lec 6

I Oligomers
- Recognition Principles
- Measurement of Affinity of Protein-Protein Interactions

Example: Pyruvate Kinase
- Structure: Contains several domains including:
- α/β barrel (red)
- Extended loop region with about 100 amino acids forming an antiparallel β strand domain (blue)
- C-terminal region of about 140 residues forming an open twisted α/β structure (green)

Issues with monomeric proteins include:
- Limits on domain size
- Rate of synthesis and folding
- Regulation of function in the cell

Oligomer: Assembly of proteins composed of two or more separate polypeptide chains.
- Spontaneous assembly occurs when the critical concentration of components is sufficient.
- Oligomers may self-associate into
- Homogeneous assemblies: Composed of the same type of monomer (e.g., homotrimer like gamma-carbonic anhydrase).
- Heterogeneous assemblies: Composed of different types of monomers (e.g., hemoglobin as a heterotetramer of two homodimers).
Oligomeric structures can vary in arrangement:
- Dimers: 2 monomers
- Trimers: 3 monomers
- Tetramers: 4 monomers
- Higher-order structures may include pentamers, hexamers, etc.

Quaternary Structure: The oligomeric state or structure of folded proteins.
- Common for subunits of hetero-oligomers to have similar structures, suggesting evolutionary duplication.

Schematic Representations (Fig 1-65):
- Homodimer: a₂
- Heterodimer: ab
- Heterotetramer: a₂b₂
- Heteropentamer: a₂bcd (example: acetylcholine receptor)
Examples of quaternary arrangements in different oligomeric proteins (Fig 1-74) include:
- D-amino acid aminotransferase, KDGP aldolase, neuraminidase, lactate dehydrogenase, cholera toxin, insulin, etc.

Functionality of Large Proteins:
- Morphological functions requiring large, stable structures.
- Cooperative functions in protein interactions like allostery and multivalent associations.
- Stability against denaturation, especially in large proteins which have extensive internal interactions.
- Reduction of surface area exposure to solvents through oligomerization.

Scaffold proteins organize signal transduction components within cells;
- Example: Ste5p scaffold in yeast, crucial for the MAPK signaling pathway.
Key Details:
- Ste5p binds various kinase components, forming multimeric complexes that enhance signaling specificity.

Toll-like Receptors (TLRs): Bind microbe-associated molecular patterns.
NOD-like Receptors (NLRs): Cytoplasmic receptors recognizing peptidoglycan; NLRP3 forms inflammasomes involved in cell death (pyroptosis).

Two pathways of apoptosis: intrinsic and extrinsic.
- Intrinsic Pathway: Activated by BCL-2 family proteins (BAK and BAX) leading to cytochrome c release.
- Extrinsic Pathway: Triggered by death receptors (like TNF receptor).

Critical for many cellular processes and include:
- Weak interactions forming dynamic complexes.
- Partner swapping allows for transient interactions crucial for signal transduction.
- Binding surfaces are specific, often involving complementary shapes and charge interactions.

Dissociation Constant (Kd): Commonly used measure of binding strength.
- For a bimolecular reaction:
- $A + B \rightleftharpoons AB$
- $K<em>d = \frac{k</em>{off}}{k_{on}}$
Binding interactions can be assessed using various experimental techniques:
- Surface Plasmon Resonance (SPR): Monitors binding interactions.
- Isothermal Titration Calorimetry (ITC): Determines affinities, enthalpy, and entropy of interactions.
- Fluorescence Resonance Energy Transfer (FRET): assesses physical associations between proteins.

The nature of protein interactions can involve broad interaction surfaces or short, linear peptide binding.
Specificity can often be influenced through structural adaptations to enhance affinity for particular ligands.

Understanding protein-protein interactions is essential for elucidating cellular processes and designing therapeutic interventions.