title: A molecular switch for biochemical logic gates: conformational studies.
abstract: This report presents the computer-assisted design of a molecular switching element, in which a molecular switch regulates the enzymatic activity of Ribonuclease A (RNase A). The molecular switch, an appropriately modified amino acid residue, is constructed with an electron donor group and an electron acceptor group, connected to one another with a conjugated double bond bridge. The switching mechanism is based on the azonium-hydrazo tautomerization, by which a charge separation induced in the excited state causes a rearrangement of the molecular electronic structure, resulting in the exchange of locations of single and double bonds. This rearrangement of bonds leads to different three-dimensional conformations of the switch. Using the electrostatically driven Monte Carlo (EDMC) method and the empirical conformational energy program for peptides (ECEPP/3) potential energy function, we carried out an exhaustive search of the conformational space of the switching element. The results of these calculations reveal two sets of conformations: in one set the access to the active site of the enzyme is preferentially blocked, while in the other set the active site is preferentially accessible. Integration of the designed element into biochemical logic gates operating under the rules of threshold value, and experimental implementation of this system, are considered.
authors.affiliation: Department of Biomedical Engineering, Julius Silver Institute of Biomedical Engineering, L&D Sherman Biomaterials Research Center, Technion-Israel Institute of Technology, Haifa, Israel.
authors.forename: G
authors.initials: G
authors.lastname: Ashkenazi
authors.forename: D R
authors.initials: DR
authors.lastname: Ripoll
authors.forename: N
authors.initials: N
authors.lastname: Lotan
authors.forename: H A
authors.initials: HA
authors.lastname: Scheraga
mesh_terms: D011487:Protein Conformation; D012260:Ribonucleases / Q000737:chemistry*
chemical_list: D012260:Ribonucleases