FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W2014066797> ?p ?o ?g. }

• W2014066797 endingPage "296" @default.
• W2014066797 startingPage "283" @default.
• W2014066797 abstract "Abstract The nature of specific RNA‐RNA and protein‐RNA interactions involved in the process of genome dimerization and isomerization in HIV‐1, which is mediated in vitro by stemloop 1 (SL1) of the packaging signal and by the nucleocapsid (NC) domain of the viral Gag polyprotein, was investigated by using archetypical nucleic acid ligands as noncovalent probes. Small‐molecule ligands make contact with their target substrates through complex combinations of H‐bonds, salt bridges, and hydrophobic interactions. Therefore, their binding patterns assessed by electrospray ionization mass spectrometry can provide valuable insights into the factors determining specific recognition between species involved in biopolymer assemblies. In the case of SL1, dimerization and isomerization create unique structural features capable of sustaining stable interactions with classic nucleic acid ligands. The binding modes exhibited by intercalators and minor groove binders were adversely affected by the significant distortion of the duplex formed by palindrome annealing in the kissing‐loop (KL) dimer, whereas the modes observed for the corresponding extended duplex (ED) confirmed a more regular helical structure. Consistent with the ability to establish electrostatic interactions with highly negative pockets typical of helix anomalies, polycationic aminoglycosides bound to the stem‐bulge motif conserved in all SL1 conformers, to the unpaired nucleotides located at the hinge between kissing hairpins in KL, and to the exposed bases flanking the palindrome duplex in ED. The patterns afforded by intercalators and minor groove binders did not display detectable variations when the corresponding NC‐SL1 complexes were submitted to probing. In contrast, aminoglycosides displayed the ability to compete with the protein for overlapping sites, producing opposite effects on the isomerization process. Indeed, displacing NC from the stem‐bulges of the KL dimer induced inhibition of stem melting and decreased the efficiency of isomerization. Competition for the hinge region, instead, eliminated the NC stabilization of a grip motif formed by nucleobases of opposite strands, thus facilitating the strand‐exchange required for isomerization. These noncovalent probes provided further evidence that the structural context of the actual binding sites has significant influence on the chaperone activities of NC, which should be taken in account when developing potential drug candidates aimed at disrupting genome dimerization and isomerization in HIV‐1. © 2008 Wiley Periodicals, Inc. Biopolymers 91: 283–296, 2009. This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com" @default.
• W2014066797 created "2016-06-24" @default.
• W2014066797 creator A5030943009 @default.
• W2014066797 creator A5045329628 @default.
• W2014066797 creator A5076177690 @default.
• W2014066797 creator A5089886800 @default.
• W2014066797 date "2008-10-22" @default.
• W2014066797 modified "2023-09-30" @default.
• W2014066797 title "Noncovalent probes for the investigation of structure and dynamics of protein-nucleic acid assemblies: The case of NC-mediated dimerization of genomic RNA in HIV-1" @default.
• W2014066797 cites W1480821243 @default.
• W2014066797 cites W1547414471 @default.
• W2014066797 cites W1599743339 @default.
• W2014066797 cites W1641947900 @default.
• W2014066797 cites W1819107170 @default.
• W2014066797 cites W1963559907 @default.
• W2014066797 cites W1965019895 @default.
• W2014066797 cites W1965252702 @default.
• W2014066797 cites W1973901059 @default.
• W2014066797 cites W1974883489 @default.
• W2014066797 cites W1980679837 @default.
• W2014066797 cites W1980779739 @default.
• W2014066797 cites W1986665516 @default.
• W2014066797 cites W1987332150 @default.
• W2014066797 cites W1989989621 @default.
• W2014066797 cites W1990109007 @default.
• W2014066797 cites W1996795030 @default.
• W2014066797 cites W2005821841 @default.
• W2014066797 cites W2011912736 @default.
• W2014066797 cites W2012695073 @default.
• W2014066797 cites W2015948549 @default.
• W2014066797 cites W2020790990 @default.
• W2014066797 cites W2021534482 @default.
• W2014066797 cites W2026741263 @default.
• W2014066797 cites W2030252178 @default.
• W2014066797 cites W2032416353 @default.
• W2014066797 cites W2032467322 @default.
• W2014066797 cites W2044410490 @default.
• W2014066797 cites W2044752471 @default.
• W2014066797 cites W2045568382 @default.
• W2014066797 cites W2047135941 @default.
• W2014066797 cites W2048331014 @default.
• W2014066797 cites W2057365035 @default.
• W2014066797 cites W2061476669 @default.
• W2014066797 cites W2062001795 @default.
• W2014066797 cites W2064093220 @default.
• W2014066797 cites W2065841577 @default.
• W2014066797 cites W2067145794 @default.
• W2014066797 cites W2068374641 @default.
• W2014066797 cites W2069469166 @default.
• W2014066797 cites W2074907465 @default.
• W2014066797 cites W2077246276 @default.
• W2014066797 cites W2078508576 @default.
• W2014066797 cites W2082140615 @default.
• W2014066797 cites W2085145164 @default.
• W2014066797 cites W2086354229 @default.
• W2014066797 cites W2088417988 @default.
• W2014066797 cites W2096985241 @default.
• W2014066797 cites W2099780173 @default.
• W2014066797 cites W2102089867 @default.
• W2014066797 cites W2102212599 @default.
• W2014066797 cites W2110812878 @default.
• W2014066797 cites W2119143098 @default.
• W2014066797 cites W2121901332 @default.
• W2014066797 cites W2122594923 @default.
• W2014066797 cites W2128582252 @default.
• W2014066797 cites W2131615898 @default.
• W2014066797 cites W2132646560 @default.
• W2014066797 cites W2142225521 @default.
• W2014066797 cites W2142516950 @default.
• W2014066797 cites W2151603866 @default.
• W2014066797 cites W2158534713 @default.
• W2014066797 cites W2158977548 @default.
• W2014066797 cites W2166393079 @default.
• W2014066797 cites W2411335959 @default.
• W2014066797 cites W32169690 @default.
• W2014066797 cites W4206362406 @default.
• W2014066797 cites W4295009278 @default.
• W2014066797 doi "https://doi.org/10.1002/bip.21107" @default.
• W2014066797 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/2776628" @default.
• W2014066797 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/18946871" @default.
• W2014066797 hasPublicationYear "2008" @default.
• W2014066797 type Work @default.
• W2014066797 sameAs 2014066797 @default.
• W2014066797 citedByCount "35" @default.
• W2014066797 countsByYear W20140667972012 @default.
• W2014066797 countsByYear W20140667972013 @default.
• W2014066797 countsByYear W20140667972014 @default.
• W2014066797 countsByYear W20140667972015 @default.
• W2014066797 countsByYear W20140667972016 @default.
• W2014066797 countsByYear W20140667972017 @default.
• W2014066797 countsByYear W20140667972018 @default.
• W2014066797 countsByYear W20140667972019 @default.
• W2014066797 countsByYear W20140667972020 @default.
• W2014066797 countsByYear W20140667972021 @default.
• W2014066797 countsByYear W20140667972022 @default.
• W2014066797 countsByYear W20140667972023 @default.
• W2014066797 crossrefType "journal-article" @default.
• W2014066797 hasAuthorship W2014066797A5030943009 @default.

• next