V. Carnevale, F. Pontiggia and C. Micheletti
Structural and dynamical alignment of enzymes with partial
structural similarity
J. Phys. Condens. Matt. 19 285206 (2007)
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ABSTRACT
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.