** structural cooperation

• Structural Cooperativity


  The ability of conformational changes to propagate through a protein molecule, facilitating allosteric regulation, which is fundamental in metabolism control
• Allosteric Regulation


  Regulation of a protein's function through binding of an effector molecule at a site other than the protein's active site
• Conformational Changes in Proteins

  • Proteins exist as an ensemble of fluctuating conformations even in the folded state due to their marginal stability
  • Only a small energy input (1-5 kcal/mol) is required to cause significant conformational changes
  • The energy required for these changes is typically provided by the Gibbs free energy upon ligand binding, which is favorable and typically in the range of -10 to -20 kcal/mol
• Protein Dynamics


  • Proteins continuously fluctuate between different conformations due to thermal energy
  • The energy provided by the surrounding environment causes proteins to explore different conformational states
  • The process by which proteins explore multiple conformations, enabling them to adapt to different functional states
• Ligand Binding and Conformational Changes

  1. Ligand binding induces conformational changes, linking ligand specificity to allosteric regulation

  2. Ligands may bind preferentially to one of multiple conformers, stabilizing the protein in that specific conformation without significant energy input
• Calmodulin (CaM)


  • A multifunctional calcium-binding messenger protein expressed in all eukaryotic cells
  • Calcium binding induces a conformational change, allowing it to interact with various target proteins such as kinases and phosphatases
• Methionine Synthase


  • Exists as an ensemble of interconverting conformers
  • Ligands and the methylation state of the cofactor redistribute the conformers, allowing for efficient catalysis
• Importance of Domains in Allosteric Regulation

  • Domains are independently folding units within a protein that often contain specific binding sites
  • Multi-domain structure facilitates allosteric control by providing structural blocks that undergo conformational changes as single units
• Maltose-Binding Protein


  • Undergoes an "open to close" transition upon maltose binding
  • The binding site topology is disrupted upon movement of a loop, demonstrating structural cooperativity
• Phosphofructokinase (PFK)


  • Conformational changes propagate from one subunit to others, enabling allosteric regulation of its activity
• Dihydrofolate Reductase


  • Mapping the propagation network shows how conformational changes affect binding sites across the protein, highlighting structural cooperativity
• Domains


  Parts of a single protein that fold independently and often contain specific binding sites
• Function of Domains


  In multi-domain proteins, the active site can be formed at the interface between two or more domains, facilitating regulation through changes in domain orientation
• Cytochrome P450 Reductase (CPR)


  • Contains domains for FAD, FMN, and NADPH binding, each facilitating specific interactions
• Sorbitol Dehydrogenase


  • Assembles as a tetramer; its activity is regulated through domain interactions
• Glyceraldehyde 3-Phosphate Dehydrogenase (GAPDH)


  • A tetramer involved in glycolysis with active sites formed at domain interfaces
• Protein Associations


  • Proteins can form dimers, trimers, or tetramers by associating identical units
  • Each protein in the assemblage is called a subunit, and this arrangement allows for cooperative interactions
  • Dimerization and tetramerization are usually reversible, existing at equilibrium
• Mechanisms of Allosteric Control

  1. Ligands bind to specific conformers, stabilizing the protein in that conformation

  2. Conformational changes require small energy inputs, often provided by ligand binding

  3. Conformational changes can propagate through the protein, affecting distant sites and enabling regulation
• Catalytic Strategies and Electrostatic Effects

  • Binding sites often exclude water to enhance electrostatic interactions between the substrate and the protein
  • Water's high dielectric constant weakens electrostatic interactions, thus binding sites tend to be very hydrophobic
• Structural Cooperativity: Summary