The interpretation of protein physical properties at the most fundamental mechanistic and thermodynamic level plays a key role in physical and molecular understanding of biology. The protein thermodynamic structure (potherse) is generated through irreversible thermodynamic possesses. Protein folding is a specific physical mechanism for the origin of natural order. It was shown that pothersal change is the basic (molecular) thermodynamic unit of any physiological reaction which acts as a molecular switch. The Weiss equation is re-derived using protein mechanics theory. Some protein physical properties are also discussed.