PROTEIN DYNAMICS DERIVED FROM CLUSTERS OF CRYSTAL-STRUCTURES

A method is presented to mathematically extract concerted structural t ransitions in proteins from collections of crystal structures. The ''e ssential dynamics'' procedure is used to filter out small-amplitude fl uctuations from such a set of structures; the remaining large conforma tional changes describe motions such as those important for the uptake /release of substrate/ligand and in catalytic reactions. The method is applied to sets of x-ray structures for a number of proteins, and the results are compared with the results from essential dynamics as appl ied to molecular dynamics simulations of those proteins. A significant degree of similarity is found, thereby providing a direct experimenta l basis for the application of such simulations to the description of large concerted motions in proteins.