Simulation of Biological Processes phần 5 docx

FIG. 4. KEGG pathway diagram for lysine biosynthesis.

native network are computable, which is like computing small perturbations

around the native structure of a protein. However, the dynamics of cell

di¡erentiation, for example, would be extremely di⁄cult to compute, which is

like computing the dynamics of protein folding from the extended chain to the

native structure. A perturbation to the network may be internal or external. An

internal perturbation is a genomic change such as a gene mutation or a molecular

change such as a protein modi¢cation, and an external perturbation is a change in

the environment of the cell.

Although we do not yet have a proper way to compute dynamic responses of the

network to small perturbations, a general consideration can be made. Figure 7

illustrates the basic system architecture that results from the interactions with the

environment. The basic principle of the native structure formation of a globular

protein is that it consists of the conserved hydrophobic core to stabilize the globule

and the divergent hydrophilic surface to perform speci¢c functions. The protein

interaction network in the cell seems to have a similar dual architecture. It consists

of the conserved core such as metabolism for the basic maintenance of life and the

divergent surface such as transporters and receptors for interactions with the

environment. The subnetwork of genetic information processing may also have a

dual architecture: the conserved core of RNA polymerase and ribosome and the

divergent surface of transcription factors. In both cases the core is encoded by a

set of orthologous genes that are conserved among organisms, and the surface is

THE KEGG DATABASE 99

FIG. 5. KEGG reference network for knowledge-based prediction.