Protein Structural Changes Based on Structural Comparison

Advances in structural biology have provided a wealth of information on protein structures. In many proteins, multiple structures under distinct functional states are available. The comparison of such structures reveals structural changes during the transition between the states, for example, those from ligand-free to -bound states. These structural changes are important for understanding the molecular mechanism of protein function. Currently, a number of computational methods have been developed to compare distinct structural states of the same protein and describe protein structural changes. The resulting structural changes are stored in databases. After a brief introduction of pre-existing methods and databases, we introduce Motion Tree, which illustrates various structural changes using a tree diagram and provides an explanation of how to use Motion Tree. We also introduce PSCDB, which presents structural changes for 837 proteins including homodimers. Structural changes are classified into seven categories based on the types of motions and bound ligands. PSCDB is available via the Internet.