Cover Image, Volume 35, Issue 24
Journal of Computational Chemistry · 2014
In proteins with buried active sites, understanding how ligands migrate through the tunnels that connect the exterior of the protein to the active site can shed light on substrate specificity and enzyme function. On page 1748 (DOI: 10.1002/jcc.23680), Laura Kingsley and Markus Lill present the new computational method IterTunnel that combines geometric tunnel prediction with steered MD to incorporate ligand migration and protein flexibility into tunnel prediction. It is demonstrated that the ligand itself can reshape tunnels due to its interaction with the protein resulting in the exposure of new, energetically favorable, tunnels.