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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 Organization01:24

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 Folding01:22

Protein Folding

Overview
Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...
Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...
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...

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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
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A modular perspective of protein structures: application to fragment based loop modeling.

Narcis Fernandez-Fuentes1, Andras Fiser

  • 1Institute of Biological, Environmental and Rural Sciences Aberystwyth University Aberystwyth, Ceredigion, SY23 3DA, UK.

Methods in Molecular Biology (Clifton, N.J.)
|September 19, 2012
PubMed
Summary

Supersecondary structure modules, or Smotifs, reveal saturation in protein geometries. This finding advances protein structure modeling and design, exemplified by the ArchPred loop conformation algorithm.

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Area of Science:

  • Structural biology
  • Bioinformatics
  • Computational chemistry

Background:

  • Proteins are fundamental biological molecules composed of complex three-dimensional structures.
  • Supersecondary structure modules (Smotifs) represent recurring patterns of protein folding.
  • Understanding Smotif diversity is crucial for deciphering protein structure-function relationships.

Purpose of the Study:

  • To explore the evolution and variety of protein supersecondary structure modules (Smotifs).
  • To investigate the saturation of Smotif geometries in known protein structures.
  • To apply these findings to enhance protein structure modeling and design, specifically for loop conformations.

Main Methods:

  • Utilized a generic definition of Smotifs (two regular secondary structures flanking a loop).
  • Analyzed recent observations on the saturation of Smotif geometries.
  • Developed and applied the ArchPred algorithm for loop conformation modeling based on Smotif classification.

Main Results:

  • Observed saturation in Smotif geometries, indicating a finite set of structural building blocks.
  • ArchPred successfully identifies likely supersecondary structure environments for loop conformations.
  • The algorithm considers anchor residue fit, steric clashes, dihedral angle preferences, and local sequence signals.

Conclusions:

  • Smotif geometry saturation provides new opportunities for protein structure modeling and design.
  • ArchPred offers an effective method for predicting loop conformations by leveraging supersecondary structure context.
  • This approach moves beyond specific loop properties to utilize broader structural environments.