PROTEINS 41
of proteins having separate and distinct functions but that are grouped together
in a cellular matrix. Proteomics, a term coined around 1995, attempts to study
the interactions of the proteins as a group, focusing on their combined molecu-
lar behavior. Proteomics can be defi ned as the analysis of all the proteins
expressed at a given time or in a given location rather than the study of one
isolated protein as has been the scientifi c practice until recently. In describing
the behavior of numbers of proteins functioning together in an organelle, the
proteome becomes defi ned as the protein complement of the organism ’ s
genome. One can think of the human proteome as the universe of proteins
encoded by gene sequences in the human genome. The genome, discussed
further in the Section 2.3.3 , is defi ned as all of the genes contained in a given
organism.
Scientists believe that the molecular function of an isolated protein may be
very different from the function of that protein in its complex cellular environ-
ment — that is, in the proteome. It is also thought that an understanding not
only of the structure and function of the individual proteins, but also of their
interactions with other proteins and other molecules, may lead to better disease
diagnosis and treatment. Proteomics is a more complex topic than genomics
because organisms may have well over an order of magnitude more proteins
than genes. Because proteomics studies large, complex groups of proteins
together at the same time, new techniques and technologies are being devel-
oped to assist in this effort. A few of these techniques and technologies are
discussed briefl y here. A good basic review of proteomics techniques and
technologies can be found in the Chembytes ezine article written by Michael
Dunn at the website http://www.chemsoc.org/chembytes/ezine/1998/dunn.
htm.
The fi rst requirement for proteome analysis, also known as protein profi ling,
is separating the complex protein mixture into its various protein components.
Two - dimensional polyacrylamide gel electrophoresis (2 - DE or 2 - D gels) is still
a common method used for separating sample proteins according to their dif-
ferent properties. The fi rst dimension separation, called isoelectric focusing
(IEF), separates proteins according to charge as the different proteins are
focused at their respective isoelectric points (pI, the pH at which the protein ’ s
net charge equals zero). The second dimension separation, by sodium dodecyl
sulfate polyacrylamide gel electrophoresis (SDS - PAGE), separates the pro-
teins by size — molecular weight, Mr. The orthogonal combination of the two
separations carried out at right angles results in the proteins being distributed
across the 2 - D gel profi le. Automated computer analysis algorithms, available
commercially, are needed at this point for rigorous qualitative and quantitative
analysis of the complex and partially overlapping patterns of proteins visual-
ized by the 2 - D separation process.
Following the separation process, the individual proteins must be identifi ed
and characterized. The 2 - D separation has provided Mr , pI, and relative abun-
dance data but no information on protein identities or functions. Computer
algorithms are available for matching theMr , pI, and relative abundance data