Abstract
Bacterial porins often exhibit ion conductance and gating behavior which can be modulated by pH. However, the underlying control mechanism of gating is often complex, and direct inspection of the protein structure is generally insufficient for full mechanistic understanding. Here we describe Pretzel, a computational framework that can effectively model loop-based gating events in membrane proteins. Our method combines Monte Carlo conformational sampling, structure clustering, ensemble energy evaluation, and a topological gating criterion to model the equilibrium gating state under the pH environment of interest. We discuss details of applying Pretzel to the porin outer membrane protein G (OmpG).
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Acknowledgements
This research was supported by the US National Institutes of Health grants R01-GM126558, R01-GM079804, and R35GM127084.
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Perez-Rathke, A., Fahie, M.A.V., Chisholm, C.M., Chen, M., Liang, J. (2021). Simulation of pH-Dependent, Loop-Based Membrane Protein Gating Using Pretzel. In: Fahie, M.A. (eds) Nanopore Technology. Methods in Molecular Biology, vol 2186. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0806-7_12
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DOI: https://doi.org/10.1007/978-1-0716-0806-7_12
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