Binding Protein

A Binding Protein is a protein that interacts with and attaches to specific molecules

• Context:
  • It can (typically) bind to DNA, RNA, or other proteins.
  • It can (often) regulate biological processes like transcription, translation, and replication.
  • It can (often) assist in molecule transportation, such as hemoglobin binding to oxygen for transport in the bloodstream.
  • ...
  • It can range from being a DNA-binding protein (that binds to specific DNA sequences) to being an RNA-binding protein (that regulates RNA processing).
  • ...
  • It can regulate the activity of enzymes by binding to them, either activating or inhibiting their function.
  • It can have specific binding sites for molecules like ions, hormones, or other macromolecules.
  • It can participate in signaling pathways, such as calcium-binding proteins involved in signal transduction.
  • It can be involved in maintaining the stability of the genome, such as single-strand binding proteins protecting DNA during replication.
  • It can play a role in post-transcriptional regulation, such as poly(A)-binding proteins that control mRNA stability.
  • It can assist in the folding or transporting of other proteins, functioning as a molecular chaperone.
  • It can interact with ligands reversibly or irreversibly depending on the physiological process.
  • It can be a Protein Binder, that specifically binds to other proteins (possibly artificially designed).
  • ...
• Example(s):
  • An RNA-binding protein that showcases its role in the regulation of alternative splicing of pre-mRNA.
  • A calcium-binding protein that demonstrates the role of calcium in cellular signaling pathways.
  • A single-strand binding protein that illustrates its function in stabilizing single-stranded DNA during replication.
  • A CREB-binding protein that interacts with the cAMP response element-binding protein to regulate gene transcription.
  • A telomere-binding protein that protects the ends of chromosomes from degradation.
  • A nuclear cap-binding protein complex that binds to the 5' cap of eukaryotic mRNA to regulate mRNA processing and export.
  • A ferritin protein that binds and stores iron, releasing it in a controlled fashion when needed by the body.
  • A transferrin protein that binds iron ions and transports them through the bloodstream to various tissues.
  • Antibody Proteins: Antibodies are natural protein binders that the immune system uses to recognize and bind to specific antigens.
  • Designed ankyrin repeat proteins (DARPins): proteins based on the structure of natural ankyrin repeat proteins.
  • Affibodies: Small engineered proteins derived from one of the IgG-binding domains of staphylococcal protein A.
  • ...
• Counter-Example(s):
  • Enzymes that catalyze chemical reactions rather than binding other molecules for regulation.
  • Transport proteins that actively move molecules across membranes without necessarily binding them.
• See: CPE-Binding Protein, Protein, Molecular Binding, DNA-Binding Protein, Single-Strand Binding Protein, Telomere-Binding Protein, RNA-Binding Protein, Poly(A)-Binding Protein, Nuclear Cap-Binding Protein Complex, CREB-Binding Protein, Calcium-Binding Protein, Calcium-Binding Protein 1.

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References

2024

• (Zambaldi et al., 2024) ⇒ Vinicius Zambaldi, David La, Alexander E. Chu, Harshnira Patani, Amy E. Danson, Tristan O. C. Kwan, Thomas Frerix, Rosalia G. Schneider, David Saxton, Ashok Thillaisundaram, Zachary Wu, Isabel Moraes, Oskar Lange, Eliseo Papa, Gabriella Stanton, Victor Martin, Sukhdeep Singh, Lai H. Wong, Russ Bates, Simon A. Kohl, Josh Abramson, Andrew W. Senior, Yilmaz Alguel, Mary Y. Wu, Irene M. Aspalter, Katie Bentley, David L. V. Bauer, Peter Cherepanov, Demis Hassabis, Pushmeet Kohli, Rob Fergus, and Jue Wang. (2024). “De Novo Design of High-affinity Protein Binders with AlphaProteo.”
  • NOTES:
    • The paper introduces AlphaProteo, a machine learning model specifically designed for the de novo creation of protein binders, utilizing a novel deep learning architecture to achieve superior performance in generating high-affinity binders for target proteins.
    • The paper demonstrates that AlphaProteo can produce binders with 3- to 300-fold better binding affinities compared to existing methods. This advance is achieved using a specialized deep generative model architecture that learns protein structure-function relationships and minimizes the need for multiple rounds of experimental testing.
    • The paper showcases successful experimental validation of binders for seven structurally diverse proteins. The AI-driven system achieved binding success rates of 9% to 88%, far surpassing previous approaches by efficiently narrowing down candidate binders for in vitro testing.

2024

• (Wikipedia, 2024) ⇒ https://en.wikipedia.org/wiki/Binding_protein Retrieved:2024-9-6.
  • A binding protein is any protein that acts as an agent to bind two or more molecules together.

    Examples include:

    • DNA-binding protein
      • Single-strand binding protein
      • Telomere-binding protein
    • RNA-binding protein
      • Poly(A)-binding protein
      • Nuclear cap-binding protein complex
    • CREB-binding protein
    • Calcium-binding protein
      • Calcium-binding protein 1
      • S100 calcium-binding protein A1
    • TATA-binding protein
    • Actin-binding protein
  • Most actin binding proteins bind on the actin surface, despite having different functions and structures.
    • Penicillin binding proteins
    • Retinol binding protein
      • Retinol binding protein 4
    • EP300
    • Binding immunoglobulin protein
    • Odorant binding protein
    • Lipopolysaccharide-binding protein
    • C4b-binding protein
    • Rap GTP-binding protein
    • Calmodulin-binding proteins
    • Iron-binding proteins
    • Thyroxine-binding proteins
    • Folate-binding protein
    • Sterol regulatory element-binding protein
    • GTP-binding protein
    • Retinaldehyde-binding protein 1
    • Ccaat-enhancer-binding proteins
    • Androgen-binding protein
    • Maltose-binding protein
    • Phosphatidylethanolamine binding protein 1
    • Syntaxin binding protein 3
    • Insulin-like growth factor-binding protein
    • Methyl-CpG-binding domain protein 2
    • Growth hormone-binding protein
    • Vitamin D-binding protein
    • Syntaxin binding protein 2
    • Oxysterol-binding protein
    • E3 binding protein
    • Iron-responsive element-binding protein
    • Polypyrimidine tract-binding protein
    • Fatty acid-binding protein
    • Myosin binding protein C, cardiac
    • CPE binding protein

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