Molecular dynamics simulation for all

SA Hollingsworth, RO Dror - Neuron, 2018 - cell.com
The impact of molecular dynamics (MD) simulations in molecular biology and drug discovery
has expanded dramatically in recent years. These simulations capture the behavior of …

Antiviral approaches against influenza virus

R Kumari, SD Sharma, A Kumar, Z Ende… - Clinical microbiology …, 2023 - Am Soc Microbiol
Preventing and controlling influenza virus infection remains a global public health
challenge, as it causes seasonal epidemics to unexpected pandemics. These infections are …

Biomolecular simulations: From dynamics and mechanisms to computational assays of biological activity

DJ Huggins, PC Biggin, MA Dämgen… - Wiley …, 2019 - Wiley Online Library
Biomolecular simulation is increasingly central to understanding and designing biological
molecules and their interactions. Detailed, physics‐based simulation methods are …

Inhibitors of the M2 proton channel engage and disrupt transmembrane networks of hydrogen-bonded waters

JL Thomaston, NF Polizzi, A Konstantinidi… - Journal of the …, 2018 - ACS Publications
Water-mediated interactions play key roles in drug binding. In protein sites with sparse polar
functionality, a small-molecule approach is often viewed as insufficient to achieve high …

Atomic structures of closed and open influenza B M2 proton channel reveal the conduction mechanism

VS Mandala, AR Loftis, AA Shcherbakov… - Nature structural & …, 2020 - nature.com
Abstract The influenza B M2 (BM2) proton channel is activated by acidic pH to mediate virus
uncoating. Unlike influenza A M2 (AM2), which conducts protons with strong inward …

Transcendent Aspects of Proton Channels

TE DeCoursey - Annual review of physiology, 2024 - annualreviews.org
A handful of biological proton-selective ion channels exist. Some open at positive or
negative membrane potentials, others open at low or high pH, and some are light activated …

Voltage and pH sensing by the voltage-gated proton channel, HV1

TE DeCoursey - Journal of the Royal Society Interface, 2018 - royalsocietypublishing.org
Voltage-gated proton channels are unique ion channels, membrane proteins that allow
protons but no other ions to cross cell membranes. They are found in diverse species, from …

How influenza virus uses host cell pathways during uncoating

EA Moreira, Y Yamauchi, P Matthias - Cells, 2021 - mdpi.com
Influenza is a zoonotic respiratory disease of major public health interest due to its pandemic
potential, and a threat to animals and the human population. The influenza A virus genome …

XFEL structures of the influenza M2 proton channel: Room temperature water networks and insights into proton conduction

JL Thomaston, RA Woldeyes… - Proceedings of the …, 2017 - National Acad Sciences
The M2 proton channel of influenza A is a drug target that is essential for the reproduction of
the flu virus. It is also a model system for the study of selective, unidirectional proton …

Structural motifs for subtype-specific pH-sensitive gating of vertebrate otopetrin proton channels

B Teng, JP Kaplan, Z Liang, Z Krieger, YH Tu… - Elife, 2022 - elifesciences.org
Otopetrin (OTOP) channels are proton-selective ion channels conserved among vertebrates
and invertebrates, with no structural similarity to other ion channels. There are three …