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Pregled bibliografske jedinice broj: 1060274

MD and DFT study of glycerol binding in B12-dependent diol dehydratase


Bilić, Luka; Tomin, Marko; Barić, Danijela; Kovačević, Boris; Smith, David Matthew
MD and DFT study of glycerol binding in B12-dependent diol dehydratase // Computational Chemistry Day / Babić, Darko ; Barić, Danijela ; Cvitaš, Marko ; Despotović, Ines ; Došlić, Nađa ; Hanževački, Marko ; Hrenar, Tomica ; Kovačević, Borislav ; Ljubić, Ivan ; Mihalić, Zlatko ; Vianello, Robert (ur.).
Zagreb: University of Zagreb Faculty of Science, 2018. str. 25-25 (poster, podatak o recenziji nije dostupan, neobjavljeni rad, znanstveni)


CROSBI ID: 1060274 Za ispravke kontaktirajte CROSBI podršku putem web obrasca

Naslov
MD and DFT study of glycerol binding in B12-dependent diol dehydratase

Autori
Bilić, Luka ; Tomin, Marko ; Barić, Danijela ; Kovačević, Boris ; Smith, David Matthew

Vrsta, podvrsta i kategorija rada
Sažeci sa skupova, neobjavljeni rad, znanstveni

ISBN
978-953-6076-45-1

Skup
Computational Chemistry Day

Mjesto i datum
Zagreb, Hrvatska, 12.05.2018

Vrsta sudjelovanja
Poster

Vrsta recenzije
Podatak o recenziji nije dostupan

Ključne riječi
B12-dependent diol dehydratase ; Substrate binding ; Glycerol inactivation ; Molecular dynamics ; QM/MM calculations

Sažetak
During biodiesel production a large amount of glycerol is created as a byproduct [1, 2]. Dehydration of glycerol to a more valuable product could be obtained by eco-friendly methods utilizing B12-dependent dehydratases which turn glycerol into 3-hydroxypropanal [3-5]. However, the unusual property of glycerol is that it is both the supstrate and the irreversible inhibitor of B12-dependent dehydratases [6]. The proposed mechanism of inactivation is based on the crystal structure of B12-dependant diol dehydratase (DDH, PDB code: 3AUJ) [7]. This mechanism relies on the position of the hydroxyl group at C(3) atom of glycerol being oriented towards the serine residue (Ser301) in the active site. However, incompleteness of the enzyme in crystal structure (missing adenosyl group), poor resolution (2.1 Å) and small electron densityaroud C(3) call for further research. Herein we compare geometrical parameters of the active site of DDH obtained by molecular dynamic simulations (MD) and quantum chemical calculations (DFT) with the crystal structure, and investigate various patterns ofglycerol binding in the active site.

Izvorni jezik
Engleski

Znanstvena područja
Kemija



POVEZANOST RADA


Projekti:
HRZZ-IP-2013-11-8238 - Računalna rješenja u bioznanostima: Značaj savitljivosti molekula (CompSoLS-MolFlex) (Matthew Smith, David, HRZZ - 2013-11) ( POIROT)

Ustanove:
Institut "Ruđer Bošković", Zagreb

Citiraj ovu publikaciju

Bilić, Luka; Tomin, Marko; Barić, Danijela; Kovačević, Boris; Smith, David Matthew
MD and DFT study of glycerol binding in B12-dependent diol dehydratase // Computational Chemistry Day / Babić, Darko ; Barić, Danijela ; Cvitaš, Marko ; Despotović, Ines ; Došlić, Nađa ; Hanževački, Marko ; Hrenar, Tomica ; Kovačević, Borislav ; Ljubić, Ivan ; Mihalić, Zlatko ; Vianello, Robert (ur.).
Zagreb: University of Zagreb Faculty of Science, 2018. str. 25-25 (poster, podatak o recenziji nije dostupan, neobjavljeni rad, znanstveni)
Bilić, L., Tomin, M., Barić, D., Kovačević, B. & Smith, D. (2018) MD and DFT study of glycerol binding in B12-dependent diol dehydratase. U: Babić, D., Barić, D., Cvitaš, M., Despotović, I., Došlić, N., Hanževački, M., Hrenar, T., Kovačević, B., Ljubić, I., Mihalić, Z. & Vianello, R. (ur.)Computational Chemistry Day.
@article{article, year = {2018}, pages = {25-25}, keywords = {B12-dependent diol dehydratase, Substrate binding, Glycerol inactivation, Molecular dynamics, QM/MM calculations}, isbn = {978-953-6076-45-1}, title = {MD and DFT study of glycerol binding in B12-dependent diol dehydratase}, keyword = {B12-dependent diol dehydratase, Substrate binding, Glycerol inactivation, Molecular dynamics, QM/MM calculations}, publisher = {University of Zagreb Faculty of Science}, publisherplace = {Zagreb, Hrvatska} }
@article{article, year = {2018}, pages = {25-25}, keywords = {B12-dependent diol dehydratase, Substrate binding, Glycerol inactivation, Molecular dynamics, QM/MM calculations}, isbn = {978-953-6076-45-1}, title = {MD and DFT study of glycerol binding in B12-dependent diol dehydratase}, keyword = {B12-dependent diol dehydratase, Substrate binding, Glycerol inactivation, Molecular dynamics, QM/MM calculations}, publisher = {University of Zagreb Faculty of Science}, publisherplace = {Zagreb, Hrvatska} }




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