Proteomics

is the large-scale study of proteins, the workhorses of the cell. It examines the structure, function, interactions, and dynamics of proteins within a biological system, providing insights into how they contribute to health and disease. Proteomics complements genomics and transcriptomics by focusing on proteins, the final functional products of gene expression.

What is proteomics?

The human genome contains the complete set of genes required to build a functional human being. However, the genome is only a source of information. In order to function, it must be expressed.

The transcription of genes is the first stage of gene expression and is followed by the translation of messenger RNA to produce proteins. The proteome is the complete set of proteins produced by the genome at any one time.

The proteome is much more complex than either the genome or the transcriptome (see transcriptomics). This is because each protein can be chemically modified in different ways after synthesis. Many proteins have carbohydrate groups added to them. Others are phosphorylated or acetylated or methylated.

The proteome is also very dynamic. Most of our cells contain the same genome regardless of the cell type, developmental stage or environmental conditions. The proteome, however, varies considerably in these differing circumstances due to different patterns of gene expression and different patterns of protein modification.

Proteomics, the study of the proteome, is important because proteins represent the actual functional molecules in the cell. When mutations occur in the DNA, it is the proteins that are ultimately affected. Drugs, when they have beneficial effects, do so by interacting with proteins. Proteomics therefore covers a number of different aspects of protein function, including the following:

Structural proteomics :

the large-scale analysis of protein structures.

Protein structure comparisons can help to identify the functions of newly discovered genes. Structural analysis can also show where drugs bind to proteins and where proteins interact with each other. This is achieved using technologies such as X-ray crystallography and NMR spectroscopy.

Expression proteomics :

the large-scale analysis of protein expression.

This can help to identify the main proteins found in a particular sample and proteins differentially expressed in related samples, such as diseased vs healthy tissue. A protein found only in a diseased sample may represent a useful drug target or diagnostic marker. Proteins with similar expression profiles may also be functionally related. Technologies such as 2D-PAGE and mass spectrometry are used here.

Interaction proteomics :

the large-scale analysis of protein interactions.

The characterization of protein-protein interactions helps to determine protein functions and can also show how proteins assemble in larger complexes. Technologies such as affinity purification, mass spectrometry and the yeast two-hybrid system are particularly useful.

The techniques for proteome analysis are not as straightforward as those used in transcriptomics. However, the advantage of proteomics is that the real functional molecules of the cell are being studied. Strong gene expression, resulting in an abundant mRNA, does not necessarily mean that the corresponding protein is also abundant or indeed active in the cell.

WHAT IS PROTEOME ANALYSIS?

Proteome analysis is the investigation of all the proteins present in a cell, tissue or organism at any one time. Since cells are constantly responding to their environment, and the proteins are the workhorses of the cell, the proteome is also changing - reflecting the life of the cell.

By using carefully controlled growth conditions, it is possible to obtain exquisitely detailed information about the molecular biology of the living cell and the organism - and for example what happens during disease development.

The dream of having genomes completely sequenced is now a reality. The complete sequence of several genomes including the human one is known. However, the understanding of probably half a million human proteins encoded by some 30'000 genes is still a long way away and the hard work to unravel the complexity of biological systems is yet to come. A new fundamental concept called proteome (PROTEin complement to a genOME) has recently emerged that should drastically help phenomics to unravel biochemical and physiological mechanisms of complex multivariate diseases at the functional molecular level. A new discipline, proteomics, has been initiated that complements physical genomic research. Proteomics can be defined as the qualitative and quantitative comparison of proteomes under different conditions to further unravel biological processes.

What is PROTEOMICS?

The word "PROTEOMICS" might come from the word "GENOMICS." Genome is a gene set which contains the total genetic information of a biological species and in molecular level, it is a set of very long DNA chains. By the study of genome (GENOMICS), full DNA sequence of several biological species including human has been determined.

Under these circumstances, the focus of life science is moving from genome to proteins, which are biologically synthesized from genome. Where are the sites of DNA which actually work as the templates of polypeptide? How do the constructed proteins work in cells? How do the proteins assemble to form complexes with multiple functions? These points will be studied for all the proteins synthesized in a cell (At present, the number of polypeptides synthesized in human cells is estimated to be about thirty thousand.). This line of study, aiming to clarify the structure and function of all the proteins of a biological species to reconstruct the total biological function of the life, is called "PROTEOMICS."

Analysis of human genome has almost been accomplished by international collaboration within these ten years. Analysis of human proteins will not be accomplished in the next ten years. However, since there are people who think proteomic studies will make money, a huge amount of money will be spent to buy hundreds of (thousands of) apparatus for systematic analysis of protein structure and function. We must be aware that the establishment of these studies must be applied for the survival of all the biological species and that this century must be a turning point from "earth for human" to "earth for life."

Background

At the turn of 2001, it was announced that the human genome had been sequenced and that this was the beginning of a new era for biological research. Essentially what had been done was to determine the order of the four building blocks (nucleotides) that are joined together to form the pairs of DNA chains called the chromosomes. Humans have 46 of these, half of which a person receives from the mother, the other half from the father. This is virtually all of the information that is handed down from one generation to the next and is essentially the book of building plans for all proteins and how these are should be put together to make our organs and tissues. The genome centres have determined the order of the billions of nucleotides (called A, C, G and T) and written this down. Theoretically we should now be able to read the building book of life, since the nucleotides are grouped into 'pages' that contain all the information needed to construct a specific protein. Currently estimates of the number of pages range between 30,000 and 40,000. These pages are called genes and are photocopied (transcribed) and the photocopies (mRNA) are transported from the cells library (the nucleus where all the chromosomes are stored) to the protein-building factory (the ribosome). Here the instructions in the photocopies are used to build proteins (translation).

Proteome

The term proteome was first used in 1995 and has been applied to several different types of biological systems. A cellular proteome is the collection of proteins found in a particular cell type under a particular set of environmental conditions such as exposure to hormone stimulation. It can also be useful to consider an organism's complete proteome. The complete proteome for an organism can be conceptualized as the complete set of proteins from all of the various cellular proteomes. This is very roughly the protein equivalent of the genome. The term "proteome" has also been used to refer to the collection of proteins in certain sub-cellular biological systems. For example, all of the proteins in a virus can be called a viral proteome.

Proteomics, the study of the proteome, has largely been practiced through the separation of proteins by two dimensional gel electrophoresis. In the first dimension, the proteins are separated by isoelectric focusing, which resolves proteins on the basis of charge. In the second dimension, proteins are separated by molecular weight using SDS-PAGE. The gel is dyed with Coomassie Blue or silver to visualize the proteins. Spots on the gel are proteins that have migrated to specific locations.

The mass spectrometer has augmented proteomics. Mass mapping identifies a protein by cleaving it into short peptides and then deduces the protein's identity by matching the observed peptide masses against a sequence database. Tandem mass spectrometry, on the other hand, can get sequence information from individual peptides by isolating them, colliding them with a nonreactive gas, and then cataloging the fragment ions produced.