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Related Concept Videos

Protein Organization01:24

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 Organization01:13

Protein Organization

Overview
Protein Folding01:22

Protein Folding

Overview
Protein Folding01:22

Protein Folding

Overview
Protein Folding01:25

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...
Protein and Protein Structures02:15

Protein and Protein Structures

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 WISDOM: A Workbench for In silico De novo Design of BioMolecules
10:58

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

PTGL: a database for secondary structure-based protein topologies.

Patrick May1, Annika Kreuchwig, Thomas Steinke

  • 1Max Planck Institute for Molecular Plant Physiology, Bioinformatics, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany. may@mpimp-golm.mpg.de

Nucleic Acids Research
|November 13, 2009
PubMed
Summary
This summary is machine-generated.

A new database, the Protein Topology Graph Library (PTGL), offers a unique graph-based method for classifying protein structures. This approach enables fast searching and deeper understanding of protein topology and function.

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Area of Science:

  • Structural biology
  • Bioinformatics

Background:

  • The increasing volume of experimental data leads to a continuous rise in known protein structures.
  • Classifying protein structures is crucial for understanding the relationship between structure and function.
  • Existing classification methods like SCOP, CATH, and TOPS, based on secondary structures, classify protein structures from different perspectives, potentially yielding varied results.

Purpose of the Study:

  • To develop a mathematically unique representation of protein structure topologies for enhanced classification and rapid data searching.
  • To introduce the Protein Topology Graph Library (PTGL) as a database for protein secondary structure topologies, offering search, visualization, and supplementary information.

Main Methods:

  • Protein topologies are represented as undirected labeled graphs in four distinct ways, enabling multi-aspectual exploration.
  • Linear notations, along with 2D and 3D diagrams, are utilized to facilitate a comprehensive understanding of protein topologies.
  • The database incorporates search functions for topologies and sub-topologies, a BLAST search capability, and links to external resources like SCOP, CATH, and PDBsum.

Main Results:

  • The PTGL database currently contains topologies for 54,859 protein structures.
  • Pre-implemented search functionalities for common structural motifs, such as TIM-barrel and Jelly Roll, are available.
  • The unique graph representation provides new classification aspects and enables efficient searching.

Conclusions:

  • The PTGL database offers a novel and efficient method for classifying and searching protein structures based on their topologies.
  • This approach enhances the understanding of protein structure-function relationships and supports both individual and large-scale investigations.