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Pregled bibliografske jedinice broj: 934286

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


Bilić, Luka; Tomin, Marko; Barić, Danijela; Kovačević, Borislav; Smith, David Matthew
MD and DFT study of glycerol binding in B12-dependent diol dehydratase // AMBER Molecular Dynamics workshop 2018 i Spring School in Computational Chemistry 2018 @ CSC
Haifa, Izrael i Espoo, Finska, 2018. (poster, nije recenziran, neobjavljeni rad, znanstveni)


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

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

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

Skup
AMBER Molecular Dynamics workshop 2018 i Spring School in Computational Chemistry 2018 @ CSC

Mjesto i datum
Haifa, Izrael i Espoo, Finska, 04-08.03.2018. / 13-16.03.2018

Vrsta sudjelovanja
Poster

Vrsta recenzije
Nije recenziran

Ključne riječi
B12 ; diol dehydratase ; DDH ; glycerol ; molecular dynamics ; MD ; DFT

Sažetak
During biodiesel production a large amount of glycerol is created as a byproduct. 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. However, the unusual property of glycerol is that it is both the supstrate and the irreversible inhibitor of B12-dependent dehydratases. The proposed mechanism of inactivation is based on the crystal structure of B12-dependant diol dehidratase (DDH, PDB code: 3AUJ). 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 density aroud 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 of glycerol 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, Borislav; Smith, David Matthew
MD and DFT study of glycerol binding in B12-dependent diol dehydratase // AMBER Molecular Dynamics workshop 2018 i Spring School in Computational Chemistry 2018 @ CSC
Haifa, Izrael i Espoo, Finska, 2018. (poster, nije recenziran, 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: AMBER Molecular Dynamics workshop 2018 i Spring School in Computational Chemistry 2018 @ CSC.
@article{article, year = {2018}, keywords = {B12, diol dehydratase, DDH, glycerol, molecular dynamics, MD, DFT}, title = {MD and DFT study of glycerol binding in B12-dependent diol dehydratase}, keyword = {B12, diol dehydratase, DDH, glycerol, molecular dynamics, MD, DFT}, publisherplace = {Haifa, Izrael i Espoo, Finska} }
@article{article, year = {2018}, keywords = {B12, diol dehydratase, DDH, glycerol, molecular dynamics, MD, DFT}, title = {MD and DFT study of glycerol binding in B12-dependent diol dehydratase}, keyword = {B12, diol dehydratase, DDH, glycerol, molecular dynamics, MD, DFT}, publisherplace = {Haifa, Izrael i Espoo, Finska} }




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