Fundamentals of Bioinformatics - Ogurtsov A.N. 2013

Foundations of Bioinformatics
Genomes and Proteomes
Proteomics

Proteomics focuses on the cataloging and Analysis of Proteins to determine:

1) the specific cellular state and stage of The life cycle at which a given protein is expressed;

2) the quantity in which a given protein is synthesized;

3) the other proteins with which a given protein can interact.

The term "proteomics" refers to all proteins expressed by The Genome. It is a systematic Analysis of Protein expression profiles synthesized across various Tissues throughout an Organism.

The word "proteome" refers to the proteins produced by a given biological species at a specific time.

The proteome changes over time and is defined as the entire Complement of proteins in a single sample or specimen (tissue, organism, Cell culture) at a given moment. Proteomics thus reflects the dynamic biological activity of the genome.

Proteomics is subdivided into:

✵ expression proteomics — The Study of global changes in protein expression;

✵ cytomapping proteomics — the systematic study of Protein-Structure/156.html">Protein Interactions through the isolation of Protein Complexes.

In recent years, there has been a rapidly growing interest in proteomics. This is because the information obtained from DNA Sequencing reflects the static Genetic information of a cell, whereas cellular life is a dynamic process.

The composition of proteins expressed by an organism changes during the growth, disease, and death of Cells and Tissues.

Proteomics systematizes and characterizes proteins, compares changes in their expression levels between healthy and diseased tissues, investigates their interactions, and determines their functional roles.

Proteomics begins with the ISOLATION OF A functionally modified protein and concludes with the identification of the Gene responsible for its expression.

The MAIN OBJECTIVES OF proteomics are as follows:

1) to identify all proteins within the proteome;

2) to determine The sequence of each protein and deposit the resulting data into Databases;

3) to perform comprehensive profiling of protein expression levels across different cell types and developmental stages.

Proteomics is divided into Structural and functional proteomics.

Structural proteomics, or protein expression profiling, measures the number and types of proteins present in healthy and diseased (or wild-type and mutant) cells.

This approach is valuable for determining The structure of cellular proteins, some of which may serve as targets for novel therapeutic drugs.

Functional proteomics is dedicated to studying the BIOLOGICAL Functions OF proteins.

Proteome research is carried out in three stages.

1. Separation of Protein Mixtures using two-dimensional (2D) Polyacrylamide gel Electrophoresis.

2. Identification of individual gel-purified proteins via mass spectrometry or N-terminal sequencing.

3. Storage, Processing, and comparison of the obtained data using bioinformatics Methods.

In the post-genomic era, The Significance of proteomics lies in the fact that proteomic methods are specifically used to investigate the expression and functions of genes discovered through Genomics.

Differential display proteomics, which focuses on comparing protein expression levels, is applied in the Treatment of a wide range of diseases.

It is often quite difficult to predict a protein's function based solely on its Homology to other proteins or even its three-dimensional structure; therefore, functional analysis via proteomics determines the components of complex Protein Assemblies.

Proteomics also plays a crucial role in Drug Discovery and development by characterizing disease processes through the direct identification of protein sets (pathways or groups) whose collective action—whether sequential or simultaneous—triggers the disease.

Proteomics can be viewed as a mass separation-based method of molecular biology that maps the overall distribution of cellular proteins to identify and characterize specific target proteins and, ultimately, elucidate their interactions and functional roles.

Such direct protein-level analysis is essential because insights gained from genomic studies alone cannot reliably predict protein structures and expression dynamics. Yet it is precisely at the protein level that the majority of regulatory mechanisms operate, pathological processes unfold, and most targets for pharmacological intervention are to be found.