Temporal fluctuations in the potential energy of proteins: 1/fα noise and diffusion

Molecular dynamics (MD) simulation methods were used to investigate temporal fluctuations in the potential energy of plastocyanin (PC), an electron transport copper-containing protein. The related power spectra, studied within a range of sampling times, revealed the presence of 1/fα noise with 1<α<2 and Gaussian statistics, that is consistent with fractional Brownian motion (fBm) models describing sublinear diffusion. Analysis of the protein trajectory in the configurational space by the essential dynamics method, allowed us to confirm, in an independent way, the occurrence of such a sublinear diffusive process. The results are discussed also in connection with the self-similar properties, involving spatial and temporal disorder, of the investigated systems.