Reaction mechanism of deamidation of asparaginyl residues in peptides: effect of solvent molecules.
Deamidation of proteins occurs spontaneously under physiological conditions. Asparaginyl (Asn) residues may deamidate into aspartyl (Asp) residues, causing a change in both the charge and the conformation of peptides. It has been previously proposed by Capasso et al. that deamidation of relatively unrestrained Asn residues proceeds through a succinimide intermediate. This mechanism has been modeled by Konuklar et al. and the rate determining step for the deamidation process in neutral media has been shown to be the cyclization step leading to the succinimide intermediate. In the present study, possible water-assisted mechanisms, for both concerted and stepwise succinimide formation, were computationally explored using the B3LYP method with 6-31+G* basis set. Single point solvent calculations were carried out in water, by means of integral equation formalism-polarizable continuum model (IEF-PCM) at the B3LYP/6-31++G* level of theory. A novel route leading to the succinimide intermediate via tautomerization of the Asn side chain amide functionality has been proposed. The energetics of these pathways have been subject to a comparative study to identify the most probable mechanism for the deamidation of peptides in solution.
Catak
Saron
S
Department of Chemistry, Bogazici University, 34342 Bebek, Istanbul, Turkey.
Monard
Gérald
G
Aviyente
Viktorya
V
Ruiz-López
Manuel F
MF
D000577:Amides / Q000737:chemistry; D000595:Amino Acid Sequence; D001216:Asparagine / Q000737:chemistry*; D019295:Computational Biology; D004735:Energy Transfer; D008958:Models, Molecular; D008969:Molecular Sequence Data; D015394:Molecular Structure; D010455:Peptides / Q000737:chemistry*; D011487:Protein Conformation; D013329:Structure-Activity Relationship; D014867:Water / Q000737:chemistry
D000577:Amides; D010455:Peptides; D014867:Water; D001216:Asparagine