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 …

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 …

Computational Lipidomics with insane: A Versatile Tool for Generating Custom Membranes for Molecular Simulations

TA Wassenaar, HI Ingólfsson… - Journal of chemical …, 2015 - ACS Publications
For simulations of membranes and membrane proteins, the generation of the lipid bilayer is
a critical step in the setup of the system. Membranes comprising multiple components pose …

Crosstalk and trade‐offs: plant responses to climate change‐associated abiotic and biotic stresses

CP Leisner, N Potnis, A Sanz‐Saez - Plant, Cell & Environment, 2023 - Wiley Online Library
As sessile organisms, plants are constantly challenged by a dynamic growing environment.
This includes fluctuations in temperature, water availability, light levels, and changes in …

[HTML][HTML] Photosynthetic, respiratory and extracellular electron transport pathways in cyanobacteria

DJ Lea-Smith, P Bombelli, R Vasudevan… - Biochimica et Biophysica …, 2016 - Elsevier
Cyanobacteria have evolved elaborate electron transport pathways to carry out
photosynthesis and respiration, and to dissipate excess energy in order to limit cellular …

[HTML][HTML] Protein post-translational modifications: In silico prediction tools and molecular modeling

M Audagnotto, M Dal Peraro - Computational and structural biotechnology …, 2017 - Elsevier
Post-translational modifications (PTMs) occur in almost all proteins and play an important
role in numerous biological processes by significantly affecting proteins' structure and …

Comparative molecular dynamics simulation studies of realistic eukaryotic, prokaryotic, and archaeal membranes

ID Pogozheva, GA Armstrong, L Kong… - Journal of chemical …, 2022 - ACS Publications
We present a comparative all-atom molecular dynamics simulation study of 18
biomembrane systems with lipid compositions corresponding to eukaryotic, bacterial, and …

[HTML][HTML] Molecular dynamics simulations of membrane proteins and their interactions: from nanoscale to mesoscale

M Chavent, AL Duncan, MSP Sansom - Current opinion in structural biology, 2016 - Elsevier
Highlights•Simulations provide a computational tool to probe membrane structure and
dynamics.•Simulations can successfully predict lipid binding sites on membrane …

Computational 'microscopy'of cellular membranes

HI Ingólfsson, C Arnarez, X Periole… - Journal of cell …, 2016 - journals.biologists.com
Computational 'microscopy'refers to the use of computational resources to simulate the
dynamics of a molecular system. Tuned to cell membranes, this computational …

Atomistic simulations of membrane ion channel conduction, gating, and modulation

E Flood, C Boiteux, B Lev, I Vorobyov… - Chemical …, 2019 - ACS Publications
Membrane ion channels are the fundamental electrical components in the nervous system.
Recent developments in X-ray crystallography and cryo-EM microscopy have revealed what …