Small interfering RNAs (siRNAs) that silence genes of infectious diseases are potentially potent drugs. A continuing obstacle for siRNA-based drugs is how to improve their efficacy for adequate dosage. To overcome this obstacle, the interactions of antiviral siRNAs, tested in vivo, were computationally examined within the RNA-induced silencing complex (RISC). Thermodynamics data show that a persistent RISC cofactor is significantly more exothermic for effective antiviral siRNAs than their ineffective counterparts. Detailed inspection of viral RNA secondary structures reveals that effective antiviral siRNAs target hairpin or pseudoknot loops. These structures are critical for initial RISC interactions since they partially lack intramolecular complementary base pairing. Importing two temporary RISC cofactors from magnesium-rich hairpins and/or pseudoknots then kickstarts full RNA hybridization and hydrolysis. Current siRNA design guidelines are based on RNA primary sequence data. Herein, the thermodynamics of RISC cofactors and targeting magnesium-rich RNA secondary structures provide additional guidelines for improving siRNA design.

• MeSH
• Argonaut proteiny chemie   metabolismus   MeSH
• guide RNA, Kinetoplastida chemie   metabolismus   MeSH
• hořčík MeSH
• hybridizace nukleových kyselin MeSH
• hydrolýza MeSH
• komplex RISC MeSH
• konformace nukleové kyseliny MeSH
• krystalografie rentgenová MeSH
• lidé MeSH
• malá interferující RNA chemie   genetika   metabolismus   MeSH
• messenger RNA chemie   metabolismus   MeSH
• metoda Monte Carlo MeSH
• párování bází MeSH
• racionální návrh léčiv MeSH
• RNA interference * MeSH
• RNA virová antagonisté a inhibitory   chemie   MeSH
• simulace molekulového dockingu MeSH
• termodynamika MeSH
• vztahy mezi strukturou a aktivitou MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

The F-ATPases (also called the F1 Fo -ATPases or ATP synthases) are multi-subunit membrane-bound molecular machines that produce ATP in bacteria and in eukaryotic mitochondria and chloroplasts. The structures and enzymic mechanisms of their F1 -catalytic domains are highly conserved in all species investigated hitherto. However, there is evidence that the F-ATPases from the group of protozoa known as Euglenozoa have novel features. Therefore, we have isolated pure and active F1 -ATPase from the euglenozoan parasite, Trypanosoma brucei, and characterized it. All of the usual eukaryotic subunits (α, β, γ, δ, and ε) were present in the enzyme, and, in addition, two unique features were detected. First, each of the three α-subunits in the F1 -domain has been cleaved by proteolysis in vivo at two sites eight residues apart, producing two assembled fragments. Second, the T. brucei F1 -ATPase has an additional subunit, called p18, present in three copies per complex. Suppression of expression of p18 affected in vitro growth of both the insect and infectious mammalian forms of T. brucei. It also reduced the levels of monomeric and multimeric F-ATPase complexes and diminished the in vivo hydrolytic activity of the enzyme significantly. These observations imply that p18 plays a role in the assembly of the F1 domain. These unique features of the F1 -ATPase extend the list of special characteristics of the F-ATPase from T. brucei, and also, demonstrate that the architecture of the F1 -ATPase complex is not strictly conserved in eukaryotes.

• MeSH
• adenosintrifosfát metabolismus   MeSH
• hydrolýza MeSH
• kinetika MeSH
• konformace proteinů MeSH
• konzervovaná sekvence MeSH
• membránový potenciál mitochondrií MeSH
• molekulární modely * MeSH
• multimerizace proteinu MeSH
• peptidové mapování MeSH
• podjednotky proteinů antagonisté a inhibitory   genetika   izolace a purifikace   metabolismus   MeSH
• proteolýza MeSH
• protonové ATPasy antagonisté a inhibitory   genetika   izolace a purifikace   metabolismus   MeSH
• protozoální proteiny antagonisté a inhibitory   genetika   izolace a purifikace   metabolismus   MeSH
• RNA interference MeSH
• sekvence aminokyselin MeSH
• sekvenční homologie aminokyselin MeSH
• sekvenční seřazení MeSH
• stabilita enzymů MeSH
• Trypanosoma brucei brucei enzymologie   růst a vývoj   MeSH
• výpočetní biologie MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH