Cooking causes denaturation of proteins as the input energy leads to covalent bond formation with other proteins and carbohydrates. The changes in carbohydrates cause browning. Protein structure is irreversibly altered by denaturation caused by solvent, heat, oxidation and may become tightly folded or unfolded. Proteins could be degraded using various proteases by inducing proteolytic effects. Protease degradation changes solubility, isoelectric points etc.
Protease can be endogenous or exogenous.