The conversion of l-lysine into l-β-lysine: the role of 5′-deoxyadenosyl radical and water—a DFT study

• Published in: Journal of molecular modeling Vol. 27; no. 1; p. 6
• Main Authors: Thuy, Phan Thi, Son, Ninh The
• Format: Journal Article
• Language: English
• Published: Berlin/Heidelberg Springer Berlin Heidelberg 01-01-2021; Springer Nature B.V
• Subjects: Characterization and Evaluation of Materials; Chemistry; Chemistry and Materials Science; Computer Appl. in Life Sciences; Computer Applications in Chemistry; Conversion; Density functional theory; Lysine; Molecular Medicine; Original Paper; Theoretical and Computational Chemistry; Water; Density functional theory; 5′-Deoxyadenosyl radical; Lysine
• ISSN: 1610-2940; 0948-5023
• DOI: 10.1007/s00894-020-04639-3

In the current study, we deal with the crucial role of 5′-deoxyadenosyl radical and water in the mechanism of the conversion of
l
-lysine into
l
-β-lysine. The DFT (density functional theory)–B3LYP method coupled with 6-31G(d) basis set has been performed to investigate the optimized structures of transition states (
TSs
) and intermediates (
IMs
) of two processes in water: (i) the attack of 5′-deoxyadenosyl radical to complex PLP-
l
-lysine and (ii) hydrolysis to liberate
l
-β-lysine. Meanwhile, M062X/6-311++g(3df,2p) level of theory is applied to compute the relative Gibbs energy ΔG. Procedure (i) has undergone various steps but includes two main structural aziridinyl rings
TS2
(ΔG = 4.1 kcal/mol) and
TS3
(ΔG = 2.3 kcal/mol). In stage (ii), hydroxy group of water would help to break the bond between β-NH
2
group of
l
-lysine and PLP better than that of Tyr389.
Graphical abstract