Biophysical characterization of the interaction of Atg8 with a disordered region of Nup159 involved in selective autophagy of the nuclear pore complex

A functional proteome in the cell is maintained by coordinate regulation of biogenesis, folding, and degradation of cellular proteins. Although the degradation pathways have been extensively characterized for various substrates, it remains elusive how large multiprotein complexes are selectively degraded. Recent investigations have discovered selective autophagic degradation of the yeast Nuclear Pore Complex (NPC) consisting of similar to 500 proteins and mediating selective nucleocytoplasmic transport. To understand the underlying molecular mechanism of NPC-phagy, we performed biophysical characterization of the interaction between Atg8 and an intrinsically disordered region (IDR) of Nup159 involved in the initial recognition step. In particular, from the systematic isothermal titration calorimetry (ITC) experiments, we determined the thermodynamic parameters and discovered a significant negative heat capacity change (Delta C-p degrees) for the interaction. Furthermore, the heat capacity change becomes more negative at higher temperatures, yielding a negative curvature in the observed enthalpy change (Delta H degrees) with respect to temperature. This thermodynamic feature was analyzed in terms of coupling between binding and conformational equilibria of Atg8 and/or Nup159 IDR. We interpret the coupled conformational equilibria as disorder-to-order transitions or local stabilizations of Nup159 IDR and/or partially unfolded Atg8 upon binding. A potential impact of the proposed coupling in the initial step of NPC-phagy is discussed. In a broader view, our study demonstrates that a negative curvature of Delta H degrees can be used as a probe for conformational selection processes in the interactions of IDRs with their target proteins. (C) 2022 Elsevier Inc. All rights reserved.

Automated summary

The selective degradation of large multiprotein complexes remains elusive, but recent investigations have discovered selective autophagic degradation of the yeast Nuclear Pore Complex (NPC). In this study, the researchers performed biophysical characterization of the interaction between Atg8 and an intrinsically disordered region (IDR) of Nup159, and identified thermodynamic parameters and a negative heat capacity change (Delta C-p degrees) for the interaction. The study demonstrates the potential impact of this coupling in the initial step of NPC-phagy and provides insights into conformational selection processes in the interactions of IDRs with their target proteins.