Computational analyses of virtual proteolytic fragments generated by naphthalene 1,2-dioxygenase. In search of native-like conformation and function

Structural and energetic properties of proteolytic fragments originated from naphthalene 1,2-dioxygenase (NDO) enzyme were investigated through a computational approach. A library of fragments was generated by using an algorithm able to identify specified regions of the primary sequence and simulating cleavages on target sites. Structure of the fragments was optimised by Monte Carlo and molecular dynamics (MD) methods and the conformational and energetic properties were compared with those of the native enzyme. Protonation states of ionizable groups were predicted on the basis of effective pK a values. Proteolytic fragments structurally similar to NDO were docked to naphthalene and interaction energies were evaluated by using MD computations. Many candidate fragments were able to maintain properties close to those which occur in the native conditions, while structures obtained by cleavages on the β-subunit of the NDO asymmetric unit were found to be rather unstable. Among the investigated structures, owin...