Modeling Protein S–Aromatic Motifs Reveals Their Structural and Redox Flexibility

Abstract

S-aromatic motifs are important noncovalent forces for protein stability and function but remain poorly understood. Hence, we performed quantum calculations at the MP2(full)/6-311++G(d,p) level on complexes between Cys (HS, MeSH) and Met (MeS) models with models of Phe (benzene, toluene), Trp (indole, 3-methylindole), Tyr (phenol, 4-methylphenol), and His (imidazole, 4-methylimidazole). The most stable gas-phase conformers exhibit binding energies of -2 to -6 kcal/mol, and the S atom lies perpendicular to the ring plane. This reveals preferential interaction with the ring π-system, except in the imidazoles where S binds edge-on to an N atom. Complexation tunes the gas-phase vertical ionization potentials of the ligands over as much as 1 eV, and strong σ- or π-type H-bonding supports charge transfer to the H-bond donor, rendering it more oxidizable. When the S atom acts as an H-bond acceptor (N/O-H···S), calibration of the CHARMM36 force field (by optimizing pair-specific Lennard-Jones parameters) is required. Implementing the optimized parameters in molecular dynamics simulations in bulk water, we find stable S-aromatic complexes with binding free energies of -0.6 to -1.1 kcal/mol at ligand separations up to 8 Å. The aqueous S-aromatics exhibit flexible binding conformations, but edge-on conformers are less stable in water. Reflecting this, only 0.3 to 10% of the S-indole, S-phenol, and S-imidazole structures are stabilized by N/O-H···S or S-H···O/N σ-type H-bonding. The wide range of energies and geometries found for S-aromatic interactions and their tunable redox properties expose the versatility and variability of the S-aromatic motif in proteins and allow us to predict a number of their reported properties.

Methionine in proteins: The Cinderella of the proteinogenic amino acids

“…Despite the potential importance of these findings, they went largely overlooked, perhaps because the physicochemical nature of this bond is only poorly understood. Although the strength of these interactions may depend on the conditions of its environment, it is accepted that the S‐aromatic interaction occurs at a greater distance (5–7 å) than a salt bridge (< 4 å), while the energies associated with either interaction are comparable. More recently, extensive surveys of the Protein Data Bank have revealed the importance of the methionine‐aromatic motif for stabilizing protein structures and for protein–protein interactions …”

Drude polarizable force field for cation–π interactions of alkali and quaternary ammonium ions with aromatic amino acid side chains

“…We thus calibrate the model for these complexes using ab initio PECs as target data. The parameter optimization follows a procedure similar to those reported previously . Agreement with the ab initio properties of the complexes is improved by manipulating the nonbonded van der Waals interaction energy terms.…”

“…b) values are binned and ρ ( r MX , θ MXY ), the number of structures in each bin, is determined. A plot of the 2D PMF function − RT ln[ ρ ( r MX , θ MXY )/2π r MX sin θ MXY ] versus r MX sin θ MXY and r MX cos θ MXY reveals the preference of the ion for either the face or the edge of the aromatic moiety …”

The Role of Methionine Residues in the Regulation of Liquid-Liquid Phase Separation

“…Thus, when this distance is below the threshold of 7 Å, the interaction can have an associated energy comparable to that of a salt bridge. However, the strength of these non-covalent bonds can vary dramatically depending on the environment around the sulfur [126,136,137], which may be exploited from a regulatory point of view, as we will discuss later.…”