Structural and dynamical alignment of enzymes with partial structural similarity

Proteins and enzymes, in order to carry our their biological tasks, often need to sustain concerted displacements of a large number of amino acids. In recent years many theoretical and computational studies have pointed out how these large- scale movements, also termed slow modes or essential dynamical spaces, are mostly dictated by the overall structural organization of the protein. Several fundamental questions arise when this fact is complemented by the observation that enzymes within the same enzymatic superfamily can have remarkable conformational differences. Could their large- scale movements be similar despite the difference in structure? In this study we address this issue and present a quantitative scheme for comparing the slow modes in proteins that, though differing in sequence, length and tertiary structure, still admit a partial structural superposition. We illustrate the application of the method to two representatives of the protease enzymatic superfamily, carboxypeptidase A and pyroglutamyl peptidase. ( Some figures in this article are in colour only in the electronic version)