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 …

Mitochondrial VDAC1: a key gatekeeper as potential therapeutic target

AKS Camara, YF Zhou, PC Wen, E Tajkhorshid… - Frontiers in …, 2017 - frontiersin.org
Mitochondria are the key source of ATP that fuels cellular functions, and they are also central
in cellular signaling, cell division and apoptosis. Dysfunction of mitochondria has been …

[HTML][HTML] Polder maps: improving OMIT maps by excluding bulk solvent

D Liebschner, PV Afonine, NW Moriarty… - Biological …, 2017 - journals.iucr.org
The crystallographic maps that are routinely used during the structure-solution workflow are
almost always model-biased because model information is used for their calculation. As …

Martini 3 coarse-grained force field for cholesterol

L Borges-Araújo, AC Borges-Araújo… - Journal of Chemical …, 2023 - ACS Publications
Cholesterol plays a crucial role in biomembranes by regulating various properties, such as
fluidity, rigidity, permeability, and organization of lipid bilayers. The latest version of the …

Protein ensembles: how does nature harness thermodynamic fluctuations for life? The diverse functional roles of conformational ensembles in the cell

G Wei, W **, R Nussinov, B Ma - Chemical reviews, 2016 - ACS Publications
All soluble proteins populate conformational ensembles that together constitute the native
state. Their fluctuations in water are intrinsic thermodynamic phenomena, and the …

[HTML][HTML] VDAC1 at the intersection of cell metabolism, apoptosis, and diseases

V Shoshan-Barmatz, A Shteinfer-Kuzmine, A Verma - Biomolecules, 2020 - mdpi.com
The voltage-dependent anion channel 1 (VDAC1) protein, is an important regulator of
mitochondrial function, and serves as a mitochondrial gatekeeper, with responsibility for …

A mechanism for the activation of the mechanosensitive Piezo1 channel by the small molecule Yoda1

WM Botello-Smith, W Jiang, H Zhang, AD Ozkan… - Nature …, 2019 - nature.com
Abstract Mechanosensitive Piezo1 and Piezo2 channels transduce various forms of
mechanical forces into cellular signals that play vital roles in many important biological …

Ceramides bind VDAC2 to trigger mitochondrial apoptosis

S Dadsena, S Bockelmann, JGM Mina… - Nature …, 2019 - nature.com
Ceramides draw wide attention as tumor suppressor lipids that act directly on mitochondria
to trigger apoptotic cell death. However, molecular details of the underlying mechanism are …

MemProtMD: automated insertion of membrane protein structures into explicit lipid membranes

PJ Stansfeld, JE Goose, M Caffrey, EP Carpenter… - Structure, 2015 - cell.com
There has been exponential growth in the number of membrane protein structures
determined. Nevertheless, these structures are usually resolved in the absence of their lipid …

Markov state models provide insights into dynamic modulation of protein function

D Shukla, CX Hernández, JK Weber… - Accounts of chemical …, 2015 - ACS Publications
Conspectus Protein function is inextricably linked to protein dynamics. As we move from a
static structural picture to a dynamic ensemble view of protein structure and function, novel …