Exploring the gating mechanism in the ClC chloride channel via metadynamics.
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Summary
The metadynamics calculations reported herein demonstrate that before reaching the periplasmic solution, chloride ions have to overcome an additional barrier arising from two different effects, namely the rearrangement of their solvation shell and a flip in the backbone angles of the residues E148 and G149, which reside at the end of the alphaF helix.
- Type
- article
- Published
- 2006-08-11
- Cited by
- 51
- References
- 38
- Access
- Open access
- OpenAlex
- https://openalex.org/W16843488
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:21021648
Keywords
Art
References
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- Crystal structure and pair potentials: A molecular-dynamics study
- All-atom empirical potential for molecular modeling and dynamics studies of proteins.
- Efficient reconstruction of complex free energy landscapes by multiple walkers metadynamics.
- The role of the peripheral anionic site and cation-pi interactions in the ligand penetration of the human AChE gorge.
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- A molecular dynamics method for simulations in the canonical ensemble
- CLC chloride channels: correlating structure with function.
- Flexible docking in solution using metadynamics.
- The calculation of the potential of mean force using computer simulations
Cited by
- The Role of a Conserved Lysine in Chloride- and Voltage-dependent ClC-0 Fast Gating
- Secondary water pore formation for proton transport in a ClC exchanger revealed by an atomistic molecular-dynamics simulation.
- Molecular mechanics investigation of the transport mechanisms in the CIC-ec1 H+/CI⁻ exchanger and P-glycoprotein/Sav1866 ABC transporter
- Statistical determinants of selective ionic complexation: ions in solvent, transport proteins, and other "hosts".
- Charge delocalization upon chloride ion binding in ClC chloride ion channels/transporters
- Transpath: A computational method for locating ion transit pathways through membrane proteins
- Molecular dynamics simulations of potassium channels
- The coupled proton transport in the ClC-ec1 Cl(-)/H(+) antiporter.
- Well-tempered metadynamics as a tool for characterizing multi-component, crystalline molecular machines.
- Structural features of aquaporin 4 supporting the formation of arrays and junctions in biomembranes.
- Proton transport pathways in [NiFe]-hydrogenase.
- Chloride ion conduction without water coordination in the pore of ClC protein
- Influences of Mutations on the Electrostatic Binding Free Energies of Chloride Ions in Escherichia Coli ClC
- CO escape from myoglobin with metadynamics simulations
- Molecular dynamics investigation of Cl- and water transport through a eukaryotic CLC transporter.
- A three-state multi-ion kinetic model for conduction properties of ClC-0 chloride channel.
- Proton transport pathway in the ClC Cl-/H+ antiporter.
- First-principles molecular dynamics simulations of condensed-phase V-type nerve agent reaction pathways and energy barriers.
- CLC-0 and CFTR: chloride channels evolved from transporters.
- Proton pathways and H+/Cl− stoichiometry in bacterial chloride transporters
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