L’État natif est-il l’État fondamental?

Résumé

Après avoir défini l’état natif d’une protéine, nous rappellerons les arguments classiques en faveur de l’identité des états natif et fondamental. Nous donnerons quelques exemples de l’influence des caractéristiques cinétiques du repliement de la chaîne polypeptidique sur l’état atteint après ‘renaturation’. Ces exemples, ainsi que l’effet de divers cofacteurs sur la restructuration de protéines dénaturées, indiquent que les propriétés cinétiques du ‘folding’ peuvent parfois l’emporter sur les propriétés énergétiques. Nous montrerons enfin comment les associations quaternaires peuvent modifier les propriétés structurales et énergétiques des protomères et étendrons ces observations au cas des chaînes peptidiques structurées en plusieurs ‘globules’.

Summary

This conference is aimed at showing how some classical molecular-biology experiments can raise some questions about the widely accepted physical-chemical conclusions concerning the identity of the native and fundamental states of a protein.

It is not intended to be either a general conference about this topics, or a review of the vast amount a work related to this subject.

To begin with, an operational definition of the ‘native state’ of a protein is given and, from this mere definition, it appears that the native and fundamental states of a protein can hardly be compared.

The main experimental arguments suggesting the identity of the two states (i.e. spontaneous re-folding of denatured proteins) are discussed and experiments proving the existence of a ‘kinetic trough’ during the refolding of urea-denatured β-D-galactosidase are reported.

By studying the kinetics of renaturation of denatured β-D-galactosidase with the kinetics of ω-complementation between incomplete fragments of the galactosidase protomer, intra- and inter-chain stereospecific associations are compared and the influence of the kinetic properties of this association is discussed.

Finally, the influence of quaternary association on the structure of a protomer is discussed and illustrated by the structural and energetical coupling between the tertiary and quaternary structure of E. coli tryptophanase.

Even though none of the experiments reported conclusively show that the native state is structurally very different from the fundamental state, it is suggested that the classical experiments do not conclusively demonstrate the identity of the two states. The main reason for that appears to be the inadequacy of the definitions of the two states, one being essentially operational while the other is solely thermodynamic.