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Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

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A BEST example of channel structure annotation by molecular simulation.

Shanlin Rao¹, Gianni Klesse^1,2, Phillip J Stansfeld¹

¹a Department of Biochemistry , University of Oxford , Oxford , UK.

Channels (Austin, Tex.)

|March 21, 2017

Summary

Simulating water behavior in ion channels predicts conductivity. This method confirms a hydrophobic gate in the BEST1 chloride channel, validating a new tool for functional annotation.

Keywords:

free energy hydrophobic gating molecular dynamics water

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Area of Science:

Structural biology
Computational biophysics
Ion channel function

Background:

Determining ion channel structures is advancing rapidly.
Computational tools are needed for functional annotation of these structures.
Pore dimensions alone do not reliably predict ion channel conductivity due to hydrophobic gating.

Purpose of the Study:

To apply a water simulation method to predict ion channel conductivity.
To compare the structure of wild-type BEST1 with a mutant BEST1 channel.
To validate the simulation approach for functional annotation of ion channel structures.

Main Methods:

Simulating water behavior within ion channel pores.
Applying the simulation method to the bestrophin chloride channel (BEST1).
Comparing wild-type BEST1 with a mutant BEST1 structure.

Main Results:

The simulation method successfully predicted the conductive status of BEST1.
Results support the presence of a hydrophobic gate in the narrow neck of BEST1.
The simulation approach provides accurate and efficient functional annotation.

Conclusions:

Simulating water behavior is a reliable method for predicting ion channel conductivity.
A hydrophobic gate is present in the BEST1 chloride channel.
This simulation approach is a validated tool for functional annotation of ion channel structures.