Water in nanopores and biological channels: a molecular simulation perspective

CI Lynch, S Rao, MSP Sansom - Chemical reviews, 2020 - ACS Publications
This Review explores the dynamic behavior of water within nanopores and biological
channels in lipid bilayer membranes. We focus on molecular simulation studies, alongside …

Put a cork in it: Plugging the M2 viral ion channel to sink influenza

PH Jalily, MC Duncan, D Fedida, J Wang, I Tietjen - Antiviral research, 2020 - Elsevier
The ongoing threat of seasonal and pandemic influenza to human health requires antivirals
that can effectively supplement existing vaccination strategies. The M2 protein of influenza A …

Hybrid Pyridine–Pyridone Foldamer Channels as M2‐Like Artificial Proton Channels

J Shen, R Ye, Z Liu, H Zeng - Angewandte Chemie, 2022 - Wiley Online Library
Currently, completely abiotic channel systems that concurrently reproduce the high
selectivity and high permeation rate of natural protein channels are rare. Here, we provide …

[HTML][HTML] Decoding the 2D IR spectrum of the aqueous proton with high-level VSCF/VCI calculations

WB Carpenter, Q Yu, JH Hack, B Dereka… - The Journal of …, 2020 - pubs.aip.org
The aqueous proton is a common and long-studied species in chemistry, yet there is
currently intense interest devoted to understanding its hydration structure and transport …

Activation of the influenza B M2 proton channel (BM2)

Z Yue, J Wu, D Teng, Z Wang, GA Voth - Biochemistry, 2024 - ACS Publications
Influenza B viruses have cocirculated during most seasonal flu epidemics and can cause
significant human morbidity and mortality due to their rapid mutation, emerging drug …

Inhibition Mechanism of Anti-TB Drug SQ109: Allosteric Inhibition of TMM Translocation of Mycobacterium Tuberculosis MmpL3 Transporter

J Carbone, NJ Paradis, L Bennet… - Journal of chemical …, 2023 - ACS Publications
The mycolic acid transporter MmpL3 is driven by proton motive forces (PMF) and functions
via an antiport mechanism. Although the crystal structures of the Mycobacterium smegmatis …

Heterocyclic inhibitors of viroporins in the design of antiviral compounds

VA Shiryaev, YN Klimochkin - Chemistry of heterocyclic compounds, 2020 - Springer
Ion channels of viruses (viroporins) represent a common type of protein targets for drugs.
The relative simplicity of channel architecture allows convenient computational modeling …

Understanding the multifaceted mechanism of Compound I formation in unspecific peroxygenases through multiscale simulations

GJ Costa, R Liang - The Journal of Physical Chemistry B, 2023 - ACS Publications
Unspecific peroxygenases (UPOs) can selectively oxyfunctionalize unactivated
hydrocarbons by using peroxides under mild conditions. They circumvent the oxygen …

Molecular dynamics simulation of complex reactivity with the rapid approach for proton transport and other reactions (RAPTOR) software package

S Kaiser, Z Yue, Y Peng, TD Nguyen… - The Journal of …, 2024 - ACS Publications
Simulating chemically reactive phenomena such as proton transport on nanosecond to
microsecond and beyond time scales is a challenging task. Ab initio methods are unable to …

Water orientation and dynamics in the closed and open influenza B virus M2 proton channels

MD Gelenter, VS Mandala, MJM Niesen… - Communications …, 2021 - nature.com
The influenza B M2 protein forms a water-filled tetrameric channel to conduct protons across
the lipid membrane. To understand how channel water mediates proton transport, we have …