Stabilization of native protein fold by intein-mediated covalent cyclization

Authors

Neal K. Williams, Australian National University
Edvards Liepinsh, Karolinska Institute
Stephen J. Watt, University of Wollongong
Pavel Prosselkov, Australian National University
Jacqueline M. Matthews, University of Sydney
Phil Attard, University of Sydney
Jennifer L. Beck, University of WollongongFollow
Nicholas E. Dixon, University of WollongongFollow
Gottfried Otting, Australian National University

RIS ID

13157

Publication Details

Williams, N., Liepinsh, E., Watt, S., Prosselkov, P., Matthews, J., Attard, P., Beck, J. L., Dixon, N. E. & Otting, G. (2005). Stabilization of native protein fold by intein-mediated covalent cyclization. Journal of Molecular Biology, 346 (4), 1095-1108.

Abstract

A mutant version of the N-terminal domain of Escherichia coli DnaB helicase was used as a model system to assess the stabilization against unfolding gained by covalent cyclization. Cyclization was achieved in vivo by formation of an amide bond between the N and C termini with the help of a split mini-intein. Linear and circular proteins were constructed to be identical in amino acid sequence. Mutagenesis of Phe102 to Glu rendered the protein monomeric even at high concentration. A difference in free energy of unfolding, ΔΔG, between circular and linear protein of 2.3(±0.5) kcal mol⁻¹ was measured at 10 °C by circular dichroism. A theoretical estimate of the difference in conformational entropy of linear and circular random chains in a three-dimensional cubic lattice model predicted ΔΔG=2.3 kcal mol⁻¹, suggesting that stabilization by protein cyclization is driven by the reduced conformational entropy of the unfolded state. Amide-proton exchange rates measured by NMR spectroscopy and mass spectrometry showed a uniform, approximately tenfold decrease of the exchange rates of the most slowly exchanging amide protons, demonstrating that cyclization globally decreases the unfolding rate of the protein. The amide proton exchange was found to follow EX1 kinetics at near-neutral pH, in agreement with an unusually slow refolding rate of less than 4 min⁻¹ measured by stopped-flow circular dichroism. The linear and circular proteins differed more in their unfolding than in their folding rates. Global unfolding of the N-terminal domain of E. coli DnaB is thus promoted strongly by spatial separation of the N and C termini, whereas their proximity is much less important for folding.