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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...

Protein Complexes with Interchangeable Parts

Protein Complexes with Interchangeable Parts

Assembly of Complex Microtubule Structures

Assembly of Complex Microtubule Structures

Complex microtubule structures are present in resting cells and in dividing cells. In resting cells, they are responsible for maintaining the cellular architecture, tracks for intracellular transport, positioning of organelles, assembly of cilia and flagella. They mediate the bipolar spindle assembly for chromosomal segregation and positioning of the cell division plate in dividing cells. The formation of microtubule complex structures depends on the cell type, cell stage, and cell function.

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

Updated: May 5, 2026

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

MMDB and VAST+: tracking structural similarities between macromolecular complexes.

Thomas Madej¹, Christopher J Lanczycki, Dachuan Zhang

¹National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38 A, Room 8N805, 8600 Rockville Pike, Bethesda, MD 20894, USA.

Nucleic Acids Research

|December 10, 2013

Summary

This summary is machine-generated.

VAST+ enhances protein structure comparison by analyzing biological assemblies and macromolecular complexes. This new tool simplifies similarity searches within the Molecular Modeling Database (MMDB), improving protein family classification and functional inference.

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Last Updated: May 5, 2026

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

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Published on: July 16, 2017

Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy

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Published on: September 17, 2017

Structural Studies of Macromolecules in Solution using Small Angle X-Ray Scattering

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Published on: November 5, 2018

Area of Science:

Structural bioinformatics
Computational biology
Molecular modeling

Background:

Protein 3D structure comparison is crucial for homology detection, protein family classification, and functional inference.
Existing tools like the Vector Alignment Search Tool (VAST) compute pairwise structural similarities for individual proteins and domains within the NCBI's Molecular Modeling Database (MMDB).

Purpose of the Study:

To introduce VAST+, an extension of the VAST service, designed to summarize and present structural similarities at the level of biological assemblies and macromolecular complexes.
To simplify the presentation of structure neighboring results for macromolecular complexes within the MMDB.

Main Methods:

Development of VAST+ as an extension to the existing VAST service.
Integration of VAST+ into NCBI's Entrez query and retrieval system to replace the previous VAST service for presenting structure neighboring data.
Tracking and ranking of similar macromolecular complexes within the MMDB based on structural similarity.

Main Results:

VAST+ provides summarized structural similarity information for biological assemblies and macromolecular complexes.
The service presents ranked lists of similar macromolecular complexes found in the MMDB.
VAST+ is now the default method for displaying structure neighboring data in NCBI's Entrez system.

Conclusions:

VAST+ offers a simplified and more biologically relevant approach to exploring structural similarities among macromolecular complexes.
The enhanced presentation of structural similarity data facilitates a deeper understanding of protein relationships and functions.
VAST+ improves the utility of the MMDB for researchers studying protein structure and function.