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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...

Protein Folding

Protein Folding

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Protein Folding

Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
Protein Structure Is Critical to Its Biological Function
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...

Molecular Chaperones and Protein Folding

Molecular Chaperones and Protein Folding

The native conformation of a protein is formed by interactions between the side chains of its constituent amino acids. When the amino acids cannot form these interactions, the protein cannot fold by itself and needs chaperones. Notably, chaperones do not relay any additional information required for the folding of polypeptides; the native conformation of a protein is determined solely by its amino acid sequence. Chaperones catalyze protein folding without being a part of the folded protein.
The...

Molecular Chaperones and Protein Folding

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Conservation of Protein Domains

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Analysis of Protein Folding, Transport, and Degradation in Living Cells by Radioactive Pulse Chase

Analysis of Protein Folding, Transport, and Degradation in Living Cells by Radioactive Pulse Chase

Published on: February 12, 2019

Fold combinations in multi-domain proteins.

Nagarajan Naveenkumar^1,2,3, Gayatri Kumar³, Ramanathan Sowdhamini¹

¹National Center for Biological Science, GKVK Campus, Bengaluru, Karnataka, India - 560065.

|June 29, 2019

Summary

This summary is machine-generated.

Multi-domain proteins exhibit limited fold-fold combinations, suggesting functional constraints. Analysis reveals a small fraction of theoretically possible combinations are utilized in nature, highlighting evolutionary preferences.

Keywords:

domain architecture domain folds multi-domain proteins protein evolution protein structure

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Area of Science:

Protein structure and function
Bioinformatics and computational biology
Molecular evolution

Background:

Multi-domain proteins integrate functions through domain-domain interactions.
Coupled domain functions limit the diversity of natural domain architectures.
Understanding fold-fold combinations is crucial for deciphering protein function and evolution.

Purpose of the Study:

To document and analyze the repertoire of fold-fold combinations in multi-domain proteins.
To compare observed combinations with theoretically possible ones.
To investigate evolutionary preferences in domain architecture.

Main Methods:

Analysis of multi-domain proteins with known structures from the Protein Data Bank.
Examination of multi-domain proteins represented in sequence databases.
Calculation of observed versus theoretically possible fold-fold combinations.

Main Results:

Approximately 860 fold-fold combinations were identified in known protein structures.
Analysis of sequence databases revealed 29,860 fold-fold combinations.
These observed combinations represent only 2.8% of the theoretically possible 1,036,080 combinations.

Conclusions:

Nature utilizes a limited subset of possible fold-fold combinations in multi-domain proteins.
This preference suggests evolutionary selection for specific domain arrangements.
Gene fusion may drive structural adaptation for expanded functional capabilities.