Thermal site energy fluctuations in photosystem I: new insights from MD/QM/MM calculations

Reiter, Sebastian; Kiss, F.; Hauer, Jürgen; Vivie‐Riedle, Regina de

doi:10.1039/d2sc06160k

Cited by 8 publications

(2 citation statements)

References 159 publications

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“…This observation was made possible through the long 3 μs MD simulation. While the protein environment primarily influences the changes in site energies through electrostatic effects, the role of changing the Mg coordination should not be overlooked in these discussions, as it can induce structural changes to the chlorophyll molecules, thereby influencing the site energies. ,,,− As observed in the present study, these changes occur on time scales longer than the excitonic dynamics and are often not accounted for in short QM/MM MD trajectories or single-point calculations, though potentially introducing static disorder. Alternatively, one can model many copies of the same LHC in slightly different environments .…”

Section: Discussionmentioning

confidence: 99%

Protein Effects on the Excitation Energies and Exciton Dynamics of the CP24 Antenna Complex

Sarngadharan,

Holtkamp,

Kleinekathöfer

2024

J. Phys. Chem. B

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In this study, the site energy fluctuations, energy transfer dynamics, and some spectroscopic properties of the minor light-harvesting complex CP24 in a membrane environment were determined. For this purpose, a 3 μs-long classical molecular dynamics simulation was performed for the CP24 complex. Furthermore, using the density functional tight binding/molecular mechanics molecular dynamics (DFTB/MM MD) approach, we performed excited state calculations for the chlorophyll a and chlorophyll b molecules in the complex starting from five different positions of the MD trajectory. During the extended simulations, we observed variations in the site energies of the different sets as a result of the fluctuating protein environment. In particular, a water coordination to Chl-b 608 occurred only after about 1 μs in the simulations, demonstrating dynamic changes in the environment of this pigment. From the classical and the DFTB/MM MD simulations, spectral densities and the (time-dependent) Hamiltonian of the complex were determined. Based on these results, three independent strongly coupled chlorophyll clusters were revealed within the complex. In addition, absorption and fluorescence spectra were determined together with the exciton relaxation dynamics, which reasonably well agrees with experimental time scales.

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Section: Discussionmentioning

confidence: 99%

Protein Effects on the Excitation Energies and Exciton Dynamics of the CP24 Antenna Complex

Sarngadharan,

Holtkamp,

Kleinekathöfer

2024

J. Phys. Chem. B

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“…Recent structural analyses have also contributed to theoretical studies on the physical processes occurring within type-I RCs. ,,,,− Adolphs et al calculated the excitonic coupling strength between every pair of Chl a molecules on PSI using the Poisson TrESP (P-TrESP) method and obtained the spatial distribution of the site energy shift (SES) values using the charge density coupling (CDC) method. SES values indicate the differences in the electrostatic interactions between the excited and ground states of the Chl a molecules and the surrounding polypeptides.…”

Section: Introductionmentioning

confidence: 99%

Experimental and Theoretical Mutation of Exciton States on the Smallest Type-I Photosynthetic Reaction Center Complex of a Green Sulfur Bacterium Chlorobaclum tepidum

Kimura,

Kitoh-Nishioka,

Kondo

et al. 2024

J. Phys. Chem. B

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The exciton states on the smallest type-I photosynthetic reaction center complex of a green sulfur bacterium Chlorobaculum tepidum (GsbRC) consisting of 26 bacteriochlorophylls a (BChl a) and four chlorophylls a (Chl a) located on the homodimer of two PscA reaction center polypeptides were investigated. This analysis involved the study of exciton states through a combination of theoretical modeling and the genetic removal of BChl a pigments at eight sites. ( 1) A theoretical model of the pigment assembly exciton state on GsbRC was constructed using Poisson TrESP (P-TrESP) and charge density coupling (CDC) methods based on structural information. The model reproduced the experimentally obtained absorption spectrum, circular dichroism spectrum, and excitation transfer dynamics, as well as explained the effects of mutation. (2) Eight BChl a molecules at different locations on the GsbRC were selectively removed by genetic exchange of the His residue, which ligates the central Mg atom of BChl a, with the Leu residue on either one or two PscAs in the RC. His locations are conserved among all type-I RC plant polypeptide, cyanobacteria, and bacteria amino acid sequences. (3) Purified mutant-GsbRCs demonstrated distinct absorption and fluorescence spectra at 77 K, which were different from each other, suggesting successful pigment removal. (4) The same mutations were applied to the constructed theoretical model to analyze the outcomes of these mutations. (5) The combination of theoretical predictions and experimental mutations based on structural information is a new tool for studying the function and evolution of photosynthetic reaction centers.

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Development of artificial photosystems based on designed proteins for mechanistic insights into photosynthesis

Serrano,

Echavarría,

Mejias

2024

Protein Science

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This review aims to provide an overview of the progress in protein‐based artificial photosystem design and their potential to uncover the underlying principles governing light‐harvesting in photosynthesis. While significant advances have been made in this area, a gap persists in reviewing these advances. This review provides a perspective of the field, pinpointing knowledge gaps and unresolved challenges that warrant further inquiry. In particular, it delves into the key considerations when designing photosystems based on the chromophore and protein scaffold characteristics, presents the established strategies for artificial photosystems engineering with their advantages and disadvantages, and underscores the recent breakthroughs in understanding the molecular mechanisms governing light‐harvesting, charge separation, and the role of the protein motions in the chromophore's excited state relaxation. By disseminating this knowledge, this article provides a foundational resource for defining the field of bio‐hybrid photosystems and aims to inspire the continued exploration of artificial photosystems using protein design.

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Thermal site energy fluctuations in photosystem I: new insights from MD/QM/MM calculations

Abstract: Cyanobacterial photosystem I (PSI) is one of the most efficient photosynthetic machineries found in nature. Due to the large scale and complexity of the system, the energy transfer mechanism from...

Cited by 8 publications

References 159 publications

Protein Effects on the Excitation Energies and Exciton Dynamics of the CP24 Antenna Complex

Protein Effects on the Excitation Energies and Exciton Dynamics of the CP24 Antenna Complex

Experimental and Theoretical Mutation of Exciton States on the Smallest Type-I Photosynthetic Reaction Center Complex of a Green Sulfur Bacterium Chlorobaclum tepidum

Development of artificial photosystems based on designed proteins for mechanistic insights into photosynthesis

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