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Related Concept Videos

Protein-protein Interfaces02:04

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-Protein Interfaces02:04

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 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 Folding01:22

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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 Folding01:22

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A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Classification of protein functional surfaces using structural characteristics.

Yan Yuan Tseng1, Wen-Hsiung Li

  • 1Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA.

Proceedings of the National Academy of Sciences of the United States of America
|January 13, 2012
PubMed
Summary
This summary is machine-generated.

Protein surface classification (PSC) uses functional surface structures to reveal protein relationships. This method aids in defining evolutionary positions and inferring functions for uncharacterized proteins.

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Area of Science:

  • Biochemistry and Structural Biology
  • Bioinformatics and Computational Biology

Background:

  • Protein structure and function are intrinsically linked, particularly at functional surfaces responsible for biological activities.
  • Protein structures evolve more slowly than their amino acid sequences, offering a stable basis for classification.

Purpose of the Study:

  • To develop and validate a novel method for protein classification based on functional surface structures, termed protein surface classification (PSC).
  • To explore the potential of PSC in identifying functional and evolutionary relationships among proteins, even those with divergent sequences.
  • To establish a comprehensive library of protein binding surface types.

Main Methods:

  • Focused on ligand-bound regions to define well-characterized functional surfaces.
  • Utilized structural attributes to quantify similarities between protein binding surfaces.
  • Constructed a protein surface classification (PSC) library comprising approximately 2,000 binding surface types from bound protein structures.

Main Results:

  • Demonstrated PSC's utility with flavin mononucleotide-binding proteins and glycosidases, enabling evolutionary positioning and functional inference for uncharacterized proteins.
  • Revealed that proteins with identical enzyme nomenclature can exhibit distinct subtypes.
  • Showed that proteins within the same CATH (Class, Architecture, Topology, Homologous superfamily) fold may belong to different surface types, highlighting the limitations of fold-based classification alone.

Conclusions:

  • PSC complements existing sequence-based and fold-domain classification methods by directly linking protein shape to biological function.
  • The PSC library serves as a valuable, expandable resource for studying the evolution of protein structure and function through spatial patterns.
  • This approach offers a unique perspective on protein evolution and functional relationships by prioritizing structural surface characteristics.