Single ion free energy calculation in ASIC1: the importance of the HG loop

Vallée, Cédric; Howlin, Brendan J.; Lewis, Rebecca

doi:10.1039/d2cp01563c

Cited by 2 publications

(2 citation statements)

References 41 publications

(63 reference statements)

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“…Taking advantage of statistical physics, MD simulations can also be used to calculate a permeation free energy profile and thus provide a detailed gating mechanism of ion permeation. The derived energy landscape helps to identify important restriction residues and energy barriers. − Mhashal et al also studied cancer mutations found in genomic-wide tumor screens . MD simulations show that mutation (R252S) leads to wider upper and lower gates than wild type, facilitating ion and water permeation (Figure B).…”

Section: Membrane Protein Simulationsmentioning

confidence: 99%

CHARMM-GUI Membrane Builder: Past, Current, and Future Developments and Applications

Feng

Park

Choi

et al. 2023

J. Chem. Theory Comput.

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Molecular dynamics simulations of membranes and membrane proteins serve as computational microscopes, revealing coordinated events at the membrane interface. As G protein-coupled receptors, ion channels, transporters, and membrane-bound enzymes are important drug targets, understanding their drug binding and action mechanisms in a realistic membrane becomes critical. Advances in materials science and physical chemistry further demand an atomistic understanding of lipid domains and interactions between materials and membranes. Despite a wide range of membrane simulation studies, generating a complex membrane assembly remains challenging. Here, we review the capability of CHARMM-GUI Membrane Builder in the context of emerging research demands, as well as the application examples from the CHARMM-GUI user community, including membrane biophysics, membrane protein drugbinding and dynamics, protein−lipid interactions, and nano-bio interface. We also provide our perspective on future Membrane Builder development.

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Section: Membrane Protein Simulationsmentioning

confidence: 99%

CHARMM-GUI Membrane Builder: Past, Current, and Future Developments and Applications

Feng

Park

Choi

et al. 2023

J. Chem. Theory Comput.

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show abstract

“…Notably, residues from the palm, ball, finger, and thumb domains combine to generate an acidic pocket in the extracellular domain, which is extremely negatively charged. Crucially, two pairs of carboxyl-carboxylate interactions that take place unusually close together between the side chains of aspartate or glutamate residues allow the molecule to sense pH [ 30 – 32 ].…”

Section: Asic1amentioning

confidence: 99%

Acid-sensing ion channel 1a modulation of apoptosis in acidosis-related diseases: implications for therapeutic intervention

Zhang,

Chen,

Zhan

et al. 2023

Cell Death Discov.

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Acid-sensing ion channel 1a (ASIC1a), a prominent member of the acid-sensing ion channel (ASIC) superfamily activated by extracellular protons, is ubiquitously expressed throughout the human body, including the nervous system and peripheral tissues. Excessive accumulation of Ca2+ ions via ASIC1a activation may occur in the acidified microenvironment of blood or local tissues. ASIC1a-mediated Ca2+‑induced apoptosis has been implicated in numerous pathologies, including neurological disorders, cancer, and rheumatoid arthritis. This review summarizes the role of ASIC1a in the modulation of apoptosis via various signaling pathways across different disease states to provide insights for future studies on the underlying mechanisms and development of therapeutic strategies.

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Single ion free energy calculation in ASIC1: the importance of the HG loop

Abstract: Acid Sensing Ion Channels (ASICs) are one of the most studied channels of the Epithelial Sodium Channel/Degenerin (ENaC/DEG) superfamily. They are responsible for excitatory responses following acidification of the extracellular...

Cited by 2 publications

References 41 publications

CHARMM-GUI Membrane Builder: Past, Current, and Future Developments and Applications

CHARMM-GUI Membrane Builder: Past, Current, and Future Developments and Applications

Acid-sensing ion channel 1a modulation of apoptosis in acidosis-related diseases: implications for therapeutic intervention

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