Biochemical switching

In an extensive study, Okamoto and co-workers [76-86] introduced a biochemical switching device based on a cyclic enzyme system in which two enzymes share two cofactors in a cyclic manner. Cyclic enzyme systems have been used as biochemical amplitiers to improve the sensitivity of enzymatic analysis [87-89], and subsequently, this technique was introduced into biosensors [90-93], In addition, cyclic enzyme systems were also widely employed in enzymic reactors, in cases where cofactor regeneration is required [94-107], Using computer simulations, Okamoto and associates [77,80-83] investigated the characteristics of the cyclic enzyme system as a switching device, and their main model characteristics and simulation results are detailed in Table 1.1, as is a similar cyclic enzyme system introduced by Hjelmfelt et al. [109,116], which can be used as a logic element. 

Models for biochemical switches, logic gates, and information-processing devices that are also based on enzymic reactions but do not use the cyclic enzyme system were also introduced [76,115,117-122]. Examples of these models are presented in Table 1.3. It should also be mentioned that in other studies [108,112-114,116], models of chemical neurons and chemical neural networks based on nonenzymic chemical reactions were also introduced. 

M. Okamoto, T. Sakai, and K. Hayashi, Biochemical switching device realizing McCulloch-Pitts type equation, Biol Cybern., 58, 295-299 (1988). 

M. Okamoto, Biochemical switching device biomimetic approach and application to neural network study, J. Biotechnol, 109, 109-127 (1992). 

Biochemical switches inside a cell are usually based on the conformational transition of a protein the protein can have little or no biological activity in one state... 

There are essentially two types of control mechanisms for biochemical switching allosteric cooperative transition and reversible chemical modification. Allosteric cooperativity, which was discussed in Chapter 4, was discovered in 1965 by Jacques Monod, Jefferies Wyman, and Jean-Picrrc Changeux [143], and independently by Daniel Koshland, George Nemethy and David Filmer [116]. The molecular basis of this phenomenon, which is well understood in terms of three-dimensional protein crystal structures and protein-ligand interaction, is covered in every biochemistry textbook [147] as well as special treatises [215],... 

Figure 5.2 A typical cellular biochemical switch consisting of a phosphorylation-dephosphorylation cycle. The substrate molecule S may be a protein or other signaling molecule. If S is a protein then the phosphorylation of S is catalyzed by a protein kinase (K) and the dephosphorylation is catalyzed by a protein phosphatase (P). The entire cycle is accompanied by the reaction ATP ADP+PI. In the context of mitogen-activation protein kinase pathway, S, K, and P correspond to MAPK, MAPKK, and MKP, respectively. In the context of the example from the PIP3 pathway, the kinase is PI3K and the phosphatase is PTEN.

Figure 5.4 Switch-like behavior of the phosphorylation-dephosphorylation cycle. The left panel illustrates the off position (unphosphorylated) of the biochemical switch, in which the phosphatase activity is higher than the kinase activity. When the kinase activity exceeds the phosphatase activity, as in the right panel, the biochemical switch is in the opposite state.

In analyzing the temporal behavior of a biochemical switching molecule, we can study either of the equivalent models of the phosphorylation-dephosphorylation cycle or the GTPase signaling module. In particular, we are interested in the duration of each activation event at the single-molecule level. 

A biochemical switch) Zebra stripes and butterfly wing patterns are two of the most spectacular examples of biological pattern formation. Explaining the development of these patterns is one of the outstanding problems of biology see Murray (1989) for an excellent review of our current knowledge. 

As one ingredient in a model of pattern formation, Lewis et al. (1977) considered a simple example of a biochemical switch, in which a gene G is activated by a biochemical signal substance S. For example, the gene may normally be inactive but can be switched on to produce a pigment or other gene product when the concentration of 5 exceeds a certain threshold. Let g(f) denote the concentration of the gene product, and assume that the concentration of S is fixed. The model is... 

Nednoor, P, Chopra, N, Gavalas, V, Bachas, LG and Hinds, BJ (2005), Reversible biochemical switching of ionic transport through ahgned carbon nanotube membranes , Chem Mater, 17(14), 3595-3599... 

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