Affinity, Specificity, and Cooperativity of DNA Binding by Bacterial Gene Regulatory Proteins

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Nearly all of biology depends on interactions between molecules: Proteins with small molecules, proteins with other proteins, nucleic acids with small molecules, and nucleic acids with proteins that regulate gene expression, our concern in this Special Issue. All those kinds of interactions, and others, constitute the vast majority of biology at the molecular level. An understanding of those interactions requires that we quantify them to learn how they interact: How strongly? With which partners? How—and how well—are different partners distinguished? This review addresses the evolution of our current understanding of the molecular origins of affinity and specificity in regulatory protein-DNA interactions, and suggests that both these properties can be modulated by cooperativity.

Original languageEnglish (US)
Article number562
JournalInternational journal of molecular sciences
Issue number1
StatePublished - Jan 1 2022

All Science Journal Classification (ASJC) codes

  • Molecular Biology
  • Spectroscopy
  • Catalysis
  • Inorganic Chemistry
  • Computer Science Applications
  • Physical and Theoretical Chemistry
  • Organic Chemistry


  • Biological constraints
  • Cryptic thermodynamic factors
  • Drug design
  • Gestalt properties of proteins
  • Host-guest chemistry
  • Pre-organization
  • Protein folding coupled to ligand binding


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