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Related Concept Videos

Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
Conservation of Protein Domains02:26

Conservation of Protein Domains

Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
Proteomics01:33

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 and Protein Structure02:15

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...
Protein Networks02:26

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-Drug Binding: Determination Methods01:22

Protein-Drug Binding: Determination Methods

Determining protein-drug binding can be achieved through indirect and direct methods, each providing valuable insights into the interaction between proteins and drugs.
Indirect methods involve isolating the bound drug from its free form in biological samples such as blood, serum, or plasma. These techniques aim to measure the percentage of drugs bound to proteins. Equilibrium dialysis is a commonly used method where the free drug concentration at equilibrium is measured by separating the bound...

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Related Experiment Video

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A New Approach for the Comparative Analysis of Multiprotein Complexes Based on 15N Metabolic Labeling and Quantitative Mass Spectrometry
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ProCoCoA: A quantitative approach for analyzing protein core composition.

Silvia Bottini1, Andrea Bernini, Matteo De Chiara

  • 1Department of Biotechnology, Chemistry and Pharmacy, University of Siena, I-53100 Siena, Italy. bottini4@unisi.it

Computational Biology and Chemistry
|January 22, 2013
PubMed
Summary

Understanding protein core amino acid composition is key for protein folding and engineering. A new tool, ProCoCoA, analyzes protein core composition, revealing specific patterns across different protein folds.

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Area of Science:

  • Structural biology
  • Bioinformatics
  • Protein science

Background:

  • Protein core composition is crucial for protein folding and stability.
  • Quantitative analysis of protein cores is needed for reliable protein engineering.

Purpose of the Study:

  • To establish unambiguous criteria for assigning amino acid residues to protein cores.
  • To develop a tool for analyzing protein core composition.
  • To investigate amino acid patterns in different protein folds.

Main Methods:

  • Development of the Protein Core Composition Analyzer (ProCoCoA) tool.
  • Utilizing atom depth considerations to classify residues as inner or outer molecular moieties.
  • Analysis of six protein architectures from the CATH database.

Main Results:

  • ProCoCoA provides accurate estimates of protein core composition.
  • Specific patterns of amino acid composition were identified in different protein folds.
  • The tool facilitates classification of inner and outer molecular moieties.

Conclusions:

  • Amino acid networks within protein cores are vital for structural stability.
  • ProCoCoA is a user-friendly tool for analyzing protein core composition.
  • Identified patterns can enhance protein engineering reliability.