Pathways research

Luciano JS. PAX of mind for pathway researchers. Drug Discov Today 2005 10 937-42. 

Generation of mutants is also a starting point in optimization experiments, and now is the time for metabolic engineering of the astaxanthin biosynthetic pathway. Researchers should be able to manage carbon fluxes within the cells and resolve competitions between enzymes such as phytoene desaturase and lycopene cyclase. 

USEPA (2001) Draft protocol for measuring children s non-occupational exposure to pesticides by all relevant pathways. Research Triangle Park, NC, United States Environmental Protection Agency, Office of Research and Development (EPA/600/R-03/026). 

Long before molecular geneticists began tinkering with the structure and function of proteins and metabolic pathways, researchers were ma-... 

McKone, T.E. (1991). Human exposure to chemicals from multiple media and through multiple pathways Research overview and comments. Risk Anal, 11, 5-10. 

To determine the order of the steps in the pathway, researchers analyzed double sec mutants. For Instance, when yeast cells contain mutations in both class B and class D functions, proteins accumulate in the rough ER, not in the Golgi clsternae. Since proteins accumulate at the earliest blocked step, this finding shows that class B mutations must act at an earlier point in the secretory pathway than class D mutations do. These studies confirmed that as a secreted protein is synthesized and processed it moves sequentially from the cytosol —> rough ER —> ER-to-Golgl transport vesicles —> Golgi clsternae —> secretory vesicles and finally is exocytosed. 

Biochemical pathways and metabolic reaction networks have recently attracted much interest and are an active and rich field for research,... 

Example Researchers have used MX DO and. AMI setn i-etn pirical methods It) calculate possible reaction pathways for the interae-... 

A transition structure is, of course, a maximum on the reaction pathway. One well-defined reaction path is the least energy or intrinsic reaction path (IRC). Quasi-Newton methods oscillate around the IRC path from one iteration to the next. Several researchers have proposed methods for obtaining the IRC path from the quasi-Newton optimization based on this observation. 

Template recognition is the process of finding the most similar sequence. The researcher must choose how to compute similarity. It is possible to run a fast, approximate search of many sequences or a slow, accurate search of a few sequences. Sequences that should be analyzed more carefully are the same protein from a different species, proteins with a similar function or from the same metabolic pathway, or a library of commonly observed substructures if available. 

Biorational approaches have proven useful in the development of classes of herbicides which inhibit essential metaboHc pathways common to all plants and thus are specific to plants and have low toxicity to mammalian species. Biorational herbicide development remains a high risk endeavor since promising high activities observed in the laboratory may be nullified by factors such as limitations in plant uptake and translocation, and the instabiHty or inactivity of biochemical en2yme inhibitors under the harsher environmental conditions in the field. Despite these recogni2ed drawbacks, biorational design of herbicides has shown sufficient potential to make the study of herbicide modes of action an important and growing research area. 

A simplified diagram representing the various reservoirs and transport mechanisms and pathways involved in the cycles of nutrient elements at and above the surface of the Earth is given in Eigure 1. The processes are those considered to be the most important in the context of this article, but others of lesser significance can be postulated. Eor some of the elements, notably carbon, sulfur, chlorine, and nitrogen, considerable research has been done to evaluate (quantitatively) the amount of the various elements in the reservoirs and the rates of transfer. 

Direct-Liquefaction Kinetics All direct-liquefac tion processes consist of three basic steps (1) coal slurrying in a vehicle solvent, (2) coal dissolution under high pressure and temperature, and (3) transfer of hydrogen to the dissolved coal. However, the specific reac tion pathways and associated kinetics are not known in detail. Overall reaction schemes and semiempirical relationships have been generated by the individual process developers, but apphcations are process specific and limited to the range of the specific data bases. More extensive research into liquefaction kinetics has been conducted on the laboratory scale, and these results are discussed below. 

The underlying assumption driving marine natural products chemistry research is that secondary metabolites produced by marine plants, animals, and microorganisms will be substantially different from those found in traditional terrestrial sources simply because marine life forms are very different from terrestrial life forms and the habitats which they occupy present very different physiological and ecological challenges. The expectation is that marine organisms will utilize completely unique biosynthetic pathways or exploit unique variations on well established pathways. The marine natural products chemistry research conducted to date has provided many examples that support these expectations. 

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/). 

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