Proteins don't always stay in the first 'low point', sometimes they stay there for a little while then change conformation. Often proteins can change significantly when bound by something.
There is a great citizen science project on it. https://fold.it/portal/ This is in the top 3 most successful citizen science projects.
You have specific enzymes in your body called "proteases" that break down the proteins. This is a good article that covers all you need to know about proteases: http://www.nature.com/nature/journal/v426/n6968/full/nature02263.html