Multiscale simulations of biological membranes: the challenge to understand biological phenomena in a living substance

G Enkavi, M Javanainen, W Kulig, T Róg… - Chemical …, 2019 - ACS Publications
Biological membranes are tricky to investigate. They are complex in terms of molecular
composition and structure, functional over a wide range of time scales, and characterized by …

Free energy methods for the description of molecular processes

C Chipot - Annual Review of Biophysics, 2023 - annualreviews.org
Efforts to combine theory and experiment to advance our knowledge of molecular processes
relevant to biophysics have been considerably enhanced by the contribution of statistical …

Identification of vacuolar phosphate efflux transporters in land plants

L Xu, H Zhao, R Wan, Y Liu, Z Xu, W Tian, W Ruan… - Nature Plants, 2019 - nature.com
Inorganic phosphate (Pi) is an essential component of all life forms. Land plants acquire Pi
from the soil through roots and associated symbioses, and it is then transported throughout …

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 …

Molecular dynamics simulations of biological membranes and membrane proteins using enhanced conformational sampling algorithms

T Mori, N Miyashita, W Im, M Feig, Y Sugita - Biochimica et Biophysica Acta …, 2016 - Elsevier
This paper reviews various enhanced conformational sampling methods and explicit/implicit
solvent/membrane models, as well as their recent applications to the exploration of the …

Structural basis for the reaction cycle of DASS dicarboxylate transporters

DB Sauer, N Trebesch, JJ Marden, N Cocco, J Song… - Elife, 2020 - elifesciences.org
Citrate, α-ketoglutarate and succinate are TCA cycle intermediates that also play essential
roles in metabolic signaling and cellular regulation. These di-and tricarboxylates are …

[HTML][HTML] Conformational landscapes of membrane proteins delineated by enhanced sampling molecular dynamics simulations

TJ Harpole, L Delemotte - Biochimica Et Biophysica Acta (BBA) …, 2018 - Elsevier
The expansion of computational power, better parameterization of force fields, and the
development of novel algorithms to enhance the sampling of the free energy landscapes of …

Proton-driven alternating access in a spinster lipid transporter

R Dastvan, A Rasouli… - Nature …, 2022 - nature.com
Spinster (Spns) lipid transporters are critical for transporting sphingosine-1-phosphate (S1P)
across cellular membranes. In humans, Spns2 functions as the main S1P transporter in …

Molecular dynamics simulations of membrane proteins: An overview

K Goossens, H De Winter - Journal of chemical information and …, 2018 - ACS Publications
Simulations of membrane proteins have been rising in popularity in the past decade.
Advancements in technology and force fields made it possible to simulate behavior of …

[HTML][HTML] Mechanism of substrate translocation in an alternating access transporter

NR Latorraca, NM Fastman, AJ Venkatakrishnan… - Cell, 2017 - cell.com
Transporters shuttle molecules across cell membranes by alternating among distinct
conformational states. Fundamental questions remain about how transporters transition …