Metabolic pathways structure

Unrean P, Trinh CT, Srienc F (2010) Rational design and construction of an efficient E. coli for production of diapolycopendioic acid. Metab Eng 12 112-122 Vijayasankaran N, Carlson R, Srienc E (2005) Metabolic pathway structures for recombinant protein synthesis in Escherichia coli. Appl Microbiol Biotechnol 68 737-746 von Kamp A, Schuster S (2006) Metatool 5.0 fast and flexible elementary modes analysis. Bioinformatics 22 1930-1931... 

The World Wide Web has transformed the way in which we obtain and analyze published information on proteins. What only a few years ago would take days or weeks and require the use of expensive computer workstations can now be achieved in a few minutes or hours using personal computers, both PCs and Macintosh, connected to the internet. The Web contains hundreds of sites of Interest to molecular biologists, many of which are listed in Pedro s BioMolecular Research Tools (http // www.fmi.ch/biology/research tools.html). Many sites provide free access to databases that make it very easy to obtain information on structurally related proteins, the amino acid sequences of homologous proteins, relevant literature references, medical information and metabolic pathways. This development has opened up new opportunities for even non-specialists to view and manipulate a structure of interest or to carry out amino-acid sequence comparisons, and one can now rapidly obtain an overview of a particular area of molecular biology. We shall here describe some Web sites that are of interest from a structural point of view. Updated links to these sites can be found in the Introduction to Protein Structure Web site (http // WWW.ProteinStructure.com/). 

Plants are constantly subject to adverse environmental conditions such as drought, flooding, extreme temperatures, excessive salts, heavy metals, high-intensity irradiation and infection by pathogenic agents. Because of their immobility, plants have to make necessary metabolic and structural adjustments to cope with the stress conditions. To this end, the expression of the genetic programme in plants is altered by the stress stimuli to induce and/or suppress the production of specific proteins which are either structural proteins or enzymes for specific metabolic pathways. 

In practice, there is only one really satisfactory solution the kinetics of the transformation must be followed. The justification for this substantial increase in effort is the dividend resulting in the form of a description of the metabolic pathway including the synthesis of possibly inhibitory metabolites. An important dividend is that it may be possible to make generalizations on the degradation of other xenobiotics—structurally related or otherwise. 

Trudgill PW (1984) Microbial degradation of the alicyclic ring structural relationships and metabolic pathways. In Microbial Degradation of Organic Compounds (Ed DT Gibson), pp. 131-180. Marcel Dekker Inc, New York. 

A common characteristic of metabolic pathways is that the product of one enzyme in sequence is the substrate for the next enzyme and so forth. In vivo, biocatalysis takes place in compartmentalized cellular structure as highly organized particle and membrane systems. This allows control of enzyme-catalyzed reactions. Several multienzyme systems have been studied by many researchers. They consist essentially of membrane- [104] and matrix- [105,106] bound enzymes or coupled enzymes in low water media [107]. 

FIGURE 20.1 Schematic illustration of lycopene metabolic pathway by CM02. (a) 5-cis Lycopene and 13-cis lycopene are preferentially cleaved by CM02 at 9, 10 -double bond. The cleavage product, apo-lO -lycopenal, can be further oxidized to apo-lO -lycopenol or reduced to apo-lO -lycopenoic acid, depending on the presence of NAD+ or NADH. (b) Chemical structures of apo-lO -lycopenoic acid, acyclo-retinoic acid, and all-frans retinoic acid. (Adapted from Hu, K.Q. et al., J. Biol. Chem., 281, 19327, 2006. With permission.)... 

Information metabolism provides a way to store and retrieve the information that guides the development of cellular structure, communication, and regulation. Like other metabolic pathways, this process is highly regulated. Information is stored by the process of DNA replication and meiosis, in which we form our germ-line cells. These processes are limited to specific portions of the cell cycle. Information is retrieved by the transcription of DNA into RNA and the ultimate translation of the signals in the mRNA into protein. 

MARSOLAIS, F GIDDA, S.K., BOYD, J., VARIN, L Plant soluble sulfotransferases structural and functional similarity with mammalian enzymes. In Evolution of Metabolic Pathways (J.T. Romeo, R. Ibrahim, L. Varin, V. de Luca, eds.), Elsevier Science Ltd., Amsterdam. 2000, pp. 433-456. 

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