Protein Function Flashcards
How does protein flexibility relate to function?
- Fast and small scale motions tend to be associated with catalysis
- Collective mid range spatial and temporal motions are associated with conformational changes upon binding or signaling
- Slow and large scale motions associated with binding events
Protein movement often involves:
- The release of bound water molecules
2. Making/breaking of non-covalent interactions as the protein moves or subunits move relative to one another
Triggered conformational changes are dependent on :
- Unique structure of proteins
2. Inherent flexibility/ instability of molecules
Molecular recognition depends on:
- Complementarity of shape
- Charge distribution between ligand and protein binding site
- Formation of specialized microenvironments in the tertiary structure (ligand-binding sites/ enzyme active sites).
Structure of binding sites
- Lined with appropriate amino acids or binding elements which interact specifically with ligand
- Higher than average amount of exposed hydrophobic groups
- Can have different shapes
For marcomolecules shape of binding site can be:
Concave, convex or flat and may be grooves
For small molecules shape of binding site can be:
Clefts, pockets or cavities
Catalytic active sites
Occur at the interface between subunits or domains in proteins.
Weak interaction between ligand and protein
Favors easy exchange of molecules
The energy for driving binding events is provided by
Displacement of water from ligand binding site
Kd =
The equilibrium constant for the release of ligand
[P.L]/[Po]
Proportion of protein that has ligand-bound
Relationship between [P.L]/[Po] and [L]
Rectangular hyperbola
Equation for ligand binding
[P.L]/[Po] = [L]/ [L] + [Kd]
Units of Kd
Molar concentration e.g. Moles/litre
