Denaturation is the term used to describe the change of a proteins shape when it is exposed to external stress. When proteins denature, the cells go through a series of changes, first loosening, then tightening.
In cooking, this stress that causes denaturation is typically heat. You can see denaturation easily when you fry an egg. As it heats, its proteins coagulate. Heat is the fastest method of denaturation. It is so fast that you rarely see the loosening stage. You can visible see the proteins tighten, however, and this is one of the keys to judging doneness of meat. The more firm the meat is, the more denatured (or cooked) it is.
Denaturation also happens with acid. Acid denaturation is slower that that of heat. In marinades, the acid slowly tenderizes protein. If left a longtime in a high acid solution, as ceviche is, the acid will completely cook the protein.
Agitation also denatures protein. We see this clearly in the whipping of egg whites. The structure changes completely, is able to hold air, and can be baked in that form to solidify it. In nature, you can see the denaturation of protein in the waves at the beach. The constant churning creates foam from various proteins in the sea water.
Salty brine is another method of denaturation. It is used to hydrate meat by opening up the cells and letting in moisture. If the salt concentration is high, the cells eventually tighten, and the product is completely cooked, as in cured meats.