The balance between side‐chain and backbone‐driven association in folding of the α‐helical influenza A transmembrane peptide

• Published in: Journal of computational chemistry 2020-09, Vol.41 (25), p.2177-2188
• Main Authors: Stylianakis, Ioannis, Shalev, Ariella, Scheiner, Steve, Sigalas, Michael P., Arkin, Isaiah T., Glykos, Nikolas, Kolocouris, Antonios
• Format: Article
• Language: English
• Subjects: adaptive tempering; B3LYP; Bonding strength; Chemical bonds; CH⋯O hydrogen bonding; circular dichroism; Coils; D95(d,p); Dichroism; Folding; Hydrogen bonding; Hydrogen bonds; Hydrogen-based energy; Influenza; influenza A M2TM; Mathematical analysis; Molecular dynamics; NBO; ONIOM; Peptides; Proteins; QTAIM; Quantum theory; α‐helix
• ISSN: 0192-8651; 1096-987X
• DOI: 10.1002/jcc.26381

The correct balance between attractive, repulsive and peptide hydrogen bonding interactions must be attained for proteins to fold correctly. To investigate these important contributors, we sought a comparison of the folding between two 25‐residues peptides, the influenza A M2 protein transmembrane domain (M2TM) and the 25‐Ala (Ala25). M2TM forms a stable α‐helix as is shown by circular dichroism (CD) experiments. Molecular dynamics (MD) simulations with adaptive tempering show that M2TM monomer is more dynamic in nature and quickly interconverts between an ensemble of various α‐helical structures, and less frequently turns and coils, compared to one α‐helix for Ala25. DFT calculations suggest that folding from the extended structure to the α‐helical structure is favored for M2TM compared with Ala25. This is due to CH⋯O attractive interactions which favor folding to the M2TM α‐helix, and cannot be described accurately with a force field. Using natural bond orbital (NBO) analysis and quantum theory atoms in molecules (QTAIM) calculations, 26 CH⋯O interactions and 22 NH⋯O hydrogen bonds are calculated for M2TM. The calculations show that CH⋯O hydrogen bonds, although individually weaker, have a cumulative effect that cannot be ignored and may contribute as much as half of the total hydrogen bonding energy, when compared to NH⋯O, to the stabilization of the α‐helix in M2TM. Further, a strengthening of NH⋯O hydrogen bonding interactions is calculated for M2TM compared to Ala25. Additionally, these weak CH⋯O interactions can dissociate and associate easily leading to the ensemble of folded structures for M2TM observed in folding MD simulations. Folding landscape of the M2TM peptide in trifluoroethanol. All minima (colored blue/cyan) correspond to various forms of helical structures. The high energy ridge separates almost fully folded structures (upper half), from partially unfolded structures (lower half).