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Database of protein complexes with multivalent binding ability: Bival-Bind.

Tim Meyer1, Ernst-Walter Knapp

  • 1Fachbereich Biologie Chemie, Pharmazie/Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195, Berlin, Germany.

Proteins
|November 23, 2013
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Summary
This summary is machine-generated.

This study introduces the Bival-Bind database, a resource for identifying multivalent receptors crucial for understanding biological binding and designing new drugs. It also analyzes receptor surface topography to predict potential binding challenges.

Keywords:
binding enhancementmultivalent bindingmultivalent receptorpolymeric drug delivery systemspolymeric spacerprotein bindingstructure property relationship

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Area of Science:

  • Biochemistry and Molecular Biology
  • Materials Science
  • Structural Biology

Background:

  • Multivalent binding, where multiple ligands interact with receptors, significantly enhances binding affinity and is vital in biological processes.
  • Understanding multivalent interactions is key for developing advanced materials and targeted therapeutics.
  • Identifying suitable bi- and multivalent receptor models is challenging but essential for mechanistic studies.

Purpose of the Study:

  • To create a comprehensive database of potential bi- and multivalent receptors from existing protein data.
  • To analyze the surface topography of these receptors to predict the impact of molecular spacers on binding affinity.
  • To provide a resource for researchers designing multivalent drugs and studying molecular recognition.

Main Methods:

  • Curated a database (Bival-Bind) of 2073 protein complexes with <90% sequence identity from the Protein Data Bank.
  • Characterized the surface topography of identified potential multivalent receptors.
  • Developed a height profile analysis to assess steric clashes between receptor binding pockets and molecular spacers.

Main Results:

  • The Bival-Bind database offers a substantial collection of potential multivalent receptors.
  • Analysis revealed that steric clashes with molecular spacers can significantly reduce binding affinity, counteracting multivalency effects.
  • Surface topography information, particularly height profiles, is critical for predicting spacer-receptor interactions.

Conclusions:

  • The Bival-Bind database serves as a valuable resource for studying multivalent interactions and designing targeted therapies.
  • Understanding receptor surface topography is crucial for optimizing the design of multivalent ligands and drugs.
  • This work provides insights into the biophysical mechanisms governing multivalent binding and its potential applications.