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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

Protein Folding

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...

Protein Folding Quality Check in the RER

Protein Folding Quality Check in the RER

ER is the primary site for the maturation and folding of soluble and transmembrane secretory proteins. The calnexin cycle is a specific chaperone system that folds and assesses the confirmation of N-glycosylated proteins before they can exit the ER lumen. The primary players of this quality check pipeline are the lectins, ER-resident chaperones, and a glucosyl transferase enzyme. In case the calnexin system in the lumen fails to salvage a misfolded protein, it is transported to the cytoplasm...

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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Related Experiment Video

Updated: Apr 21, 2026

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

Protein design with a comprehensive statistical energy function and boosted by experimental selection for

Peng Xiong¹, Meng Wang¹, Xiaoqun Zhou¹

¹School of Life Sciences, University of Science and Technology of China, 443 Huangshan Road, Hefei, Anhui 230027, China.

Nature Communications

|October 28, 2014

Summary

We developed a new computational model for de novo protein design, improving our understanding of protein folding and enabling advanced protein engineering. Experimental validation confirmed the designed proteins are well-folded.

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Assessment of Immunologically Relevant Dynamic Tertiary Structural Features of the HIV-1 V3 Loop Crown R2 Sequence by ab initio Folding

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Published on: September 15, 2010

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Assessment of Immunologically Relevant Dynamic Tertiary Structural Features of the HIV-1 V3 Loop Crown R2 Sequence by ab initio Folding

Published on: September 15, 2010

Area of Science:

* Computational biology
* Structural biology
* Protein engineering

Background:

* De novo protein design aims to create novel amino acid sequences encoding specific protein structures.
* Current computational protein design methods have limitations requiring complementary approaches.
* Experimental feedback is crucial for refining theoretical models in protein design.

Purpose of the Study:

* To develop a comprehensive statistical energy function for de novo protein design.
* To create computational models that complement and rival existing protein design tools.
* To establish an experimental approach for assessing and improving designed protein foldability.

Main Methods:

* Development of a novel statistical energy function for protein sequence design.
* Implementation of a general strategy for de novo protein design.
* Experimental verification of designed protein foldability and structure determination.

Main Results:

* A new statistical energy function was developed and validated.
* Four de novo proteins were designed for distinct targets.
* All designed proteins were experimentally verified as well-folded, with two structures matching design targets.

Conclusions:

* The developed computational model and strategy effectively complement existing protein design methods.
* Experimental validation is a viable approach to assess and enhance designed protein foldability.
* This work advances the field of de novo protein design and protein engineering.