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Protein Folding

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
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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.
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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.
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Amyloid Fibrils

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Protein Organization

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Related Experiment Video

Updated: Jun 13, 2025

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

Inventing Novel Protein Folds.

Nobuyasu Koga¹, Rie Tatsumi-Koga²

¹Laboratory for Protein Design, Institute for Protein Research (IPR), Osaka University, Suita, Osaka 565-0871, Japan; Protein Design Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Aichi 444-8585, Japan.

Journal of Molecular Biology

|September 11, 2024

Summary

This summary is machine-generated.

Nature has explored only a small fraction of possible protein folds. Systematic de novo design reveals vast unexplored protein fold universe, opening new avenues for functional protein design.

Keywords:

novel fold protein design protein fold protein sequence space protein topology

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Published on: September 15, 2010

Area of Science:

Protein engineering
Structural biology
Biochemistry

Background:

The diversity of protein structures is vast, yet the extent of naturally occurring protein folds is unknown.
Understanding the "protein fold universe" is crucial for advancing protein design and function prediction.

Purpose of the Study:

To explore the unexplored protein fold universe using de novo protein design.
To demonstrate that numerous possible protein folds remain undiscovered by nature.
To discuss the potential for designing novel functional proteins with unique folds.

Main Methods:

Systematic de novo design of proteins.
Focus on novel alpha-beta (αβ) folds.
Computational and experimental validation of designed protein structures.

Main Results:

Demonstrated the existence of a vast unexplored protein fold space.
Successfully designed proteins with novel αβ-folds, distinct from known natural folds.
Indicated that nature has sampled only a minor subset of potential protein folds.

Conclusions:

The theoretical space of protein folds far exceeds those currently observed in nature.
De novo protein design is a powerful approach to access novel protein architectures.
Future prospects include the design of functional proteins with entirely new folds for various applications.