FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W2215463534> ?p ?o ?g. }

• W2215463534 endingPage "15190" @default.
• W2215463534 startingPage "15176" @default.
• W2215463534 abstract "We report an extensive set of explicit solvent molecular dynamics (MD) simulations (∼25 μs of accumulated simulation time) of the RNA kissing-loop complex of the HIV-1 virus initiation dimerization site. Despite many structural investigations by X-ray, NMR, and MD techniques, the position of the bulged purines of the kissing complex has not been unambiguously resolved. The X-ray structures consistently show bulged-out positions of the unpaired bases, while several NMR studies show bulged-in conformations. The NMR studies are, however, mutually inconsistent regarding the exact orientations of the bases. The earlier simulation studies predicted the bulged-out conformation; however, this finding could have been biased by the short simulation time scales. Our microsecond-long simulations reveal that all unpaired bases of the kissing-loop complex stay preferably in the interior of the kissing-loop complex. The MD results are discussed in the context of the available experimental data and we suggest that both conformations are biochemically relevant. We also show that MD provides a quite satisfactory description of this RNA system, contrasting recent reports of unsatisfactory performance of the RNA force fields for smaller systems such as tetranucleotides and tetraloops. We explain this by the fact that the kissing complex is primarily stabilized by an extensive network of Watson-Crick interactions which are rather well described by the force fields. We tested several different sets of water/ion parameters but they all lead to consistent results. However, we demonstrate that a recently suggested modification of van der Waals interactions of the Cornell et al. force field deteriorates the description of the kissing complex by the loss of key stacking interactions stabilizing the interhelical junction and excessive hydrogen-bonding interactions." @default.
• W2215463534 created "2016-06-24" @default.
• W2215463534 creator A5009175551 @default.
• W2215463534 creator A5026399646 @default.
• W2215463534 creator A5041529029 @default.
• W2215463534 creator A5046741316 @default.
• W2215463534 creator A5065501960 @default.
• W2215463534 creator A5083895400 @default.
• W2215463534 creator A5085363071 @default.
• W2215463534 date "2015-11-30" @default.
• W2215463534 modified "2023-10-16" @default.
• W2215463534 title "Microsecond-Scale MD Simulations of HIV-1 DIS Kissing-Loop Complexes Predict Bulged-In Conformation of the Bulged Bases and Reveal Interesting Differences between Available Variants of the AMBER RNA Force Fields" @default.
• W2215463534 cites W1480821243 @default.
• W2215463534 cites W171539743 @default.
• W2215463534 cites W1964670587 @default.
• W2215463534 cites W1966078827 @default.
• W2215463534 cites W1976499671 @default.
• W2215463534 cites W1980779739 @default.
• W2215463534 cites W1981225934 @default.
• W2215463534 cites W1983169232 @default.
• W2215463534 cites W1984481443 @default.
• W2215463534 cites W1986961755 @default.
• W2215463534 cites W1987224264 @default.
• W2215463534 cites W1993146975 @default.
• W2215463534 cites W2005313434 @default.
• W2215463534 cites W2008593229 @default.
• W2215463534 cites W2012293288 @default.
• W2215463534 cites W2013902881 @default.
• W2215463534 cites W2016133492 @default.
• W2215463534 cites W2020304050 @default.
• W2215463534 cites W2021272531 @default.
• W2215463534 cites W2023462216 @default.
• W2215463534 cites W2023735050 @default.
• W2215463534 cites W2029667189 @default.
• W2215463534 cites W2032416353 @default.
• W2215463534 cites W2032467322 @default.
• W2215463534 cites W2035687084 @default.
• W2215463534 cites W2036888427 @default.
• W2215463534 cites W2037003688 @default.
• W2215463534 cites W2038354555 @default.
• W2215463534 cites W2040809566 @default.
• W2215463534 cites W2042285588 @default.
• W2215463534 cites W2043476833 @default.
• W2215463534 cites W2045914731 @default.
• W2215463534 cites W2048057039 @default.
• W2215463534 cites W2049475242 @default.
• W2215463534 cites W2050595677 @default.
• W2215463534 cites W2051564720 @default.
• W2215463534 cites W2053819163 @default.
• W2215463534 cites W2055720064 @default.
• W2215463534 cites W2057806291 @default.
• W2215463534 cites W2060555689 @default.
• W2215463534 cites W2061476669 @default.
• W2215463534 cites W2062065338 @default.
• W2215463534 cites W2067145794 @default.
• W2215463534 cites W2067174909 @default.
• W2215463534 cites W2073197460 @default.
• W2215463534 cites W2074660775 @default.
• W2215463534 cites W2077100489 @default.
• W2215463534 cites W2077246276 @default.
• W2215463534 cites W2078051106 @default.
• W2215463534 cites W2078508576 @default.
• W2215463534 cites W2079438618 @default.
• W2215463534 cites W2079954040 @default.
• W2215463534 cites W2081046982 @default.
• W2215463534 cites W2086817352 @default.
• W2215463534 cites W2087984168 @default.
• W2215463534 cites W2088417988 @default.
• W2215463534 cites W2093654118 @default.
• W2215463534 cites W2093887772 @default.
• W2215463534 cites W2096184392 @default.
• W2215463534 cites W2101136532 @default.
• W2215463534 cites W2101874060 @default.
• W2215463534 cites W2103488640 @default.
• W2215463534 cites W2106140689 @default.
• W2215463534 cites W2108511484 @default.
• W2215463534 cites W2112154906 @default.
• W2215463534 cites W2112957275 @default.
• W2215463534 cites W2115729502 @default.
• W2215463534 cites W2116413427 @default.
• W2215463534 cites W2119966574 @default.
• W2215463534 cites W2120339119 @default.
• W2215463534 cites W2128582252 @default.
• W2215463534 cites W2130479394 @default.
• W2215463534 cites W2131288855 @default.
• W2215463534 cites W2134216529 @default.
• W2215463534 cites W2136729627 @default.
• W2215463534 cites W2142225521 @default.
• W2215463534 cites W2145583354 @default.
• W2215463534 cites W2146942655 @default.
• W2215463534 cites W2149655632 @default.
• W2215463534 cites W2152576103 @default.
• W2215463534 cites W2154671795 @default.
• W2215463534 cites W2167905636 @default.
• W2215463534 cites W2170595734 @default.
• W2215463534 cites W2286580685 @default.
• W2215463534 cites W2313946562 @default.
• W2215463534 cites W2316421631 @default.

• next