Dynamic properties of bovine Cu,Zn superoxide dismutase from crystallographic data

The Cu,Zn superoxide dismutase (SOD) enzyme from bovine erythrocytes has been the subject of several crystallographic studies over the last fifteen years. Nine crystal structures in space groups C2, P2(1)2(1)2(1) and C222(1), have been refined at high resolution and are available from the Protein Data Bank and our laboratory. We have performed a comparative analysis based on the experimentally determined structural variability in order to study the dynamics of the enzyme in terms of molecular flexibility. We have been able to show that information on molecular motions of different types occurring on different timescales may be obtained from the data by comparing thermal motion analysis with that of backbone C alpha fluctuations. We have found that the most mobile parts of Cu,Zn SOD are located in turns and loops and that there is a strict correlation between thermal motion and flexibility of the molecule, with the only exception of the two residues Asp11 and Glu38. The analysis of crystal polymorphism established the existence of a quite strict correlation between crystal contacts and mobility in space group C2, while in P2(1)2(1)2(1) and C222(1) the opposite was observed. Comparison with the results of molecular dynamics simulation revealed a good agreement between the two approaches although some differences emerge when active site residues are considered. The results of this work indicate the feasibility of an 'experimental' approach to the study of protein dynamics. (C) 1998 Elsevier Science S.A. All rights reserved