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Shaping the water crevice to accommodate the voltage sensor in a down conformation: a molecular dynamics simulation
Sunan Kitjaruwankul1, Panisak Boonamnaj2, Sunit Fuklang2
1†Graduate School of Nanoscience and Technology, Chulalongkorn University, Bangkok 10330, Thailand.
The Journal of Physical Chemistry. B
|May 15, 2015
Summary
Voltage sensor domains undergo conformational changes to regulate ion channel function. Molecular dynamics simulations reveal how water molecules in the intracellular crevice influence these voltage-dependent gating states.
Area of Science:
- Biophysics
- Molecular Biology
- Structural Biology
Background:
- Voltage sensor domains (VSDs) are crucial for voltage-dependent ion channel function.
- VSDs share structural similarities with voltage-sensing phosphatases and proton channels.
- Charged arginines on the S4 segment mediate response to membrane potential changes.
Purpose of the Study:
- To investigate the structure and dynamics of VSD conformations at an atomic level.
- To elucidate the principle of voltage-dependent gating.
- To understand the role of the intracellular crevice in VSD conformational changes.
Main Methods:
- All-atom molecular dynamics (MD) simulations.
- Utilized spin labeling electron paramagnetic resonance (EPR) spectrometry data.
- Investigated both Up-state (activated) and Down-state (resting) VSD conformations.
Main Results:
- MD simulations revealed distinct aqueous crevice shapes in Down-state conformations.
- More water molecules were observed in the intracellular crevice in the Down state compared to the Up state.
- The solvent accessible surface shape suggests water-mediated interactions between the VSD and lipid bilayer.
Conclusions:
- The study provides a detailed atomic-level explanation for voltage-dependent gating.
- Water molecules play a significant role in the conformational dynamics of VSDs.
- Findings support and expand upon previously reported experimental data regarding VSD function.
