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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...

Conserved Binding Sites

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...

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 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

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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

Designing novel solenoid proteins with in silico evolution.

Daniella Pretorius¹, Georgi I Nikov¹, Kono Washio¹

¹Department of Life Sciences, Imperial College London, Exhibition Road, London, UK.

Communications Chemistry

|December 4, 2025

Summary

We developed an AI platform for designing novel solenoid proteins. This method successfully created alpha-solenoids and, after refinement, beta-solenoids, advancing de novo protein design.

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

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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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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

Area of Science:

Protein engineering
Computational biology
Biophysics

Background:

Solenoid proteins, characterized by tandem repeats, are crucial for various biological functions and are key targets for protein design.
Machine learning advancements have significantly improved understanding of protein sequence-structure relationships, paving the way for de novo protein design.

Purpose of the Study:

To develop an in silico evolution platform for de novo design of solenoid proteins.
To explore the design space of alpha-, beta-, and alpha-beta solenoid backbones.
To validate computational designs through experimental characterization.

Main Methods:

Utilized a genetic algorithm coupled with a solenoid discriminator network and AlphaFold2 as an oracle.
Generated random sequences to design various solenoid backbones.
Experimentally characterized 41 designed solenoid proteins.

Main Results:

Successfully designed alpha-solenoid backbones that consistently folded as intended, with one structurally validated design.
Initial beta-solenoid designs failed, highlighting the challenges in designing beta-strand rich proteins.
Refined beta-solenoid designs, incorporating terminal capping elements, resulted in two proteins with expected biophysical properties.

Conclusions:

The developed platform enables fold-specific, hallucination-based de novo protein design without reliance on explicit structural templates.
The study demonstrates the feasibility of designing novel solenoid proteins computationally and validating them experimentally.
This approach expands the possibilities for creating proteins with tailored functions.