Xenbase Image ID: 170242

Appendix 1—figure 2. Estimates of free energy and coordination results for modified CHARMM27* NBFIX (Na+-carboxylate rmin = 3.19 Å and K+-carboxylate rmin = 3.52 Å), using post-simulation adjustment for the LJ parameter (see Appendix text).(A) Umbrella Sampling for Na+ and K+ crossing the pore of 4NTW. A preference of ~0.5 kcal/mol for Na+ over K+ remains around E18’ and D21’ (B) Umbrella Sampling for Na+ and K+ crossing the pore of 2QTS. Na+ binding and preference of ~1 kcal/mol can be observed around D21’. Values deep in the channel (above −10 Å) are considered unreliable in this closed pore. (C) Adjusted analysis of ion occupancies for 4NTW. Double ion occupancies are reduced by these more repulsive ion parameters, but remain more common for Na+ than for K+, (D) Adjusted analysis of ion occupancies for 2QTS. Double ion occupancy is favoured both for Na+ and K+, but Na+ ions prefer tight clusters, as seen with the unmodified parameter.DOI: http://dx.doi.org/10.7554/eLife.24630.012 Image published in: Lynagh T et al. (2017) © 2017, Lynagh et al. This image is reproduced with permission of the journal and the copyright holder. This is an open-access article distributed under the terms of the Creative Commons Attribution license Larger Image Printer Friendly View

Return to previous page