Local fluctuations are important for protein binding and molecular recognition because they provide conformational states that can be trapped through a selection mechanism of binding. Thus, an accurate characterization of local fluctuations may be important for modeling the kinetic mechanism that leads to the biological activity of a protein. In this paper, we study the fluctuation dynamics of the regulatory protein ubiquitin and propose a novel theoretical approach to model its fluctuations. A coarse-grained, diffusive, mode-dependent description of fluctuations is accomplished using the Langevin Equation for Protein Dynamics (LE4PD). This equation decomposes the dynamics of a protein, simulated by molecular dynamics, into dynamical pathways that explore mode-dependent free energy surfaces. We calculate the time scales of the slow, high-amplitude fluctuations by modeling the kinetics of barrier crossing in the two-dimensional free energy surfaces using Markov state modeling. We find that the LE4PD predicts slow fluctuations in three important binding regions in ubiquitin: the C-terminal tail, the Lys11 loop, and the 50 s loop. These results suggest that the LE4PD can provide useful information on the role of fluctuations in the process of molecular recognition regulating the biological activity of ubiquitin.