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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

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 Organization

Protein Organization

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....

Conservation of Protein Domains

Conservation of Protein Domains

Protein and Protein Structure

Protein and Protein Structure

Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
A protein's shape is critical to its function. For example, an enzyme...

Protein and Protein Structures

Protein and Protein Structures

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Related Experiment Video

Updated: Sep 16, 2025

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

Advancing protein evolution with inverse folding models integrating structural and evolutionary constraints.

Hongyuan Fei¹, Yunjia Li², Yijing Liu²

¹New Cornerstone Science Laboratory, Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.

|July 8, 2025

Summary

AI-informed constraints for protein engineering (AiCE) improves protein evolution efficiency. This method uses inverse folding models and constraints to design high-fitness mutations, outperforming traditional techniques.

Keywords:

AiCE base editor optimization evolutionary coupling genome editing high-fitness mutations inverse folding protein evolution structure-informed constraints

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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

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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

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Last Updated: Sep 16, 2025

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

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Published on: July 8, 2025

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

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

Area of Science:

Biotechnology
Computational Biology
Protein Engineering

Background:

Traditional protein engineering methods face challenges with low success rates and high costs.
Current approaches often rely on human expertise and task-specific models, limiting scalability.

Purpose of the Study:

To introduce AI-informed constraints for protein engineering (AiCE) for efficient artificial protein evolution.
To demonstrate AiCE's versatility and superiority over conventional protein engineering methods.

Main Methods:

Utilizing generic protein inverse folding models to sample sequences.
Integrating structural and evolutionary constraints to identify high-fitness mutations.
Applying AiCE to diverse protein engineering tasks, including deaminases, nuclear localization sequences, nucleases, and reverse transcriptase.

Main Results:

Achieved success rates ranging from 11% to 88% across eight distinct protein engineering applications.
Developed novel base editors: enABE8e (5-bp window), enSdd6-CBE (1.3-fold improved fidelity), and enDdd1-DdCBE (up to 14.3-fold enhanced mitochondrial activity).
Demonstrated AiCE's effectiveness on proteins of varying sizes, from tens to thousands of residues.

Conclusions:

AiCE is a versatile and user-friendly mutation-design method.
AiCE significantly enhances efficiency, scalability, and generalizability in protein engineering.
The developed base editors show promise for applications in precision medicine and agriculture.