A general scheme to model a protein-like chain is introduced to facilitate the exploration of the connection between the morphology of the free energy surface of the protein and its folding dynamics. A microscopic theory for the dynamics of the system is developed that reduces to a Markovian model of the kinetics under well-defined conditions. We consider a particular model of a helical-folding protein and characterize the morphology of the free energy landscape as a function of temperature. The dynamics of the system are analyzed within the Markov state model and it is demonstrated that the behavior of the equilibration profile as the temperature is lowered can be understood in terms of the initial formation of local structure through many pathways followed by more sequential passage through a series of configurations leading to the final structure. The effect of the presence of mis-folded states on the dynamics of the frustration is discussed.