These wide range of Pimozide motions show interdependency, leading to a highly complex organization of the conformational and energetic landscape. Several studies have shown that the protein’s conformational and energetic landscape is organized in a multi-level hierarchy. In the familiar representation, one can imagine the potential energy landscape to be rugged and be formed of hills and valleys of varying heights and depths, populated by conformations of the protein. Within each valley, the population of conformations share Catharanthine sulfate significant similarity in terms of their structures as well as internal energies. The sub-population of protein conformations within each of these valleys represent a sub-state. The multiple levels in the hierarchy stem from the energetic differences between the various sub-states. Internal protein motions driven by thermodynamical energy fluctuations allow the protein to transition from one sub-state to another. In cases where several sub-states are separated by small energy barriers from each other but collectively by a larger barrier from other sub-states, together the collection of these sub-states can be viewed as a new sub-state in the multi-level hierarchy. Internal protein motions correspond to the inter-conversion of protein conformations as they move within a sub-state or as they visit from one sub-state to another. Analyses of internal protein motions based on experimental and theoretical/computational approaches have established the importance of sampling multiple sub-states as being vital for a number of protein functions including molecular recognition, enzyme catalysis and allosteric modulation. A number of enzymes have attracted considerable interest due to the connection between conformational fluctuations and the catalytic mechanisms. An intriguing observation has been that large conformation fluctuations occur in distal regions of the protein, far away from the active-site, which influence the catalytic step. However, it is not known if these distal motions are somehow related to the ability of enzymes to sample conformations that facilitates the attainment of the transition state during the reaction mechanism. More recently, fascinating insights from X-ray crystallographic studies have indicated that there may be rare conformations and sub-states that critically alter the active site environment for catalysis. Internal motions have also been implicated in biomolecular recognition by proteins. Hence, apart from implicating the flexibility of a protein, it is also equally critical to elucidate possible conformational sub-states and the structural changes that enable the protein to explore these sub-states. Experimental techniques revealed a wealth of information about the inter-connection between conformational fluctuations and protein function. X-ray studies and nuclear magnetic resonance methods have provided information about the most populated states for an increasing number of proteins. Further, pioneering work of Hammes and co-workers have provided information about conformations associated with single molecules during enzyme catalysis. Recently, enzyme cyclophilin A has been investigated extensively for connection between protein dynamics and enzyme catalysis. NMR spin relaxation studies performed by Kern and coworkers linked the motions of several residues with the substrate turnover step in cyclophilin A, and also indicated that the rate of enzyme conformational changes coincides with the ratelimiting step of substrate turnover. NMR studies by Lange and co-workers have provided insights into the structural heterogeneity of ubiquitin, relevant to its function of binding multiple proteins, at the ms time-scales. Even though surface regions of ubiquitin and their collective motions have been implicated in binding, the conformational sub-states involved in the mechanism of molecular recognition have been difficult to characterize. Similarly, correlated motions have been implicated in sub-domain motions for lysozyme. The detailed characterization of how these motions lead the protein to sample specific sub.