Extended Data Fig. 10: The MD simulations of ThDP-acyl donor-Breslow intermediates and acyl acceptors in the active sites of CsmA or BbmA. | Nature Chemistry

Extended Data Fig. 10: The MD simulations of ThDP-acyl donor-Breslow intermediates and acyl acceptors in the active sites of CsmA or BbmA.

From: Structural insights into two thiamine diphosphate-dependent enzymes and their synthetic applications in carbon–carbon linkage reactions

Extended Data Fig. 10

a, Model I: the initial binding of BbmA (cyan) with HPPA (green) and ThDP-CBOA-Breslow intermediate (blue) allowing an Si face attack. b, Model II: the initial binding of BbmA (cyan) with HPPA (orange) and ThDP-CBOA-Breslow intermediate (blue) allowing an Re face attack. c, Changes in the dihedral angle between the O-Cα-Cβ face and Cα-Cβ-Ha face during the 200 ns MD simulations for Model I and Model II. d, A representative MD snapshot at 110 ns for Model II, in which HPPA are shown as grey sticks. e, The MD simulations of CsmA (wheat) with HPPA (green) and ThDP-IPA-Breslow intermediate (blue) after 200 ns. f, The MD simulations of CsmA (wheat) with HPPA (green) and ThDP-OPBA-Breslow intermediate (blue) after 200 ns. g, The MD simulations of BbmA (cyan) with IPA (green) and ThDP-CBOA-Breslow intermediate (blue) after 200 ns. h, The MD simulations of BbmA (cyan) with HPPA (green) and ThDP-4-MOVA-Breslow intermediate (blue) after 200 ns.

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