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 …

Lipidomics for studying metabolism

X Han - Nature Reviews Endocrinology, 2016 - nature.com
Many thousands of lipid species exist and their metabolism is interwoven via numerous
pathways and networks. These networks can also change in response to cellular …

CHARMM-GUI input generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM simulations using the CHARMM36 additive force field

J Lee, X Cheng, S Jo, AD MacKerell, JB Klauda, W Im - Biophysical journal, 2016 - cell.com
Proper treatment of nonbonded interactions is essential for the accuracy of molecular
dynamics (MD) simulations, especially in studies of lipid mono-and bilayers. The use of the …

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 …

Understanding nanoparticle cellular entry: a physicochemical perspective

CM Beddoes, CP Case, WH Briscoe - Advances in colloid and interface …, 2015 - Elsevier
Understanding interactions between nanoparticles (NPs) with biological matter, particularly
cells, is becoming increasingly important due to their growing application in medicine and …

[HTML][HTML] Permeability across lipid membranes

W Shinoda - Biochimica et Biophysica Acta (BBA)-Biomembranes, 2016 - Elsevier
Molecular permeation through lipid membranes is a fundamental biological process that is
important for small neutral molecules and drug molecules. Precise characterization of free …

Nanocarrier‐mediated cytosolic delivery of biopharmaceuticals

W He, X **ng, X Wang, D Wu, W Wu… - Advanced functional …, 2020 - Wiley Online Library
Biopharmaceuticals have emerged to play a vital role in disease treatment and have shown
promise in the rapidly expanding pharmaceutical market due to their high specificity and …

Mechanistic understanding from molecular dynamics simulation in pharmaceutical research 1: drug delivery

A Bunker, T Róg - Frontiers in Molecular Biosciences, 2020 - frontiersin.org
In this review, we outline the growing role that molecular dynamics simulation is able to play
as a design tool in drug delivery. We cover both the pharmaceutical and computational …

Quantitative comparison against experiments reveals imperfections in force fields' descriptions of popc–cholesterol interactions

M Javanainen, P Heftberger, JJ Madsen… - Journal of Chemical …, 2023 - ACS Publications
Cholesterol is a central building block in biomembranes, where it induces orientational
order, slows diffusion, renders the membrane stiffer, and drives domain formation. Molecular …

Matrix vesicles from chondrocytes and osteoblasts: Their biogenesis, properties, functions and biomimetic models

M Bottini, S Mebarek, KL Anderson… - … et Biophysica Acta (BBA …, 2018 - Elsevier
Abstract Background Matrix vesicles (MVs) are released from hypertrophic chondrocytes
and from mature osteoblasts, the cells responsible for endochondral and membranous …