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. 2017 Apr 4;7:632. doi: 10.1038/s41598-017-00256-y

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© The Author(s) 2017

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Automatic coordinate discovery using molecular dynamics data identifies an up-down coordinate from a set of high-dimensional input data. Modeling the observed dynamics by construction of an MSM permits rapid analysis of conformational dynamics. From our analysis, we discover a novel selectivity filter (SF) conformation. (A) MSM analysis permits generation of a 500 μs representative trajectory which contains transitions between up, down, and intermediate conformations, see movie in SI. (B) We find four metastable conformational macrostates, shown as contours in tIC space. Transition rates show a rapid relaxation from I ₁ to I ₂, and a fast exchange between I ₂ and Down. (C) Automatic coordinate discovery on the selectivity filter finds a structurally distinct pinched state. Inset enumerates the SF open probability as a function of intracellular macrostate. The Up and intermediate intracellular states favor an open SF, while the Down intracellular state strongly favors a pinched SF.