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On the Reaction of Glycerol Dehydratase with But-3-ene-1, 2-diol


Sandala, Gregory M.; Kovačević, Borislav; Barić, Danijela; Smith, David M.; Radom, Leo
On the Reaction of Glycerol Dehydratase with But-3-ene-1, 2-diol // Chemistry : a European journal, 15 (2009), 19; 4865-4873 doi:10.1002/chem.200802640 (međunarodna recenzija, članak, znanstveni)


Naslov
On the Reaction of Glycerol Dehydratase with But-3-ene-1, 2-diol

Autori
Sandala, Gregory M. ; Kovačević, Borislav ; Barić, Danijela ; Smith, David M. ; Radom, Leo

Izvornik
Chemistry : a European journal (0947-6539) 15 (2009), 19; 4865-4873

Vrsta, podvrsta i kategorija rada
Radovi u časopisima, članak, znanstveni

Ključne riječi
Ab initio calculations ; density functional calculations ; enzyme inhibitors ; radicals ; reaction mechanisms

Sažetak
Ntriguing inactivation: Calculations suggest that the ability of relatively high-energy radical intermediates to inactivate glycerol dehydratase (GDH) may reflect a general and hitherto unidentified inactivation mechanism in the reaction of coenzyme B12-dependent enzymes and 3-unsaturated 1, 2-diols. High-level conventional ab initio and density functional theory (DFT) calculations have been performed to examine the fate of the native substrate glycerol (1) and its analogue but-3-ene-1, 2-diol (7) in the coenzyme B12-dependent enzyme glycerol dehydratase (GDH). Experimental studies find that 7 irreversibly inactivates GDH, though the mechanism for the inactivation remains unknown. Interestingly, the EPR data suggest that the spin density for an observed radical is located in the vicinity of the C1 atom, which has been interpreted to indicate termination of the pathway at the substrate-derived radical 8. Our calculations show that if analogue 7 were to follow a similar mechanistic pathway to that followed by 1, then the reaction would be unlikely to stop at 8 but would rather proceed to the highly stabilized product-related radical 9. However, the EPR characteristics of 9 would not be consistent with the observed EPR data. Calculations involving an initial H-atom abstraction from the C2 position of 7 identify alternative radicals that might account for the EPR data, though they are of relatively high energy. A proposal that could explain the experimental observations is that the enzyme binds 7 in such a manner as to prevent the efficient transformation of 8. Recent work with the related enzyme diol dehydratase suggests that a common, but as yet unexplained, inactivation mechanism may be operative for both enzymes. Finally, we note the good overall performance of the MPWB1K, BMK, M05-2X, and B2-PLYP DFT procedures for these reactions, with the BMK method producing the best results.

Izvorni jezik
Engleski

Znanstvena područja
Kemija



POVEZANOST RADA


Projekt / tema
098-0982933-2937 - Računalno proučavanje strukture i funkcije proteina (David Matthew Smith, )

Ustanove
Institut "Ruđer Bošković", Zagreb

Časopis indeksira:


  • Current Contents Connect (CCC)
  • Web of Science Core Collection (WoSCC)
    • Science Citation Index Expanded (SCI-EXP)
    • SCI-EXP, SSCI i/ili A&HCI
  • Scopus
  • MEDLINE


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