Overview
This lecture covers how proteins interact with ligands, the chemical nature of these interactions, and how to measure and interpret binding affinity using the dissociation constant (Kd).
Protein-Ligand Interactions
- Proteins bind ligands, which can be any molecule: another protein, DNA, nucleotides, etc.
- Binding usually involves a specific binding pocket or interface on the protein.
- Not all interactions are with a "pocket"; some involve flat binding surfaces.
- Protein-ligand interactions are typically mediated by non-covalent bonds (weaker and reversible).
Non-Covalent Bonds and Affinity
- Non-covalent bonds include hydrogen bonds, ionic bonds, and van der Waals interactions.
- Binding specificity depends on shape compatibility and chemical properties of side chains (R groups) in the binding site.
- The fit between protein and ligand (three-dimensional and chemical) determines the number and strength of bonds.
- More and stronger non-covalent bonds result in higher binding affinity (longer binding time).
Measuring and Describing Affinity
- Affinity describes how tightly a protein binds its ligand; higher affinity means longer binding.
- Affinity is measured using the dissociation constant (Kd).
- Kd is found by titrating ligand into a fixed protein concentration and identifying the ligand concentration where half the protein is bound.
- A lower Kd means higher affinity; a higher Kd means lower affinity.
- Kd is expressed in molar units (commonly micromolar or nanomolar in cells).
- The relationship is inverse: high affinity = low Kd, low affinity = high Kd.
Key Terms & Definitions
- Ligand — Any molecule that binds to a protein (could be small or large).
- Binding Pocket — The specific region on a protein where a ligand binds.
- Non-Covalent Bond — A chemical bond that does not involve sharing electrons; weaker than covalent bonds.
- Affinity — The strength or tightness of the protein-ligand interaction.
- Dissociation Constant (Kd) — The concentration of ligand at which half the protein is bound; lower values indicate higher affinity.
Action Items / Next Steps
- Watch movie 2.4 in the movies folder to see molecular interactions.
- Review provided readings on protein-ligand interactions and Kd.
- Prepare for next lecture on enzyme function.