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Proteomics

Proteomics

A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term proteomics...

Protein Organization

Protein Organization

Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence.

Protein-protein Interfaces

Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...

Protein Networks

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...

Protein and Protein Structure

Protein and Protein Structure

Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
A protein's shape is critical to its function. For example, an enzyme can...

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[Protein Structure Discovery: software package to perform computational proteomics tasks].

V A Ivanisenko, P S Demenkov, T V Ivanisenko

Bioorganicheskaia Khimiia

|April 5, 2011

Summary

This summary is machine-generated.

A new software system, Protein Structure Discovery, aids computer proteomics by predicting protein function, structure, and immunological properties. It also evaluates mutation effects on protein characteristics, offering a comprehensive tool for researchers.

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Area of Science:

Computational Biology
Bioinformatics
Structural Biology

Background:

Proteomics research requires advanced computational tools for analyzing protein structure and function.
Understanding protein properties is crucial for drug discovery and understanding biological processes.

Purpose of the Study:

To introduce the Protein Structure Discovery (PSD) software system.
To highlight PSD's capabilities in predicting protein characteristics and evaluating mutation impacts.
To provide a web-accessible platform for computational proteomics tasks.

Main Methods:

Integration of 19 specialized programs within a unified software system.
Inclusion of databases like PDBSite for protein functional sites.
Development of tools such as PDBSiteScan for site prediction and WebProAnalyst for structure-activity relationship analysis.
Implementation of a web interface for user accessibility.

Main Results:

The PSD system offers a wide range of computational proteomics functionalities.
It enables quantitative and qualitative assessment of mutation effects on proteins.
The PDBSiteScan tool demonstrated stability in recognizing functional sites even with reconstruction errors in protein structures.
The system successfully identified functional sites like zinc ion and ADP binding sites.

Conclusions:

Protein Structure Discovery is a versatile and valuable tool for computational proteomics.
Its integrated approach and web accessibility facilitate diverse protein analysis tasks.
The system's methods show robustness in identifying critical protein functional sites.