All-Atom Molecular Dynamics Simulation of a Photosystem I/Detergent Complex

Abstract

All-atom molecular dynamics (MD) simulation was used to investigate the solution structure and dynamics of the photosynthetic pigment-protein complex photosystem I (PSI) from Thermosynechococcus elongatus embedded in a toroidal belt of n-dodecyl-β-d-maltoside (DDM) detergent. Evaluation of root-mean-square deviations (RMSDs) relative to the known crystal structure show that the protein complex surrounded by DDM molecules is stable during the 200 ns simulation time, and root-mean-square fluctuation (RMSF) analysis indicates that regions of high local mobility correspond to solvent-exposed regions such as turns in the transmembrane α-helices and flexible loops on the stromal and lumenal faces. Comparing the protein-detergent complex to a pure detergent micelle, the detergent surrounding the PSI trimer is found to be less densely packed but with more ordered detergent tails, contrary to what is seen in most lipid bilayer models. We also investigated any functional implications for the observed conformational dynamics and protein-detergent interactions, discovering interesting structural changes in the psaL subunits associated with maintaining the trimeric structure of the protein. Importantly, we find that the docking of soluble electron mediators such as cytochrome c6 and ferredoxin to PSI is not significantly impacted by the solubilization of PSI in detergent.

Molecular dynamics simulations in photosynthesis

“…Various MD studies have shown that there is a heterogeneity in flexibility along the structure both at the level of the photosystems and of the single LHCs: as it could be expected, the most flexible domains are the ones more exposed to the membrane/water environment, i.e., external protein subunits in the case of PSII and PSI (Ogata et al 2013;Harris et al 2014;van Eerden et al 2017a, b, c) or exposed protein domains in the case of isolated LHCs Thallmair et al 2019). The most rigid parts are instead the core protein subunits of the photosystems and the core domains of the LHCs.…”

Molecular dynamics simulations of large macromolecular complexes

“…A remarkable example is the 200 ns MD simulation of the 3-million-atom system comprising the trimeric photosynthetic pigment-protein complex, photosystem I (PSI), embedded in a detergent belt of n-dodecyl- β -D-maltoside (DDM). The study performed by Frymier and coworkers [73]* 9 gave atomic resolution insight into the impact of the detergent on conformational dynamics of the system and its possible implications on PSI functionality.…”

“… 9 [73]* MD simulations provide insight into the in vitro behavior of photosystem I (PSI) in detergent. …”

Sortase-Mediated Ligation of PsaE-Modified Photosystem I from Synechocystis sp. PCC 6803 to a Conductive Surface for Enhanced Photocurrent Production on a Gold Electrode

“…12 Furthermore, for efficient energy conversion of PSI-integrated technologies, it is important to develop technologies that are reproducible and are able to control the orientation of PSI molecules on conductive substrates, while maintaining the functionality of the protein. 13 4 In such a process, the primary electron donor, the P 700 reaction center in PSI, is excited to P 700 * (E m = -1.3 V vs. SHE). The excited electron in P 700 * is passed to the primary electron acceptors, F A /F B (E m = -520 mV/-580 mV vs. SHE), which in turn reduces ferredoxin (E m = -440 mV vs. SHE).…”