Structural variability of peptide deformylase

A. Hrádková¹, M. H. Kolář¹, J. Kubíček²

¹Department of Physical Chemistry, University of Chemistry and Technology, Praha

²Gymnázium, Nad Kavalírkou 1, Praha

hradkova@vscht.cz

The first enzyme that bacterial proteins encounter after their birth is the peptide deformylase (PDF). PDF binds to the ribosome surface and removes the formyl group from the N terminus of the nascent protein, which emerges from the ribosomal exit tunnel. Based upon structure and sequence similarity, PDFs are divided into Type I, II, and III, with Type I being further divided into subgroups IA and IB. Type I PDFs feature a C-terminal α-helix that serves as the connection point between the PDF's catalytic domain and the ribosome's surface. Conversely, Type II PDFs exhibit an intrinsically disordered C-terminal region and the mechanism by which Type II PDFs bind to the ribosome is unknown. Due to sequence divergence of Type III in otherwise conserved motifs in Type I and II, Type III PDFs are suggested to be inactive. In our study, we investigate the folding behaviour of the C-terminal region by conducting all-atom molecular dynamics simulations of PDFs derived from various organisms. Our findings reveal significant differences in the conformational ensembles of the C-termini between Type I and Type II PDFs. We quantified the secondary structure propensities of the simulated systems and found notable differences as well. The catalytic domain of PDF plays a pivotal role in shaping the C-terminal fragments. Our results shed light on the potential binding mode of PDF to the ribosomal surface.

Figure 1. Peptide deformylase 5JEZ

This work was supported by the Ministry of Education, Youth and Sports of the Czech Republic through the e-INFRA CZ (ID:90254), and by the Czech Science Foundation (project 23-05764S).