BASICS OF PROTEOMICS:

Proteome: It is the entire protein component of a given organism. The term was coined by
Wasinger in 1995. A proteome is a quantitatively expressed protein of a genome providing
information on the gene products that are translated, amount of products and any post
translational modifications.

Fig. Simple representation of Proteomics

Proteomics is an emerging area of research in the post-genomic era. It involves identifying the
structures and functions of all proteins of a proteome. It is sometimes also treated as structural
based functional genomics.

From bioinformatics point of view proteomics is the databases of (a) protein sequence, (b)
predicted protein structures and (c) protein expression analysis. As more protein structures are
identified, the relationship between structure and functions became easier to predict.

Fig. General scheme of Proteomics

Types of Proteomics:
i. Structural Proteomics: One of the main targets of proteomics investigation is to map the
structure of protein complexes or the proteins present in a specific cellular organelle known as
cell map or structural proteins. Structural proteomics attempt to identify all the proteins within a
protein complex and their interactions. Isolation of specific protein complex by purification can
simplify the proteomic analysis.
ii. Functional Proteomics is concerned with the isolation of protein complexes or the use of
protein ligands to isolate specific types of proteins. Proteomics can provide important
information about protein signalling and disease mechanism etc.

Methods of Proteome Analysis: A major challenge facing plant biotechnology and other
bioinformatics research community is the translation of complete genome (DNA) sequence data
into protein structure and predicted functions. Such a step provides the key link between the
genotypes of an organism and its expressed phenotype.

Fig. Analysis of a Proteomics

The growth of proteomics is a direct result of advances made in large scale nucleotide
sequencing of expressed sequence tags (EST).
Resolution and identification of proteins are possible by 2D-PAGE (Polyacrylamide Gel
Electrophoresis) and Mass Spectrometry. Comparative 2-D gel approach or protein chip
approach helps to identify the proteins in up or down regulated system.
Protein identification is also done by Matrix Assisted Laser Desorption Ionization Time-Of-
Flight Mass Spectrometry (MALDI-TOF MS). The hybrid Electro Spray Ionization (ESI)
method of Quadrupole TOF-MS with its increased mass accuracy is becoming increasingly
established.

These methods are performed using modern technology resulting in large-scale characterization
of protein location, protein-protein interaction and protein functions.

Insilico methodologies are being developed to identify protein interaction from genome
sequence. For example, 6809 putative protein-protein interaction has been identified in
Escherichia coli. More than 45,000 protein interactions have been identified in yeast and large
number of these interactions are functionally related.

Scope of Proteomics:
 Fig. Scope of Proteomics

Proteomics deals with significant problems like

(a) Identification of functional domains in protein sequences.

(b) Single, multiple protein alignment (homology).

(c) Determining sequence-structure, sequence-function relationships (structural bio- informatics).

(d) Discovery of protein pattern and providing the framework for the analysis of signaling
networks.

Reverse Genetics: The research in proteomics has made it possible to get the knowledge of all
the proteins produced in an organism. It may or may not be directly responsible for any
phenotypic trait, but this may be helpful to know the functions of all the genes in that organism.
This has made the approach of reverse genetics feasible. From the study of proteins, one can
deduce the function of gene and the trait through reverse genetics.
Significance of Proteomics:
The knowledge of proteomics is complementary to genomics and has become a major thrust area
of genetics, molecular biology and biotechnology research. From the whole genome sequence,
functional genes are identified as open reading frames (ORFs) having initiation and termination
codon, but ORF always does not represent any functional gene.
Verification of gene product by proteome analysis serves a very useful purpose for annotation of
the genome.

Fig. Proteomics and its Applications

i. Protein profiling: Bioinformatics has been widely employed in protein-profiling. It explores
the changes in the protein complement of a cell type during development in response to
environmental stress.
ii. Protein arrays: Protein microarrays facilitate the detection of protein interaction and protein
expression.
iii. Proteomics to a phosphorylation: A proteomics approach for phosphorylation has an
advantage that one can study all the phosphorylating proteins in a cell at the same time.
iv. Proteome mining: It is a functional proteomic approach used to extract information from the
analysis of specific sub-proteomics.
Yeast Proteome:The complete sequence of the whole genome of yeast has been worked out in
1996 and nearly 6200 genes are present in this small organism. In 2001, the functions of 93% of
the proteins (5800 proteins) encoded in the genes were also elucidated.
Later (2002-2005) networks involving the interactions have also been studied. Study of yeast
proteome in great details will be very useful for the study of functions of genes of higher
organisms including human, since yeast is the simplest eukaryote.

Fig. Mass spectroscopy of Proteomics