Molecular Dynamics Simulations in Photosynthesis

Overview

Journal Photosynth Res

Publisher Springer

Date 2020 Apr 17

PMID 32297102

Citations 20

Authors

Nicoletta Liguori

Roberta Croce

Siewert J Marrink

Sebastian Thallmair

Affiliations

Soon will be listed here.

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.

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References

Prandi I, Viani L, Andreussi O, Mennucci B . Combining classical molecular dynamics and quantum mechanical methods for the description of electronic excitations: The case of carotenoids. J Comput Chem. 2016; 37(11):981-91. DOI: 10.1002/jcc.24286. View

Janosi L, Kosztin I, Damjanovic A . Theoretical prediction of spectral and optical properties of bacteriochlorophylls in thermally disordered LH2 antenna complexes. J Chem Phys. 2006; 125(1):014903. DOI: 10.1063/1.2210481. View

de Jong D, Liguori N, van den Berg T, Arnarez C, Periole X, Marrink S . Atomistic and Coarse Grain Topologies for the Cofactors Associated with the Photosystem II Core Complex. J Phys Chem B. 2015; 119(25):7791-803. DOI: 10.1021/acs.jpcb.5b00809. View

Schmid N, Eichenberger A, Choutko A, Riniker S, Winger M, Mark A . Definition and testing of the GROMOS force-field versions 54A7 and 54B7. Eur Biophys J. 2011; 40(7):843-56. DOI: 10.1007/s00249-011-0700-9. View

Ogata K, Yuki T, Hatakeyama M, Uchida W, Nakamura S . All-atom molecular dynamics simulation of photosystem II embedded in thylakoid membrane. J Am Chem Soc. 2013; 135(42):15670-3. DOI: 10.1021/ja404317d. View

Narzi D, Coccia E, Manzoli M, Guidoni L . Impact of molecular flexibility on the site energy shift of chlorophylls in Photosystem II. Biophys Chem. 2017; 229:93-98. DOI: 10.1016/j.bpc.2017.06.013. View

Hashemi Shabestari M, Wolfs C, Spruijt R, van Amerongen H, Huber M . Exploring the structure of the 100 amino-acid residue long N-terminus of the plant antenna protein CP29. Biophys J. 2014; 106(6):1349-58. PMC: 3985499. DOI: 10.1016/j.bpj.2013.11.4506. View

Daskalakis V . Protein-protein interactions within photosystem II under photoprotection: the synergy between CP29 minor antenna, subunit S (PsbS) and zeaxanthin at all-atom resolution. Phys Chem Chem Phys. 2018; 20(17):11843-11855. DOI: 10.1039/c8cp01226a. View

Monticelli L, Kandasamy S, Periole X, Larson R, Tieleman D, Marrink S . The MARTINI Coarse-Grained Force Field: Extension to Proteins. J Chem Theory Comput. 2015; 4(5):819-34. DOI: 10.1021/ct700324x. View

10.

Oostenbrink C, Soares T, van der Vegt N, van Gunsteren W . Validation of the 53A6 GROMOS force field. Eur Biophys J. 2005; 34(4):273-84. DOI: 10.1007/s00249-004-0448-6. View

11.

Uusitalo J, Ingolfsson H, Akhshi P, Tieleman D, Marrink S . Martini Coarse-Grained Force Field: Extension to DNA. J Chem Theory Comput. 2015; 11(8):3932-45. DOI: 10.1021/acs.jctc.5b00286. View

12.

Umena Y, Kawakami K, Shen J, Kamiya N . Crystal structure of oxygen-evolving photosystem II at a resolution of 1.9 Å. Nature. 2011; 473(7345):55-60. DOI: 10.1038/nature09913. View

13.

Seo S, Shinoda W . SPICA Force Field for Lipid Membranes: Domain Formation Induced by Cholesterol. J Chem Theory Comput. 2018; 15(1):762-774. DOI: 10.1021/acs.jctc.8b00987. View

14.

Guerra F, Adam S, Bondar A . Revised force-field parameters for chlorophyll-a, pheophytin-a and plastoquinone-9. J Mol Graph Model. 2015; 58:30-9. DOI: 10.1016/j.jmgm.2015.03.001. View

15.

Alessandri R, Souza P, Thallmair S, Melo M, De Vries A, Marrink S . Pitfalls of the Martini Model. J Chem Theory Comput. 2019; 15(10):5448-5460. PMC: 6785803. DOI: 10.1021/acs.jctc.9b00473. View

16.

Niyogi K, Truong T . Evolution of flexible non-photochemical quenching mechanisms that regulate light harvesting in oxygenic photosynthesis. Curr Opin Plant Biol. 2013; 16(3):307-14. DOI: 10.1016/j.pbi.2013.03.011. View

17.

Atilgan A, Durell S, Jernigan R, Demirel M, Keskin O, Bahar I . Anisotropy of fluctuation dynamics of proteins with an elastic network model. Biophys J. 2001; 80(1):505-15. PMC: 1301252. DOI: 10.1016/S0006-3495(01)76033-X. View

18.

Damjanovic A, Kosztin I, Kleinekathofer U, Schulten K . Excitons in a photosynthetic light-harvesting system: a combined molecular dynamics, quantum chemistry, and polaron model study. Phys Rev E Stat Nonlin Soft Matter Phys. 2002; 65(3 Pt 1):031919. DOI: 10.1103/PhysRevE.65.031919. View

19.

Liguori N, Roy L, Opacic M, Durand G, Croce R . Regulation of light harvesting in the green alga Chlamydomonas reinhardtii: the C-terminus of LHCSR is the knob of a dimmer switch. J Am Chem Soc. 2013; 135(49):18339-42. DOI: 10.1021/ja4107463. View

20.

Kim C, Choi B, Rhee Y . Excited state energy fluctuations in the Fenna-Matthews-Olson complex from molecular dynamics simulations with interpolated chromophore potentials. Phys Chem Chem Phys. 2017; 20(5):3310-3319. DOI: 10.1039/c7cp06303b. View