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Protein Complexes with Interchangeable Parts

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 Parts

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...

Conservation of Protein Domains Over Different Proteins

Conservation of Protein Domains Over Different Proteins

Protein domains are small structurally independent units that are part of a single amino acid chain. Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...

Conservation of Protein Domains

Conservation of Protein Domains

Protein domains are small structurally independent units that are part of a single amino acid chain. Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...

Protein Complex Assembly

Protein Complex Assembly

Proteins can form homomeric complexes with another unit of the same protein or heteromeric complexes with different types. Most protein complexes self-assemble spontaneously via ordered pathways, while some proteins need assembly factors that guide their proper assembly. Despite the crowded intracellular environment, proteins usually interact with their correct partners and form functional complexes.
Many viruses self-assemble into a fully functional unit using the infected host cell to...

Protein Complex Assembly

Protein Complex Assembly

Proteins can form homomeric complexes with another unit of the same protein or heteromeric complexes with different types. Most protein complexes self-assemble spontaneously via ordered pathways, while some proteins need assembly factors that guide their proper assembly. Despite the crowded intracellular environment, proteins usually interact with their correct partners and form functional complexes.
Many viruses self-assemble into a fully functional unit using the infected host cell to...

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Related Experiment Video

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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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ConPlex: a server for the evolutionary conservation analysis of protein complex structures.

Yoon Sup Choi¹, Seong Kyu Han, Jinho Kim

¹School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, 790-784, Republic of Korea.

Nucleic Acids Research

|May 4, 2010

Summary

ConPlex is a new web tool for analyzing protein-protein interactions using evolutionary conservation. It helps researchers understand protein complex structures by identifying conserved residues at interfaces.

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Area of Science:

Structural biology
Bioinformatics
Computational biology

Background:

Evolutionary conservation analysis is crucial for identifying protein-protein interactions.
Sequence conservation aids in determining protein oligomerization, native interfaces, and distinguishing real structures from artifacts.

Purpose of the Study:

To develop a user-friendly web-based service for evolutionary conservation analysis of protein complexes.
To provide a tool for analyzing protein interactions within protein quaternary structures.

Main Methods:

Developed ConPlex, a web application for evolutionary conservation analysis of protein complexes.
Automated identification of protein interfaces and conservation analysis of interface regions.
Visualization of residue-specific conservation on protein complex structures with customizable display options.

Main Results:

ConPlex enables evolutionary conservation analysis of protein interactions within protein quaternary structures.
The tool automatically identifies protein interfaces and analyzes conservation in these regions.
Residue-specific conservation results can be visualized directly on the protein complex structure.

Conclusions:

ConPlex provides a convenient platform for analyzing protein complex structures.
The tool leverages the evolutionary conservation of protein-protein interface residues.
It facilitates a deeper understanding of protein complex organization and function.