Normal mode analysis of biomolecular structures: Functional mechanisms of membrane proteins

A normal mode analysis (NMA) of biomolecular structures and functional mechanisms of membrane proteins was studied. Normal mode analysis provides information on the equilibrium modes accessible to a system, assuming that the system is stabilized by harmonic potentials. A striking feature of NMA and other PCAs of biomolecular structures is the observed robustness of the global modes to details in atomic coordinates or specific interatomic interactions. A major reason behind the broadening recognition of NMA as a tool for exploring functional motions of proteins is the observation that global modes elucidated by NMA bear functional significance. Membrane proteins are classified into two broad groups, integral membrane proteins (IMPs) and peripheral membrane proteins. The biological function of many membrane proteins involves a transient change in structure, with the associated processes usually spanning a broad range of time scales. The function of membrane proteins involves many other specific and subtle interactions that cannot be studied by CG models and NMA.