Combining High-Pressure NMR and Geometrical Sampling to Obtain a Full Topological Description of Protein Folding Landscapes: Application to the Folding of Two MAX Effectors from Magnaporthe oryzae

• Published in: International journal of molecular sciences 2022-05, Vol.23 (10), p.5461
• Main Authors: Dubois, Cécile, Lahfa, Mounia, Pissarra, Joana, de Guillen, Karine, Barthe, Philippe, Kroj, Thomas, Roumestand, Christian, Padilla, André
• Format: Article
• Language: English
• Subjects: Biochemistry, Molecular Biology; Computer applications; Conserved sequence; Cyana3 calculations; Effectors; Folding; high hydrostatic pressure; Hydrostatic pressure; Life Sciences; Magnetic resonance spectroscopy; MAX effectors; NMR; NMR spectroscopy; Nuclear magnetic resonance; Polypeptides; Probability; Protein folding; Proteins; Simulation; Spectrum analysis; Structural Biology; Topology
• ISSN: 1422-0067; 1661-6596; 1422-0067
• DOI: 10.3390/ijms23105461

Despite advances in experimental and computational methods, the mechanisms by which an unstructured polypeptide chain regains its unique three-dimensional structure remains one of the main puzzling questions in biology. Single-molecule techniques, ultra-fast perturbation and detection approaches and improvement in all-atom and coarse-grained simulation methods have greatly deepened our understanding of protein folding and the effects of environmental factors on folding landscape. However, a major challenge remains the detailed characterization of the protein folding landscape. Here, we used high hydrostatic pressure 2D NMR spectroscopy to obtain high-resolution experimental structural information in a site-specific manner across the polypeptide sequence and along the folding reaction coordinate. We used this residue-specific information to constrain calculations, in order to obtain a topological description of the entire folding landscape. This approach was used to describe the conformers populating the folding landscape of two small globular proteins, AVR-Pia and AVR-Pib, that belong to the structurally conserved but sequence-unrelated MAX effectors superfamily. Comparing the two folding landscapes, we found that, in spite of their divergent sequences, the folding pathway of these two proteins involves a similar, inescapable, folding intermediate, even if, statistically, the routes used are different.