Protein Dynamics: Fluorescence Lifetime Distributions

Abstract

It is now well established that proteins in their native conformation can exist in a large number of subconformations slightly different one from the other (Lakowicz & Weber, 1973; Austin et al., 1975; Careri et al., 1975, 1979; Karplus & McCammon, 1983). Subconformations originate from small structural fluctuations around the main conformation. The protein structure is very flexible and it allows rotations around the phi and psi angles of the polypeptide chain and around the C-alpha carbon on the side chain. The stabilization of one particular native structure depends on a large number of interactions which are affected by solvent, ions of the medium and chemico-physical parameters. Some parts of the protein structure are more stable than others due to a more favorable interaction between the amino acid residues and they form structural domains. Frequently, these domains are associated with secondary structural elements such as alpha helical segments or beta sheets. The connections or loops between domains are generally more flexible. Within a domain, a side chain exposed to the solvent can have large rotational freedom and fast motions can result with rates comparable to the rates of motion of the residue in the solvent. Alternatively, a side chain at the interface between two distinct domains can move only if the domains separate enough to allow the side chain to rotate. The resultant motion of this side chain is then modulated by the relatively slow motion of the two domains.