Exploring the Structure of the 100 Amino-Acid Residue Long N-Terminus of the Plant Antenna Protein CP29

Shabestari, Maryam Hashemi; Wolfs, C.J.A.M.; Spruijt, Ruud B.; Amerongen, Herbert van; Huber, Martina

doi:10.1016/j.bpj.2013.11.4506

Cited by 11 publications

(13 citation statements)

References 49 publications

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“…This work provided structural insights to a series of previous experimental findings. For example, high disorder was systematically observed via simulations at the N-terminus, in agreement with EPR/ESR results (Dockter et al 2012;Shabestari et al 2014). The MD simulations revealed that the motions of the N-terminus correlate with changes in the excitonic interactions of the lowest energy site of the complex, represented by a couple of Chls (Remelli et al 1999;Novoderezhkin et al 2005;Müh et al 2010) (Fig.…”

Section: (Sub)μs Timescale: Fast Conformational Changes Of the Photossupporting

confidence: 76%

Molecular dynamics simulations in photosynthesis

Liguori¹,

Croce²,

Marrink

et al. 2020

Photosynth Res

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Photosynthesis is regulated by a dynamic interplay between proteins, enzymes, pigments, lipids, and cofactors that takes place on a large spatio-temporal scale. Molecular dynamics (MD) simulations provide a powerful toolkit to investigate dynamical processes in (bio)molecular ensembles from the (sub)picosecond to the (sub)millisecond regime and from the Å to hundreds of nm length scale. Therefore, MD is well suited to address a variety of questions arising in the field of photosynthesis research. In this review, we provide an introduction to the basic concepts of MD simulations, at atomistic and coarse-grained level of resolution. Furthermore, we discuss applications of MD simulations to model photosynthetic systems of different sizes and complexity and their connection to experimental observables. Finally, we provide a brief glance on which methods provide opportunities to capture phenomena beyond the applicability of classical MD.Publisher's Note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

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Section: (Sub)μs Timescale: Fast Conformational Changes Of the Photossupporting

confidence: 76%

Molecular dynamics simulations in photosynthesis

Liguori¹,

Croce²,

Marrink

et al. 2020

Photosynth Res

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“…It can be shown that while during the simulation the helix regions maintain an almost identical structure to that of the crystal, the stromal loop and especially the N-terminus of the protein strongly deviate from the crystal structure. EPR/ESR studies on LHCII and on the homologous antenna CP29 have previously shown that the N-terminus is indeed highly flexible 27 29 , adopting various conformations in solution, suggesting that this domain is constitutively highly disordered. It can be concluded that compared to the crystal, LHCII in the membrane maintains the rigid alpha-helix core structure, while differs in the peripheral region, especially in the stromal-exposed domains.…”

Section: Resultsmentioning

confidence: 99%

From light-harvesting to photoprotection: structural basis of the dynamic switch of the major antenna complex of plants (LHCII)

Liguori¹,

Periole

Marrink

et al. 2015

Sci Rep

124

181

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Light-Harvesting Complex II (LHCII) is largely responsible for light absorption and excitation energy transfer in plants in light-limiting conditions, while in high-light it participates in photoprotection. It is generally believed that LHCII can change its function by switching between different conformations. However, the underlying molecular picture has not been elucidated yet. The available crystal structures represent the quenched form of the complex, while solubilized LHCII has the properties of the unquenched state. To determine the structural changes involved in the switch and to identify potential quenching sites, we have explored the structural dynamics of LHCII, by performing a series of microsecond Molecular Dynamics simulations. We show that LHCII in the membrane differs substantially from the crystal and has the signatures that were experimentally associated with the light-harvesting state. Local conformational changes at the N-terminus and at the xanthophyll neoxanthin are found to strongly correlate with changes in the interactions energies of two putative quenching sites. In particular conformational disorder is observed at the terminal emitter resulting in large variations of the excitonic coupling strength of this chlorophyll pair. Our results strongly support the hypothesis that light-harvesting regulation in LHCII is coupled with structural changes.

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“…3c,d ). Spectroscopic analyses 44 revealed that Ile65 is highly mobile, likely serving as a point of flexibility in the loop, while the Thr48–Ile65 region contains a helical stretch and a random coil. It is therefore plausible that the distal part of the long hairpin is responsible for “tying the knot” by homodimerizing to form the structured area at the center of the connecting density between the two Lhcb4 subunits.…”

Section: Resultsmentioning

confidence: 99%

Pea PSII-LHCII supercomplexes form pairs by making connections across the stromal gap

Albanese

Melero

Engel

et al. 2017

Sci Rep

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In higher plant thylakoids, the heterogeneous distribution of photosynthetic protein complexes is a determinant for the formation of grana, stacks of membrane discs that are densely populated with Photosystem II (PSII) and its light harvesting complex (LHCII). PSII associates with LHCII to form the PSII-LHCII supercomplex, a crucial component for solar energy conversion. Here, we report a biochemical, structural and functional characterization of pairs of PSII-LHCII supercomplexes, which were isolated under physiologically-relevant cation concentrations. Using single-particle cryo-electron microscopy, we determined the three-dimensional structure of paired C2S2M PSII-LHCII supercomplexes at 14 Å resolution. The two supercomplexes interact on their stromal sides through a specific overlap between apposing LHCII trimers and via physical connections that span the stromal gap, one of which is likely formed by interactions between the N-terminal loops of two Lhcb4 monomeric LHCII subunits. Fast chlorophyll fluorescence induction analysis showed that paired PSII-LHCII supercomplexes are energetically coupled. Molecular dynamics simulations revealed that additional flexible physical connections may form between the apposing LHCII trimers of paired PSII-LHCII supercomplexes in appressed thylakoid membranes. Our findings provide new insights into how interactions between pairs of PSII-LHCII supercomplexes can link adjacent thylakoids to mediate the stacking of grana membranes.

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Exploring the Structure of the 100 Amino-Acid Residue Long N-Terminus of the Plant Antenna Protein CP29

Cited by 11 publications

References 49 publications

Molecular dynamics simulations in photosynthesis

Molecular dynamics simulations in photosynthesis

From light-harvesting to photoprotection: structural basis of the dynamic switch of the major antenna complex of plants (LHCII)

Pea PSII-LHCII supercomplexes form pairs by making connections across the stromal gap

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