Molecular motions and properties of water and biomacromolecules change when confined in nanoporous matrices. Freezing and melting points of water are depressed, and generally, the activity of enzymes and stability of proteins are increased. We performed temperature ramp FTIR analyses of silica matrix confined water and proteins to identify the kinetic and thermodynamic transitions of water at cryogenic temperatures and to understand the water-protein interactions in confinement. In our studies, confined water did not freeze at temperatures as low as -180 °C but underwent liquid-liquid and liquid-glass transitions during cooling. During warming from cryogenic temperatures, the formations of cubic and hexagonal ice were detected. Additionally, the changes in the secondary structures of proteins correlated to the changes in the H-bonding characteristics of the confined water. Our results showed that the kinetic and thermodynamic transitions of water dictate the structural transitions of encapsulated proteins. Evidence was obtained for the universal behavior of water in close proximity to surfaces and in the hydration shells of isolated and cytoplasmic proteins (in intact encapsulated bacteria and mammalian cells).