deltavirus
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- MeSH
- hepatitida D diagnóza epidemiologie farmakoterapie komplikace MeSH
- lidé MeSH
- virus hepatitidy delta fyziologie genetika MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- souhrny MeSH
The hepatitis delta virus (HDV) ribozyme is an RNA motif embedded in human pathogenic HDV RNA. Previous experimental studies have established that the active-site nucleotide C75 is essential for self-cleavage of the ribozyme, although its exact catalytic role in the process remains debated. Structural data from X-ray crystallography generally indicate that C75 acts as the general base that initiates catalysis by deprotonating the 2'-OH nucleophile at the cleavage site, while a hydrated magnesium ion likely protonates the 5'-oxygen leaving group. In contrast, some mechanistic studies support the role of C75 acting as general acid and thus being protonated before the reaction. We report combined quantum chemical/molecular mechanical calculations for the C75 general base pathway, utilizing the available structural data for the wild type HDV genomic ribozyme as a starting point. Several starting configurations differing in magnesium ion placement were considered and both one-dimensional and two-dimensional potential energy surface scans were used to explore plausible reaction paths. Our calculations show that C75 is readily capable of acting as the general base, in concert with the hydrated magnesium ion as the general acid. We identify a most likely position for the magnesium ion, which also suggests it acts as a Lewis acid. The calculated energy barrier of the proposed mechanism, approximately 20 kcal/mol, would lower the reaction barrier by approximately 15 kcal/mol compared with the uncatalyzed reaction and is in good agreement with experimental data.
- MeSH
- antivirové látky aplikace a dávkování terapeutické užití MeSH
- chronické selhání ledvin terapie MeSH
- dialýza ledvin MeSH
- hepatitida B diagnóza etiologie terapie MeSH
- hepatitida C diagnóza etiologie terapie MeSH
- virová hepatitida u lidí prevence a kontrola přenos terapie MeSH
- virus hepatitidy delta MeSH
- Publikační typ
- přehledy MeSH
- MeSH
- dítě MeSH
- dospělí MeSH
- hepatitida D epidemiologie imunologie MeSH
- lidé MeSH
- přenašečství epidemiologie imunologie MeSH
- protilátky virové analýza MeSH
- virus hepatitidy delta imunologie MeSH
- Check Tag
- dítě MeSH
- dospělí MeSH
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- srovnávací studie MeSH
- Geografické názvy
- Československo MeSH
- SSSR MeSH
- MeSH
- antivirové látky terapeutické užití MeSH
- fosforothioátové oligonukleotidy terapeutické užití MeSH
- hepatitida D * imunologie patofyziologie terapie MeSH
- lidé MeSH
- randomizované kontrolované studie jako téma MeSH
- RNA virová MeSH
- virus hepatitidy B * genetika MeSH
- virus hepatitidy delta * genetika MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- práce podpořená grantem MeSH
- přehledy MeSH
The hepatitis delta virus (HDV) ribozyme is an RNA enzyme from the human pathogenic HDV. Cations play a crucial role in self-cleavage of the HDV ribozyme, by promoting both folding and chemistry. Experimental studies have revealed limited but intriguing details on the location and structural and catalytic functions of metal ions. Here, we analyze a total of approximately 200 ns of explicit-solvent molecular dynamics simulations to provide a complementary atomistic view of the binding of monovalent and divalent cations as well as water molecules to reaction precursor and product forms of the HDV ribozyme. Our simulations find that an Mg2+ cation binds stably, by both inner- and outer-sphere contacts, to the electronegative catalytic pocket of the reaction precursor, in a position to potentially support chemistry. In contrast, protonation of the catalytically involved C75 in the precursor or artificial placement of this Mg2+ into the product structure result in its swift expulsion from the active site. These findings are consistent with a concerted reaction mechanism in which C75 and hydrated Mg2+ act as general base and acid, respectively. Monovalent cations bind to the active site and elsewhere assisted by structurally bridging long-residency water molecules, but are generally delocalized.
- MeSH
- financování organizované MeSH
- hořčík chemie MeSH
- kationty dvojmocné chemie MeSH
- kationty jednomocné chemie MeSH
- konformace nukleové kyseliny MeSH
- molekulární modely MeSH
- molekulární sekvence - údaje MeSH
- RNA katalytická chemie MeSH
- sekvence nukleotidů MeSH
- sodík chemie MeSH
- vazebná místa MeSH
- virus hepatitidy delta enzymologie MeSH
- voda chemie MeSH
- vodíková vazba MeSH
Hepatitis D virus (HDV) is a small, RNA-containing virus that requires the concomitant presence of Hepatitis B virus (HBV) in an obligate manner for its survival and pathogenicity. HDV infection is very uncommon in Czech Republic. The results of antiviral therapy of hepatitis D patients are not satisfactory. Alpha-interferon (alpha-IFN) in high doses (9-10 MU three times a week for 12 months) is usually recommended.
The hepatitis delta virus (HDV) ribozyme is a member of the class of small, self-cleaving catalytic RNAs found in a wide range of genomes from HDV to human. Both pre- and post-catalysis (precursor and product) crystal structures of the cis-acting genomic HDV ribozyme have been determined. These structures, together with extensive solution probing, have suggested that a significant conformational change accompanies catalysis. A recent crystal structure of a trans-acting precursor, obtained at low pH and by molecular replacement from the previous product conformation, conforms to the product, raising the possibility that it represents an activated conformer past the conformational change. Here, using fluorescence resonance energy transfer (FRET), we discovered that cleavage of this ribozyme at physiological pH is accompanied by a structural lengthening in magnitude comparable to previous trans-acting HDV ribozymes. Conformational heterogeneity observed by FRET in solution appears to have been removed upon crystallization. Analysis of a total of 1.8 µsec of molecular dynamics (MD) simulations showed that the crystallographically unresolved cleavage site conformation is likely correctly modeled after the hammerhead ribozyme, but that crystal contacts and the removal of several 2'-oxygens near the scissile phosphate compromise catalytic in-line fitness. A cis-acting version of the ribozyme exhibits a more dynamic active site, while a G-1 residue upstream of the scissile phosphate favors poor fitness, allowing us to rationalize corresponding changes in catalytic activity. Based on these data, we propose that the available crystal structures of the HDV ribozyme represent intermediates on an overall rugged RNA folding free-energy landscape.
- MeSH
- katalytická doména MeSH
- katalýza MeSH
- kinetika MeSH
- konformace nukleové kyseliny MeSH
- krystalografie rentgenová MeSH
- molekulární modely MeSH
- rezonanční přenos fluorescenční energie metody MeSH
- RNA katalytická chemie MeSH
- RNA malá jaderná chemie metabolismus MeSH
- RNA virová chemie MeSH
- simulace molekulární dynamiky MeSH
- štěpení RNA MeSH
- virus hepatitidy delta enzymologie genetika MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Research Support, N.I.H., Extramural MeSH
- Research Support, U.S. Gov't, Non-P.H.S. MeSH
- MeSH
- antivirové látky farmakologie terapeutické užití MeSH
- hepatitida D * diagnóza farmakoterapie patologie MeSH
- imunizace metody MeSH
- interferon alfa terapeutické užití MeSH
- lidé MeSH
- lipopeptidy farmakologie terapeutické užití MeSH
- screeningové diagnostické programy MeSH
- virus hepatitidy delta metabolismus patogenita MeSH
- Check Tag
- lidé MeSH
