Abstract
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.
Highlights
The photosynthetic membrane, or thylakoid, is a continuous membrane system consisting of a lipid bilayer composed mainly of galactolipids and phospholipids (Duchêne and Siegenthaler 2000), with embedded protein complexes and cofactors
The pigment-to-protein ratio is generally very high in the antennae: in the case of plants and green algae, for example, ~ 25 kDa of protein can bind ~ 15 kDa of pigments (Nicol and Croce 2018). Such a large pigment/protein ratio results in crowded supercomplexes, e.g., in the example of the largest photosystem II (PSII) supercomplex isolated from plants (Caffarri et al 2009), this packing corresponds to a dimeric core binding 18 light-harvesting complexes (LHCs) for a total of ~ 314 Chls and ~ 88 Cars and 4 pheophytins plus additional cofactors and lipids (Su et al 2017)
This review aims to introduce the reader to the basic principles of Molecular dynamics (MD) simulations, their strengths, and limitations as well as their synergetic potential if employed in combination with experimental techniques
Summary
The photosynthetic membrane, or thylakoid, is a continuous membrane system consisting of a lipid bilayer composed mainly of galactolipids and phospholipids (Duchêne and Siegenthaler 2000), with embedded protein complexes and cofactors. Besides the lower number of particles, CG simulations come with another advantage with respect to their computational efficiency: the potential energy landscape is smoothened compared to atomistic FFs which allows the use of a larger time step
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