron transfer in the “nanowires” computed with density functional theory are ≤0.015 eV. Pathways analyses also indicate that couplings match within a factor of 5 for all “nanowires”, but some alternative tunneling routes are found involving covalent protein backbone bonds (Omc- S and Z) or propionic acid-ligating His H-bonds on adjacent hemes (OmcZ). Reorganization energies computed from electrostatic vertical energy gaps or a version of the Marcus continuum expression parameterized on the total (donor + acceptor) solvent-accessible surface area typically agree within 20% and fall within the range 0.48–0.98 eV. Reaction free energies in all three “nanowires” are ≤|0.28| eV, even though Coulombic interactions primarily tune the site redox energies by 0.7–1.2 eV. Given the conserved energetic parameters, redox conductivity differs by < 103-fold among the cytochrome “nanowires”. Redox currents do not exceed 3.0 × 10–3 pA at a physiologically relevant 0.1 V bias, with the slowest electron transfers being on a (μs) timescale much faster than typical (ms) enzymatic turnovers. Thus, the “nanowires” are proposed to be functionally robust to variations in structure that provide a habitat-customized protein interface. The 30 pA to 30 nA variation in conductivity previously reported from atomic force microscopy experiments is not intrinsic to the structures and/or does not result from the physiologically relevant redox conduction mechanism.

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Section: Marcus Electron Transfer Rate (K Et )mentioning

confidence: 99%

Structural Determinants of Redox Conduction Favor Robustness over Tunability in Microbial Cytochrome Nanowires

Guberman‐Pfeffer

2023

J. Phys. Chem. B

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“…DLPNO−STEOM–CCSD calculations predict two excited states in the Q region, at 1.75 and 2.24 eV for chla in gas phase 62 . while the absorption peaks of chla were observed in (600–700) nm range 63 . Our TDDFT calculations show that the absorption wavelengths of the carotenoids are in visible region (432–452) nm, while chl a and chl b has (356, 380) nm wavelength (water) respectively.…”

Section: Resultsmentioning

confidence: 96%

“…See Table 4 . chlaz diade has absorption wavelength (340 nm) using CAM-B3LYP/6‐31+G(d,p) method 42 , while chlap diade has two absorption wavelength peaks in (440–480) nm range in aqueous state with MM/QM method 63 .…”

Section: Resultsmentioning

confidence: 99%

Physicochemical, antioxidant properties of carotenoids and its optoelectronic and interaction studies with chlorophyll pigments

Srivastava

2021

Sci Rep

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The physicochemical and antioxidant properties of seven carotenoids: antheraxanthin, β-carotene, neoxanthin, peridinin, violaxanthin, xanthrophyll and zeaxanthin were studied by theoretical means. Then the Optoelectronic properties and interaction of chlorophyll-carotenoid complexes are analysed by TDDFT and IGMPLOT. Global reactivity descriptors for carotenoids and chlorophyll (Chla, Chlb) are calculated via conceptual density functional theory (CDFT). The higher HOMO–LUMO (HL) gap indicated structural stability of carotenoid, chlorophyll and chlorophyll-carotenoid complexes. The chemical hardness for carotenoids and Chlorophyll is found to be lower in the solvent medium than in the gas phase. Results showed that carotenoids can be used as good reactive nucleophile due to lower µ and ω. As proton affinities (PAs) are much lower than the bond dissociation enthalpies (BDEs), it is anticipated that direct antioxidant activity in these carotenoids is mainly due to the sequential proton loss electron transfer (SPLET) mechanism with dominant solvent effects. Also lower PAs of carotenoid suggest that antioxidant activity by the SPLET mechanism should be a result of a balance between proclivities to transfer protons. Reaction rate constant with Transition-State Theory (TST) were estimated for carotenoid-Chlorophyll complexes in gas phase. Time dependent Density Functional Theory (TDDFT) showed that all the chlorophyll (Chla, Chlb)–carotenoid complexes show absorption wavelength in the visible region. The lower S1–T1 adiabatic energy gap indicated ISC transition from S1 to T1 state.

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“…The accuracy of the coupling calculations (0.061 eV) is evident in the close comparison between the eigenvalues and the two lowest excitation energies of the full dimer calculation at the QM/MM level. It is interesting to compare the magnitude of the excitonic coupling (0.061 eV = 492 cm −1 ) with recent calculations by our group on the antenna peridinin chlorophyl a protein (PCP) [ 21 ]. In PCP, there is a 4:1 peridinin (Per) to Chl a ratio.…”

Section: Resultsmentioning

confidence: 99%

Spectral Features of Canthaxanthin in HCP2. A QM/MM Approach

et al. 2021

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The increased interest in sequencing cyanobacterial genomes has allowed the identification of new homologs to both the N-terminal domain (NTD) and C-terminal domain (CTD) of the Orange Carotenoid Protein (OCP). The N-terminal domain homologs are known as Helical Carotenoid Proteins (HCPs). Although some of these paralogs have been reported to act as singlet oxygen quenchers, their distinct functional roles remain unclear. One of these paralogs (HCP2) exclusively binds canthaxanthin (CAN) and its crystal structure has been recently characterized. Its absorption spectrum is significantly red-shifted, in comparison to the protein in solution, due to a dimerization where the two carotenoids are closely placed, favoring an electronic coupling interaction. Both the crystal and solution spectra are red-shifted by more than 50 nm when compared to canthaxanthin in solution. Using molecular dynamics (MD) and quantum mechanical/molecular mechanical (QM/MM) studies of HCP2, we aim to simulate these shifts as well as obtain insight into the environmental and coupling effects of carotenoid–protein interactions.

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Carotenoid-Chlorophyll Interactions in a Photosynthetic Antenna Protein: A Supramolecular QM/MM Approach

Cited by 10 publications

References 32 publications

Structural Determinants of Redox Conduction Favor Robustness over Tunability in Microbial Cytochrome Nanowires

Structural Determinants of Redox Conduction Favor Robustness over Tunability in Microbial Cytochrome Nanowires

Physicochemical, antioxidant properties of carotenoids and its optoelectronic and interaction studies with chlorophyll pigments

Spectral Features of Canthaxanthin in HCP2. A QM/MM Approach

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