A theoretical QM/MM study of the [NiFe] hydrogenase from Desulfovibrio fructosovorans has been performed to investigate possible routes of proton transfer between the active site and the protein surface. We obtained the minimum energy paths, with a modified version of the nudged elastic band method, for a set of proposed pathways. The calculations were carried out for the crystallographic structure and for several structures of the protein obtained from a molecular dynamics simulation. The results show one of the studied pathways to be preferred for transport from the active site to the surface, but the preference is not so strong when transport occurs in the opposite direction. Proteins 2008. © 2008 Wiley-Liss, Inc.