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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...

Newman Projections

Newman Projections

Different notations are used to represent the three-dimensional structure of molecules on two-dimensional surfaces. One of the most commonly used representations is the dash-wedge formula. The dashed wedges, solid wedges, and the plane lines indicate the groups situated behind the plane, coming out of the plane, and in the plane, respectively.
The organic molecules rotate across the single bonds leading to numerous temporary three-dimensional structures of varying energy known as conformers.

Fischer Projections

Fischer Projections

Learning to draw Fischer projections of molecules and understanding their relevance plays a crucial role in the visual depiction of organic molecules. A Fischer projection is a two-dimensional projection on a planar surface to simplify the three-dimensional wedge–dash representation of molecules. This is especially helpful in the case of molecules with multiple chiral centers that can be difficult to draw. Here, all the bonds of interest are represented as horizontal or vertical lines. While...

Three-Dimensional Microscopy in Microbiology

Three-Dimensional Microscopy in Microbiology

Three-dimensional imaging techniques are essential in cell biology, allowing researchers to visualize intricate cellular structures with high resolution. Two prominent methods, Differential Interference Contrast Microscopy (DIC) and Confocal Scanning Laser Microscopy (CSLM), provide distinct advantages for imaging live and thick specimens, respectively.Differential Interference Contrast MicroscopyDIC microscopy enhances contrast in transparent, unstained samples by converting phase...

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...

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Updated: May 24, 2026

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

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

Published on: July 16, 2017

Three-dimensional domain swapping in the protein structure space.

Yongqi Huang¹, Huaiqing Cao, Zhirong Liu

¹College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.

|March 14, 2012

Summary

Domain swapping is a common protein assembly mechanism, found in about 10% of protein folds. Hinge loops are crucial for stabilizing these domain-swapped protein structures.

Related Experiment Videos

Last Updated: May 24, 2026

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

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

Published on: July 16, 2017

Area of Science:

Structural Biology
Protein Science

Background:

Three-dimensional (3D) domain swapping is a structural phenomenon where protein domains exchange between molecules.
While numerous 3D domain-swapped structures exist, its prevalence as a general protein assembly mechanism remains debated.

Purpose of the Study:

To investigate the generality of 3D domain swapping across the protein structure space.
To analyze the structural features and distribution of domain-swapped proteins.

Main Methods:

Construction of a comprehensive dataset of over 500 domain-swapped protein structures.
Mapping these structures into the broader protein structure space.
Analysis of protein folds, families, superfamilies, and interface regions, particularly hinge loops.

Main Results:

Approximately 10% of protein folds and 5% of protein families exhibit domain-swapping.
Proteins within the same family/superfamily can engage in domain swapping through diverse mechanisms.
Hinge loops are identified as key contributors, forming over half the open interface in 70% of domain-swapped dimers, stabilizing the swapped conformations.

Conclusions:

The findings support the hypothesis that domain swapping is a general property inherent to proteins.
This study enhances the understanding of the underlying mechanisms driving 3D domain swapping in proteins.