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Related Concept Videos

Protein Organization01:24

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....
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Protein-protein Interfaces02:04

Protein-protein Interfaces

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Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...
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Protein Families02:47

Protein Families

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Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism.   Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members.   If these new proteins contain similar amino acids in key...
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Protein Networks02:26

Protein Networks

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An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
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Ligand Binding and Linkage00:49

Ligand Binding and Linkage

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Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence...
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Ligand Binding Sites02:40

Ligand Binding Sites

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Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
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Updated: Sep 10, 2025

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions
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ProDualNet: dual-target protein sequence design method based on protein language model and structure model.

Liu Cheng1, Ting Wei1, Xiaochen Cui2

  • 1Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.

Briefings in Bioinformatics
|August 26, 2025
PubMed
Summary
This summary is machine-generated.

Designing proteins to bind two targets is crucial for new therapies. A new AI method, Protein Dual-Target Design Network (ProDualNet), successfully designs dual-target proteins, outperforming existing approaches.

Keywords:
dual-target protein sequence designprotein sequence designstructure-based protein sequence design

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Area of Science:

  • Computational biology
  • Protein engineering
  • Bioinformatics

Background:

  • Proteins interacting with multiple partners are key to biological regulation.
  • Multi-target peptide drugs show therapeutic promise, necessitating multi-target protein design strategies.
  • Current protein design methods primarily focus on single-receptor interactions, limiting dual-target design capabilities.

Purpose of the Study:

  • To introduce ProDualNet, a novel structure-based computational method for designing protein sequences that bind to two distinct receptors.
  • To address the challenge of limited experimental data for dual-target protein structures.

Main Methods:

  • ProDualNet utilizes a heterogeneous graph network for pretraining.
  • The model is fine-tuned using a combination of noise-augmented single-target data and real dual-target data.
  • It integrates sequence and structure information from two target receptors.

Main Results:

  • ProDualNet demonstrated superior performance in recovery and success rates compared to existing multi-state design methods across various test sets.
  • In silico evaluations showed potential for designing dual-target proteins, including cases with allosteric binding and non-overlapping interfaces.
  • The method effectively overcomes limitations posed by scarce dual-target protein structural data.

Conclusions:

  • ProDualNet represents a significant advancement in computational protein design for multi-target applications.
  • The developed method holds promise for accelerating the design of novel therapeutic proteins and biologics.
  • Availability of code and data facilitates further research and application in protein engineering.