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. 2018 Nov 6;8:16380. doi: 10.1038/s41598-018-34622-1

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© The Author(s) 2018

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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Free energy change accompanying the binding of E64 to FP2. Free energy landscapes (ΔG_binding = −12.2 ± 1.1 kJ/mol) obtained from ABMD (a) using collective variable 1 (CV1) and CV2, (b) CV1 and CV3, and (c) CV2 and CV3 are shown. CV1 is the distance between centres of mass (COM) of “the first 5 (E64_F5) and the last 5 (E64_L5) heavy atoms of E64” and “the heavy atoms of G83 and N173 of FP2”. CV2 is the angle between the COMs of E64_F5, E64_L5, and “the heavy atoms of G83”. CV3 is the torsion angle between COMs of E64_F5, E64_L5, “the heavy atoms of G83”, and “the heavy atoms of N173”. Sample positions and conformations of E64 corresponding to the energy minima obtained from each of the three systems are shown in red (using sticks representation) below each energy landscape. The conformation of E64 in the X-ray structure is depicted in blue (using sticks representation). The positions and conformations of the E64 at the energy minima in the systems shown in (a), (b), and (c) have RMSD of 3.19 Å, 3.08 Å, and 2.90 Å from the E64 derived from the X-ray respectively.