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Biochim Biophys Acta Biomembr. 2018 Apr;1860(4):927-942. doi: 10.1016/j.bbamem.2017.12.013. Epub 2017 Dec 16.

Permeating disciplines: Overcoming barriers between molecular simulations and classical structure-function approaches in biological ion transport.

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Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Box 1031, 17121 Solna, Sweden. Electronic address:
Institute for Computational Molecular Science, Department of Chemistry, Temple University, Philadelphia, PA 19122, USA. Electronic address:
Science for Life Laboratory, Department of Theoretical Physics, KTH Royal Institute of Technology, Box 1031, 17121 Solna, Sweden. Electronic address:
Johannes Gutenberg University Mainz, Institute for Pharmacy and Biochemistry, Johann-Joachim-Becherweg 30, 55128 Mainz, Germany; Centre for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue Str. 9, 60438 Frankfurt, Germany. Electronic address:
Department of Medical Genetics and Molecular Biochemistry, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA. Electronic address:


Ion translocation across biological barriers is a fundamental requirement for life. In many cases, controlling this process-for example with neuroactive drugs-demands an understanding of rapid and reversible structural changes in membrane-embedded proteins, including ion channels and transporters. Classical approaches to electrophysiology and structural biology have provided valuable insights into several such proteins over macroscopic, often discontinuous scales of space and time. Integrating these observations into meaningful mechanistic models now relies increasingly on computational methods, particularly molecular dynamics simulations, while surfacing important challenges in data management and conceptual alignment. Here, we seek to provide contemporary context, concrete examples, and a look to the future for bridging disciplinary gaps in biological ion transport. This article is part of a Special Issue entitled: Beyond the Structure-Function Horizon of Membrane Proteins edited by Ute Hellmich, Rupak Doshi and Benjamin McIlwain.


Electrophysiology; Ion channel; Ion transport; Kinetic modeling; Molecular dynamics; Structural biology

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