We found that that disulfide-bonding patterns can be used to discriminate structure similarity. Our method, based on the hierarchical clustering scheme, is applicable to proteins with two or more disulfide bonds and is able to detect the structural similarities of proteins of low sequence identities (<25%). Our results show the surprisingly close relationship between disulfide-bonding patterns and proteins structures. Our findings should be useful in protein structure modeling.

Artificial molecular machines are a growing field in nanoscience and nanotechnology. This study proposes a new class of artificial molecular machines, the second-generation single-molecule electric revolving doors (2G S-MERDs), a direct extension of our previous work [Hsu, L.-Y.; Li, E.-Y.; Rabitz, H. Nano Lett. 2013, 13, 5020]. We investigate destructive quantum interference with tunneling and conductance dependence upon molecular conformation in the 2G S-MERDs by using the Green’s function method together with density functional theory. The simulations with four types of functionals (PBE, PZ, PW91, and BLYP) show that the 2G S-MERDs have a large on–off conductance ratio (>104) and that their open and closed door states can be operated by an experimentally feasible external electric field (∼1 V/nm). In addition, the simulations indicate that the potential energy difference between the open and closed states of the S-MERDs can be engineered. Conductance–gate electric field characteristics are also introduced to illustrate the operation of the 2G S-MERDs.