Restricting the ψ Torsion Angle Has Stereoelectronic Consequences on a Scissile Bond: An Electronic Structure Analysis.
Protein motion is intimately linked to enzymatic catalysis, yet the stereoelectronic changes that accompany different conformational states of a substrate are poorly defined. Here we investigate the relationship between conformation and stereoelectronic effects of a scissile amide bond. Structural studies have revealed that the C-terminal glycine of ubiquitin and ubiquitin-like proteins adopts a syn (ψ ∼ 0°) or gauche (ψ ∼ ±60°) conformation upon interacting with deubiquitinases/ubiquitin-like proteases. We used hybrid density functional theory and natural bond orbital analysis to understand how the stereoelectronic effects of the scissile bond change as a function of φ and ψ torsion angles. This led to the discovery that when ψ is between 30° and -30° the scissile bond becomes geometrically and electronically deformed. Geometric distortion occurs through pyramidalization of the carbonyl carbon and amide nitrogen. Electronic distortion is manifested by a decrease in the strength of the donor-acceptor interaction between the amide nitrogen and antibonding orbital (π*) of the carbonyl. Concomitant with the reduction in nN → π* delocalization energy, the sp(2) hybrid orbital of the carbonyl carbon becomes richer in p-character, suggesting the syn configuration causes the carbonyl carbon hybrid orbitals to adopt a geometry reminiscent of a tetrahedral-like intermediate. Our work reveals important insights into the role of substrate conformation in activating the reactive carbonyl of a scissile bond. These findings have implications for designing potent active site inhibitors based on the concept of transition state analogues.
Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States.
Eric R
ER
Strieter
Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States.
Trisha L
TL
Andrew
D005998:Glycine / Q000737:chemistry; D008958:Models, Molecular; D010447:Peptide Hydrolases / Q000737:chemistry*; D011487:Protein Conformation; D011789:Quantum Theory; D025801:Ubiquitin / Q000737:chemistry; D064570:Ubiquitin-Specific Proteases / Q000737:chemistry; D014452:Ubiquitins / Q000737:chemistry*
D025801:Ubiquitin; D014452:Ubiquitins; D010447:Peptide Hydrolases; D064570:Ubiquitin-Specific Proteases; D005998:Glycine