COMPARISON OF 3-DIMENSIONAL STRUCTURES OF FLEXIBLE PROTEIN MOLECULES

An original technique was developed for comparing 3D protein structure s, which obviates superposition and is based on the use of intramolecu lar coordinate systems (ICS). With atomic coordinates refined at high resolution, and with observance of certain requirements for reference points used to construct the ICS, the method provides a fuller picture of the differences in the mutual positions of atoms in the compared p rotein molecules than the conventional approaches. It also allows a su bstantial reduction of the calculations in pair comparison of a large number of homologous structures. Converted into the ICS, the protein a tomic coordinates prove to be automatically ''overlaid'' when working with graphic devices; simultaneously converted are the atomic coordina tes for bound water, which makes it possible to reveal its conserved p ositions. Application of the method is exemplified with the data for r ibonuclease A and its complexes with deoxynucleosides, as well as for pepsin versus pepsinogen.