SLO | ENG | Piškotki in zasebnost

Večja pisava | Manjša pisava

Izpis gradiva

Naslov:Role of magnesium ions in the reaction mechanism at the interface between Tm1631 protein and its DNA ligand
Avtorji:Ogrizek, Mitja (Avtor)
Konc, Janez (Avtor)
Bren, Urban (Avtor)
Hodošček, Milan (Avtor)
Janežič, Dušanka (Avtor)
Datoteke:.pdf Chemistry_Central_Journal_2016_Ogrizek_et_al._Role_of_magnesium_ions_in_the_reaction_mechanism_at_the_interface_between_Tm1631_protein_a.pdf (2,91 MB)
 
URL http://ccj.springeropen.com/articles/10.1186/s13065-016-0188-6
 
Jezik:Angleški jezik
Vrsta gradiva:Znanstveno delo (r2)
Tipologija:1.01 - Izvirni znanstveni članek
Organizacija:FKKT - Fakulteta za kemijo in kemijsko tehnologijo
Opis:A protein, Tm1631 from the hyperthermophilic organism Thermotoga maritima belongs to a domain of unknown function protein family. It was predicted that Tm1631 binds with the DNA and that the Tm1631–DNA complex is an endonuclease repair system with a DNA repair function (Konc et al. PLoS Comput Biol 9(11): e1003341, 2013). We observed that the severely bent, strained DNA binds to the protein for the entire 90 ns of classical molecular dynamics (MD) performed; we could observe no significant changes in the most distorted region of the DNA, where the cleavage of phosphodiester bond occurs. In this article, we modeled the reaction mechanism at the interface between Tm1631 and its proposed ligand, the DNA molecule, focusing on cleavage of the phosphodiester bond. After addition of two Mg2+ ions to the reaction center and extension of classical MD by 50 ns (totaling 140 ns), the DNA ligand stayed bolted to the protein. Results from density functional theory quantum mechanics/molecular mechanics (QM/MM) calculations suggest that the reaction is analogous to known endonuclease mechanisms: an enzyme reaction mechanism with two Mg2+ ions in the reaction center and a pentacovalent intermediate. The minimum energy pathway profile shows that the phosphodiester bond cleavage step of the reaction is kinetically controlled and not thermodynamically because of a lack of any energy barrier above the accuracy of the energy profile calculation. The role of ions is shown by comparing the results with the reaction mechanisms in the absence of the Mg2+ ions where there is a significantly higher reaction barrier than in the presence of the Mg2+ ions.
Ključne besede:methods of analysis, computer science, magnesium ions, preteins, DNA
Leto izida:2016
Št. strani:str. 1-9
Številčenje:Letn. 10
ISSN:1752-153X
UDK:543.2/.9
COBISS_ID:5947930 Povezava se odpre v novem oknu
DOI:10.1186/s13065-016-0188-6 Povezava se odpre v novem oknu
ISSN pri članku:1752-153X
Licenca:CC BY 4.0
To delo je dosegljivo pod licenco Creative Commons Priznanje avtorstva 4.0 Mednarodna
Število ogledov:154
Število prenosov:67
Metapodatki:XML RDF-CHPDL DC-XML DC-RDF
Področja:Ostalo
:
  
Skupna ocena:(0 glasov)
Vaša ocena:Ocenjevanje je dovoljeno samo prijavljenim uporabnikom.
Objavi na:AddThis
AddThis uporablja piškotke, za katere potrebujemo vaše privoljenje.
Uredi privoljenje...

Postavite miškin kazalec na naslov za izpis povzetka. Klik na naslov izpiše podrobnosti ali sproži prenos.

Gradivo je del revije

Naslov:Chemistry Central Journal
Založnik:Springer
ISSN:1752-153X
COBISS.SI-ID:3877914 Novo okno

Sekundarni jezik

Jezik:Slovenski jezik
Ključne besede:analizne metode, računalništvo, magnezijevi ioni, proteini, DNA


Komentarji

Dodaj komentar

Za komentiranje se morate prijaviti.

Komentarji (0)
0 - 0 / 0
 
Ni komentarjev!

Nazaj
Logotipi partnerjev Univerza v Mariboru Univerza v Ljubljani Univerza na Primorskem Univerza v Novi Gorici