FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W2057478725> ?p ?o ?g. }

• W2057478725 endingPage "638" @default.
• W2057478725 startingPage "626" @default.
• W2057478725 abstract "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." @default.
• W2057478725 created "2016-06-24" @default.
• W2057478725 creator A5009040971 @default.
• W2057478725 creator A5016259851 @default.
• W2057478725 creator A5017944702 @default.
• W2057478725 creator A5020303614 @default.
• W2057478725 creator A5026399646 @default.
• W2057478725 creator A5062695629 @default.
• W2057478725 date "2006-07-01" @default.
• W2057478725 modified "2023-10-16" @default.
• W2057478725 title "Cations and Hydration in Catalytic RNA: Molecular Dynamics of the Hepatitis Delta Virus Ribozyme" @default.
• W2057478725 cites W1881326155 @default.
• W2057478725 cites W1968524596 @default.
• W2057478725 cites W1974000520 @default.
• W2057478725 cites W1976499671 @default.
• W2057478725 cites W1977169697 @default.
• W2057478725 cites W1985012591 @default.
• W2057478725 cites W1988286515 @default.
• W2057478725 cites W1988550390 @default.
• W2057478725 cites W1989973566 @default.
• W2057478725 cites W1990447102 @default.
• W2057478725 cites W1996036703 @default.
• W2057478725 cites W1999606717 @default.
• W2057478725 cites W2000670326 @default.
• W2057478725 cites W2002730194 @default.
• W2057478725 cites W2006112806 @default.
• W2057478725 cites W2006521039 @default.
• W2057478725 cites W2009690079 @default.
• W2057478725 cites W2010345100 @default.
• W2057478725 cites W2013902881 @default.
• W2057478725 cites W2020304050 @default.
• W2057478725 cites W2020909889 @default.
• W2057478725 cites W2022889126 @default.
• W2057478725 cites W2023219682 @default.
• W2057478725 cites W2025232734 @default.
• W2057478725 cites W2025529107 @default.
• W2057478725 cites W2029667189 @default.
• W2057478725 cites W2032518125 @default.
• W2057478725 cites W2035266068 @default.
• W2057478725 cites W2035687084 @default.
• W2057478725 cites W2039255128 @default.
• W2057478725 cites W2040882599 @default.
• W2057478725 cites W2043251659 @default.
• W2057478725 cites W2043951259 @default.
• W2057478725 cites W2044235066 @default.
• W2057478725 cites W2047518536 @default.
• W2057478725 cites W2049289210 @default.
• W2057478725 cites W2053471524 @default.
• W2057478725 cites W2055177061 @default.
• W2057478725 cites W2059397561 @default.
• W2057478725 cites W2060954131 @default.
• W2057478725 cites W2064592675 @default.
• W2057478725 cites W2065463519 @default.
• W2057478725 cites W2068434764 @default.
• W2057478725 cites W2070777040 @default.
• W2057478725 cites W2074312400 @default.
• W2057478725 cites W2078334480 @default.
• W2057478725 cites W2082905252 @default.
• W2057478725 cites W2082968605 @default.
• W2057478725 cites W2083061759 @default.
• W2057478725 cites W2084143455 @default.
• W2057478725 cites W2084903245 @default.
• W2057478725 cites W2087572417 @default.
• W2057478725 cites W2091565965 @default.
• W2057478725 cites W2091765441 @default.
• W2057478725 cites W2101136532 @default.
• W2057478725 cites W2103488640 @default.
• W2057478725 cites W2109477938 @default.
• W2057478725 cites W2114772003 @default.
• W2057478725 cites W2115729502 @default.
• W2057478725 cites W2118956677 @default.
• W2057478725 cites W2120883316 @default.
• W2057478725 cites W2122199548 @default.
• W2057478725 cites W2130681953 @default.
• W2057478725 cites W2131288855 @default.
• W2057478725 cites W2132466716 @default.
• W2057478725 cites W2134709176 @default.
• W2057478725 cites W2135839939 @default.
• W2057478725 cites W2139601032 @default.
• W2057478725 cites W2150945052 @default.
• W2057478725 cites W2159741345 @default.
• W2057478725 cites W2159946246 @default.
• W2057478725 cites W2163151016 @default.
• W2057478725 cites W2165032708 @default.
• W2057478725 cites W2170841043 @default.
• W2057478725 cites W2337120805 @default.
• W2057478725 doi "https://doi.org/10.1529/biophysj.105.079368" @default.
• W2057478725 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/1483112" @default.
• W2057478725 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/16617077" @default.
• W2057478725 hasPublicationYear "2006" @default.
• W2057478725 type Work @default.
• W2057478725 sameAs 2057478725 @default.
• W2057478725 citedByCount "119" @default.
• W2057478725 countsByYear W20574787252012 @default.
• W2057478725 countsByYear W20574787252013 @default.
• W2057478725 countsByYear W20574787252014 @default.
• W2057478725 countsByYear W20574787252015 @default.
• W2057478725 countsByYear W20574787252016 @default.

• next