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Biotech / Medical : PROTEOMICS -- Ignore unavailable to you. Want to Upgrade?

To: Jim Oravetz who wrote (130)	10/3/2000 12:36:48 PM
From: Jim Oravetz	Respond to of 539

Molecular Biology PARSING CELLS Proteomics is an attempt to devise industrial-scale techniques to map the identity and activities of all the proteins in a cell Biological cells are not genetic reductionists. The readouts from a gene-sequencing machine do not tell you much about the ultimate structure and function of the cellular proteins made by the genes. After a protein comes off the gene-to-amino-acid assembly line, it is altered as it assumes its place as a cog in the cellular machinery. Carbohydrates, phosphates, sulfates and other residues are pasted onto it. Enzymes may chop the amino acid chain into smaller pieces. A single gene may thus code for several different proteins. A new biological subdiscipline called proteomics tries to circumvent the information gap between DNA and its end products. Proteomics envisions deducing the structure and interactions of all the proteins in a given cell. Comparing proteomic maps of healthy and diseased cells may allow researchers to understand changes in cell signaling and metabolic pathways better. And pharmaceutical companies might devise diagnostic tests and identify new drug targets. Molecular biologists have tried to parse a cell's protein makeup for decades. "There's nothing new about identifying proteins in a cell," notes Marvin Cassman, director of the National Institute of General Medical Sciences (NIGMS). "What's different here is to do things in a global sense rather than looking at one protein here and there." Similar in concept to genomics, which seeks to identify all genes, the field's success will depend on the ability to develop techniques that can rapidly identify the type, amount and activities of the thousands of proteins in a cell. A slew of new biotechnology companies have started marketing technologies and services for mining protein information en masse. Oxford Glycosciences (OGS) in Abingdon, England, has automated a time-worn technique, two-dimensional gel electrophoresis. In the OGS process, an electric current applied to a sample on a polymer gel separates the proteins, first by their unique electric charge characteristics and then by size. A dye attaches to each separated protein arrayed across the gel. Then a digital imaging device automatically detects protein levels by how much the dye fluoresces. Each of the 5,000 to 6,000 proteins that may be assayed in a sample in the course of a few days is channeled through a mass spectrometer that determines its amino acid sequence. The identity of the protein can be determined by comparing the amino acid sequence with information contained in numerous gene and protein databases. One imaged array of proteins can be contrasted with another to find proteins specific to a disease. Proteomics aspires to know more than just the identity of a set of proteins. Small Molecule Therapeutics, based in Monmouth Junction, N.J., has developed one approach to understanding what a protein actually does. Its technique first finds two proteins that interact with each other and then creates fragments of one of the proteins. Some of the fragments may block any further interactions with the intact protein. Researchers assess how a cell's biological functions are altered by this inhibition. The company has used the technique to pinpoint inhibitors of the signaling protein RAS, which can trigger cancer. The suite of techniques under development for proteomics have yet to become as routine as gene sequencing. Doubts persist, for instance, about how ably two-dimensional gel electrophoresis can separate all the proteins in a cell. Researchers are working on linking mass spectrometry with newer separation methods, which could improve both speed and sensitivity of protein identification. Companies such as Ciphergen Biosystems, based in Palo Alto, Calif., labor on the protein equivalent of gene chips. One of these rapid assays consists of an array of up to 96 millimeter-square metal or plastic wells, each filled with an antibody, a receptor or a synthetic molecule that traps a protein. The proteins can then be desorbed and identified with a mass spectrometer. The possibility of a Human Proteomics Initiative intrigues some scientists. But the exact focus of a program remains unclear: Should it try to determine the levels of proteins in all the 250 or so human cell types? Or should it try to elicit the billions of possible protein-to-protein interactions? "It would need to have well-defined goals and milestones," says Francis S. Collins, who oversees the Human Genome Project at the National Institutes of Health. "Again, that will be much more difficult than for nucleic acids. How do you decide when you're done?" The NIGMS, for one, has taken a step toward a large-scale proteomics effort by initiating a program that would determine whether crystallographic and nuclear magnetic resonance techniques could become highly automated. The project will attempt to ascertain the three-dimensional structure of 10,000 proteins in the next five to 10 years, a rapid-fire pace for this painstakingly slow process. Proteomics is only the beginning. Other biological endeavors have been rear-ended by a new suffix. Buzzwords ranging from metabolomics to transcriptomics to phenomics have proliferated as entire areas of the life sciences are analyzed. Perhaps someday all things biological will be classified and jammed into an enormous database--leading to some hypothetical metadiscipline called biomics. --Gary Stix This came from Scientific American web site. Jim