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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
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...

Protein Folding

Protein Folding

Protein Folding

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Protein Organization

Protein Organization

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Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence....

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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Updated: Mar 27, 2026

Formation of Ordered Biomolecular Structures by the Self-assembly of Short Peptides

Formation of Ordered Biomolecular Structures by the Self-assembly of Short Peptides

Published on: November 21, 2013

Polymerized Short Sequences as a Template for Protein Folding and Evolution.

Tianyi Jin^1,2, Jacob I Sass¹, Wenhao Gao¹

¹Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States.

|March 25, 2026

Summary

This study designed novel repeat proteins using evolutionary methods and AlphaFold 2, achieving high foldability and stability. These findings show the potential for new peptide-based pharmaceuticals and functional materials.

Keywords:

AlphaFold Aβ Molecular dynamics Peptide linker Protein design Protein evolution Repeat protein

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Synthesis of Information-bearing Peptoids and their Sequence-directed Dynamic Covalent Self-assembly

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Published on: February 6, 2020

Area of Science:

Biochemistry
Structural Biology
Computational Biology

Background:

Repeat proteins are highly versatile and modular, making them key targets for de novo protein design.
Understanding the evolutionary potential of repeat proteins is crucial for advancing protein engineering.

Purpose of the Study:

To explore and discover novel repeat proteins using evolutionary approaches.
To investigate the foldability, stability, and mutational tolerance of computationally designed repeat protein structures.

Main Methods:

Utilized AlphaFold 2 for initial sequence design, integrating amyloid β42 with a hexapeptide linker.
Employed segmental mutations and genetic algorithms for structure evolution.
Conducted molecular dynamics simulations to assess in silico stability and medial strand compatibility.

Main Results:

Achieved high foldability (>12%) in initial de novo protein designs.
Demonstrated good in silico stability for the majority of evolved structures.
Identified a trade-off between foldability, structural variation, and sequence similarity upon mutation.

Conclusions:

The study highlights the significant evolvability and versatility of repeat proteins.
The findings suggest potential applications in developing peptide-based pharmaceuticals and functional materials.