Conformational Insights into the Control of CNF1 Toxin Activity by Peptidyl-Prolyl Isomerization: A Molecular Dynamics Perspective

• Main Authors: Eléa Paillares, Maud Marechal, Léa Swistak, Landry Tsoumtsa Meda, Emmanuel Lemichez, Thérèse E. Malliavin
• Format: Article
• Language: English
• Published: MDPI AG 2021-09-01
• Series: International Journal of Molecular Sciences
• Subjects: <i>Escherichia coli</i>; CNF1; deamidase; X-Pro imide bond; peptidyl prolyl <i>cis</i>-<i>trans</i> isomerization; molecular dynamics
• Online Access: https://www.mdpi.com/1422-0067/22/18/10129
• ISSN: 1661-6596; 1422-0067

The cytotoxic necrotizing factor 1 (CNF1) toxin from uropathogenic <i>Escherichia coli</i> constitutively activates Rho GTPases by catalyzing the deamidation of a critical glutamine residue located in the switch II (SWII). In crystallographic structures of the CNF1 catalytic domain (CNF1^CD), surface-exposed P768 and P968 peptidyl-prolyl imide bonds (X-Pro) adopt an unusual <i>cis</i> conformation. Here, we show that mutation of each proline residue into glycine abrogates CNF1^CD in vitro deamidase activity, while mutant forms of CNF1 remain functional on RhoA in cells. Using molecular dynamics simulations coupled to protein-peptide docking, we highlight the long-distance impact of peptidyl-prolyl <i>cis</i>-<i>trans</i> isomerization on the network of interactions between the loops bordering the entrance of the catalytic cleft. The energetically favorable isomerization of P768 compared with P968, induces an enlargement of loop L1 that fosters the invasion of CNF1^CD catalytic cleft by a peptide encompassing SWII of RhoA. The connection of the P968 <i>cis</i> isomer to the catalytic cysteine C866 via a ladder of stacking interactions is alleviated along the <i>cis-trans</i> isomerization. Finally, the <i>cis-trans</i> conversion of P768 favors a switch of the thiol side chain of C866 from a resting to an active orientation. The long-distance impact of peptidyl-prolyl <i>cis</i>-<i>trans</i> isomerizations is expected to have implications for target modification.