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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 Organization

Protein Organization

Protein Organization

Protein Organization

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 Folding

Protein Folding

Protein Folding

Protein Folding

Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
Protein Structure Is Critical to Its Biological Function
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...

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Extending CATH: increasing coverage of the protein structure universe and linking structure with function.

Alison L Cuff¹, Ian Sillitoe, Tony Lewis

¹Institute of Structural and Molecular Biology, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK. cuff@biochem.ucl.ac.uk

Nucleic Acids Research

|November 25, 2010

Summary

The CATH database version 3.4 enhances protein structure classification by improving functional and sequence information presentation for superfamilies. It also features a more efficient search function for exploring protein fold space.

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Area of Science:

Structural biology
Bioinformatics
Protein classification

Background:

The CATH database classifies protein structures into classes, architectures, topologies, and homologies.
Previous versions focused on structural genomics and transmembrane proteins, increasing fold space coverage.
Version 3.3 contained 128,688 domains and 2386 superfamilies.

Purpose of the Study:

To enhance the presentation of sequence and functional information for CATH superfamilies.
To improve the search functionality and user experience of the CATH database.
To increase the representation of novel protein structures within the CATH database.

Main Methods:

Implemented improved presentation of sequence and functional data for CATH superfamilies.
Integrated structural alignments of related proteins with functional annotations and conserved residue details.
Deployed the Solr search server for a more efficient CATH search function.
Utilized the Catalyst web framework for building the CATH v3.4 webpages.

Main Results:

CATH version 3.4 significantly improved the display of functional and sequence data for superfamilies.
Superfamily pages now showcase functional and structural diversity with detailed alignments.
A more efficient search capability was implemented using the Solr search server.
The CATH v3.4 webpages offer enhanced access to protein structural and functional information.

Conclusions:

CATH version 3.4 provides a richer, more informative resource for exploring protein structure-function relationships.
The enhanced search functionality improves discoverability and accessibility of protein domain information.
Continued updates to CATH ensure comprehensive coverage of protein fold space, incorporating novel structures.