Two decades of Martini: Better beads, broader scope

SJ Marrink, L Monticelli, MN Melo… - Wiley …, 2023 - Wiley Online Library
The Martini model, a coarse‐grained force field for molecular dynamics simulations, has
been around for nearly two decades. Originally developed for lipid‐based systems by the …

Light harvesting in oxygenic photosynthesis: Structural biology meets spectroscopy

R Croce, H van Amerongen - Science, 2020 - science.org
BACKGROUND The harvesting of photons is the first step in photosynthesis, the biological
process that transforms solar energy into chemical energy. The photosynthetic membranes …

Martini 3: a general purpose force field for coarse-grained molecular dynamics

PCT Souza, R Alessandri, J Barnoud, S Thallmair… - Nature …, 2021 - nature.com
The coarse-grained Martini force field is widely used in biomolecular simulations. Here we
present the refined model, Martini 3 (http://cgmartini. nl), with an improved interaction …

In situ structure of the red algal phycobilisome–PSII–PSI–LHC megacomplex

X You, X Zhang, J Cheng, Y Xiao, J Ma, S Sun… - Nature, 2023 - nature.com
In oxygenic photosynthetic organisms, light energy is captured by antenna systems and
transferred to photosystem II (PSII) and photosystem I (PSI) to drive photosynthesis,. The …

Solar energy conversion by photosystem II: principles and structures

D Shevela, JF Kern, G Govindjee, J Messinger - Photosynthesis research, 2023 - Springer
Photosynthetic water oxidation by Photosystem II (PSII) is a fascinating process because it
sustains life on Earth and serves as a blue print for scalable synthetic catalysts required for …

Computational modeling of realistic cell membranes

SJ Marrink, V Corradi, PCT Souza, HI Ingolfsson… - Chemical …, 2019 - ACS Publications
Cell membranes contain a large variety of lipid types and are crowded with proteins,
endowing them with the plasticity needed to fulfill their key roles in cell functioning. The …

Emerging diversity in lipid–protein interactions

V Corradi, BI Sejdiu, H Mesa-Galloso… - Chemical …, 2019 - ACS Publications
Membrane lipids interact with proteins in a variety of ways, ranging from providing a stable
membrane environment for proteins to being embedded in to detailed roles in complicated …

Protein–ligand binding with the coarse-grained Martini model

PCT Souza, S Thallmair, P Conflitti… - Nature …, 2020 - nature.com
The detailed understanding of the binding of small molecules to proteins is the key for the
development of novel drugs or to increase the acceptance of substrates by enzymes …

Water networks in photosystem II using crystalline molecular dynamics simulations and room-temperature XFEL serial crystallography

MD Doyle, A Bhowmick, DC Wych… - Journal of the …, 2023 - ACS Publications
Structural dynamics of water and its hydrogen-bonding networks play an important role in
enzyme function via the transport of protons, ions, and substrates. To gain insights into these …

Multifaceted computational modeling in glycoscience

S Perez, O Makshakova - Chemical Reviews, 2022 - ACS Publications
Glycoscience assembles all the scientific disciplines involved in studying various molecules
and macromolecules containing carbohydrates and complex glycans. Such an ensemble …