Molecular dynamics simulations in photosynthesis

Nicoletta Liguori, Roberta Croce, Siewert J Marrink, Sebastian Thallmair*

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

7 Citations (Scopus)
53 Downloads (Pure)

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.

Original languageEnglish
Pages (from-to)273-295
Number of pages23
JournalPhotosynthesis Research
Volume144
Issue number2
Early online date15-Apr-2020
DOIs
Publication statusPublished - May-2020

Keywords

  • Molecular dynamics
  • Photosynthesis
  • Light harvesting
  • Thylakoid membrane
  • Conformational switch
  • Coarse-grained
  • LIGHT-HARVESTING-COMPLEX
  • GRAINED FORCE-FIELD
  • ENERGY-TRANSFER PATHWAYS
  • EVOLVING PHOTOSYSTEM-II
  • CHLAMYDOMONAS-REINHARDTII
  • PROTEIN INTERACTIONS
  • COMPUTER-SIMULATION
  • THYLAKOID MEMBRANES
  • LHCII SUPERCOMPLEX
  • ELECTRON-TRANSFER

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