Modeling the enolization of succinimide derivatives, a key step of racemization of aspartic acid residues: importance of a two-H2O mechanism.
Racemization of aspartic acid residues in peptides and proteins is assumed to proceed via succinimide intermediates. An enolization of the succinimide intermediate is required for the racemization to occur. In this study, we modeled the enolization step by density-functional theory (DFT) calculations (B3LYP/6-31+G**), using two model compounds, N-methylsuccinimide (1) and its formylamino derivative 2. Three mechanisms were investigated for 1, i.e., the direct mechanism without active participation of H(2)O molecules, and one-H(2)O and two-H(2)O mechanisms, in which one or two H(2)O molecules actively participate in the reaction. We found that the two-H(2)O mechanism was the most favorable with an activation barrier of 37 kcal mol(-1). In the two-H(2)O mechanism, a concerted bond reorganization involving a triple H-atom transfer occurred in an eight-membered cyclic structure formed between the imide and two H(2)O molecules. For 2, we investigated only the two-H(2)O mechanism and found that the activation barrier was lowered to 31 kcal mol(-1) due to an H-bond between the CO O-atom of the formylamino group ('the neighboring residue') and one of the H(2)O molecules. Our results suggest that, in proteins, the Asp racemization is severely controlled by the accessibility of H(2)O molecules to the reaction site of the succinimide intermediate.
Takahashi
Ohgi
O
Faculty of Pharmaceutical Sciences, Tohoku Pharmaceutical University, 4-4-1 Komatsushima, Aoba-ku, Sendai, Miyagi 981-8558, Japan. ohgi@tohoku-pharm.ac.jp
Kobayashi
Kana
K
Oda
Akifumi
A
D001224:Aspartic Acid / Q000737:chemistry*; D006863:Hydrogen-Ion Concentration; D008956:Models, Chemical; D008958:Models, Molecular; D013237:Stereoisomerism; D013388:Succinimides / Q000737:chemistry*; D013816:Thermodynamics; D014867:Water / Q000737:chemistry*
D013388:Succinimides; D014867:Water; D001224:Aspartic Acid