Sunday, March 8, 2009

What are the Various Types of Proteomics

Even though proteomics can be defined as the study of the protein complement of the genome, the dynamic nature of the proteome made it difficult to study and understand. The total protein expression profile always changes with time and micro- and macro-environmental conditions. Only a small percentage of the total gene is expressed at a particular time. Information about the genome and gene structure can predict the structure and function of its protein complement to a limited extent because of the post-transcriptional modifications that the protein undergoes. These modifications are not represented in the respective gene. This is what makes proteomics difficult to study compared to genomics.

The following are the major types of proteomics:

Expression Proteomics:
This is the qualitative and quantitative study of the expression of total proteins under two different conditions. For example, expression proteomics of normal cells and diseased cells can be compared to understand the protein that is responsible for the diseased state or the protein that is expressed due to disease. Using this method disease-specific protein can be identified and characterized by comparing the protein-expression profile of the entire proteome or of the subproteome between the two samples.

For example, tumor tissue samples from a cancer patient and the same type of tissue from a normal person can be analyzed for differential protein expression. Using two-dimensional gel electrophoresis, mass spectrometry combined with chromatography and microarray techniques, additional proteins that are expressed in the cancer tissues or the proteins, which are absent, or those, which are over expressed and under-expressed can be identified and characterized. Identification of these proteins will give valuable information about the molecular biology of tumor formation.

Structural Proteomics:
Structural proteomics, as the name indicates, is about the structural aspects, including the three-dimensional shape and structural complexities, of functional proteins. This includes the structural prediction of a protein when its amino acid sequence is determined directly by sequencing or from the gene with a method called homology modeling. This can be carried out by doing a homology search and computational methods of protein structural studies and predictions.

Apart from this, structural proteomics can map out the structure and function of protein complexes present in a specific cellular organelle. It is possible to identify all the proteins present in a complex system such as ribosomes, membranes, or other cellular organelles and to characterize or predict all the proteins and protein interactions that can be possible between these proteins and protein complexes. Structural proteomics of a specific organelle or protein complex can give information regarding supra-molecular assemblies and their molecular architecture in cells, organelles, and in molecular complexes.

Functional Proteomics:
This is an assembly type of proteomic method to analyze and understand the properties of macromolecular networks involved in the life activities of a cell. With these methods it will be possible to identify specific protein molecules and their role in individual metabolic activities and their contribution to the metabolic network that operates in the system. This forms one of the major objectives of functional proteomics. For example, the recent elucidation of the protein network involved in the functioning of a nuclear pore complex has led to the identification of novel proteins involved in the translocation of macromolecules between the cytoplasm and nucleus through these complex pores.

Functional proteomics is yielding large databases of interacting proteins, and extensive pathway maps of these interactions are being scored and deciphered by novel high-throughput technologies. However, traditional methods of screening have not been very successful in identifying protein-protein interactions and their inhibitors. The identification and measurement of changes in the concentration of specific proteins that cells make as a result of their genetic response to specific toxicants, and how these proteins are related to each other and to the specific biological condition of the cell, also fall under functional proteomics.

Tags: Bio Technology, Bio Genetics , Proteomics

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