Structural Function Relationships in Proteins

• There are four levels of protein structure:
• The primary structure (linear sequence of amino acids within the protein)
• The secondary structure (a regular, repeating pattern of hydrogen bonds stabilizing a particular structure)
• The tertiary structure (the folding of the secondary structure elements into a three-dimensional conformation)
• The quaternary structure (the association of subunits within a protein)
• The primary structure of a protein determines the way a protein folds into a unique three-dimensional structure, called its native conformation.
• When globular proteins fold, the tertiary structure generally forms a densely packed hydrophobic core with polar amino acid side chains on the outside, facing the aqueous environment.
• The tertiary structure of a protein consists of structural domains, which may be similar between different proteins and perform similar functions for the different proteins.
• Certain structural domains are binding sites for specific molecules, called a ligand, or for other proteins.
• The affinity of a binding site for its ligand is quantitatively characterized by an association or affinity constant, K_a (or dissociation constant, K_d).
• Protein denaturation is the loss of tertiary (and/or secondary) structure within a protein, which can be caused by heat, acid, or other agents that interfere with hydrogen bonding and usually causes a decrease in solubility (precipitation).