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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 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 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 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...

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Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
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Low-resolution structural modeling of protein interactome.

Ilya A Vakser1

  • 1Center for Bioinformatics, The University of Kansas, Lawrence, KS 66047, USA. vakser@ku.edu

Current Opinion in Structural Biology
|January 9, 2013
PubMed
Summary

Understanding protein interactions is crucial for molecular biology. Low-resolution methods and template-based modeling are essential for large-scale protein interaction network analysis, especially with limited experimental data.

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Area of Science:

  • Molecular Biology
  • Structural Biology
  • Bioinformatics

Background:

  • Structural characterization of protein-protein interactions is fundamental to understanding molecular life.
  • Large-scale modeling of protein interaction networks requires low-resolution approaches due to inherent uncertainties and high-throughput demands.
  • Experimental determination of protein structures is limited, necessitating computational methods for interactome analysis.

Purpose of the Study:

  • To highlight the need for low-resolution methods in protein interaction studies.
  • To discuss the advancements and relevance of template-based modeling for protein-protein interactions.
  • To assess the availability and reliability of protein-protein templates for structure prediction.

Main Methods:

  • Review of current trends in structure prediction for individual proteins and complexes.
  • Analysis of the availability of template-based models for protein-protein interactions.
  • Assessment of the accuracy of existing protein-protein templates.

Main Results:

  • Template-based modeling is advancing rapidly for protein-protein complexes, mirroring progress in individual protein structure prediction.
  • Protein-protein templates are accessible for nearly all structurally characterized protein interactions.
  • Approximately one-third of these protein-protein templates are considered likely correct.

Conclusions:

  • Low-resolution and template-based modeling approaches are vital for studying large-scale protein interaction networks.
  • The increasing availability and accuracy of protein-protein templates support computational modeling of the interactome.
  • Further development in these areas will enhance our understanding of molecular life.