203 related articles for article (PubMed ID: 26051557)
1. Kissing loop interaction in adenine riboswitch: insights from umbrella sampling simulations.
Di Palma F; Bottaro S; Bussi G
BMC Bioinformatics; 2015; 16 Suppl 9(Suppl 9):S6. PubMed ID: 26051557
[TBL] [Abstract][Full Text] [Related]
2. Loop-loop interaction in an adenine-sensing riboswitch: a molecular dynamics study.
Allnér O; Nilsson L; Villa A
RNA; 2013 Jul; 19(7):916-26. PubMed ID: 23716711
[TBL] [Abstract][Full Text] [Related]
3. Using reweighted pulling simulations to characterize conformational changes in riboswitches.
Di Palma F; Colizzi F; Bussi G
Methods Enzymol; 2015; 553():139-62. PubMed ID: 25726464
[TBL] [Abstract][Full Text] [Related]
4. Molecular dynamics simulation of the binding process of ligands to the add adenine riboswitch aptamer.
Bao L; Wang J; Xiao Y
Phys Rev E; 2019 Aug; 100(2-1):022412. PubMed ID: 31574664
[TBL] [Abstract][Full Text] [Related]
5. Ligand-induced stabilization of the aptamer terminal helix in the add adenine riboswitch.
Di Palma F; Colizzi F; Bussi G
RNA; 2013 Nov; 19(11):1517-24. PubMed ID: 24051105
[TBL] [Abstract][Full Text] [Related]
6. Role of the adenine ligand on the stabilization of the secondary and tertiary interactions in the adenine riboswitch.
Priyakumar UD; MacKerell AD
J Mol Biol; 2010 Mar; 396(5):1422-38. PubMed ID: 20026131
[TBL] [Abstract][Full Text] [Related]
7. A kissing loop is important for btuB riboswitch ligand sensing and regulatory control.
Lussier A; Bastet L; Chauvier A; Lafontaine DA
J Biol Chem; 2015 Oct; 290(44):26739-51. PubMed ID: 26370077
[TBL] [Abstract][Full Text] [Related]
8. Thermal adaptation of structural dynamics and regulatory function of adenine riboswitch.
Wu L; Liu Z; Liu Y
RNA Biol; 2021 Nov; 18(11):2007-2015. PubMed ID: 33573442
[TBL] [Abstract][Full Text] [Related]
9. Ligand-modulated folding of the full-length adenine riboswitch probed by NMR and single-molecule FRET spectroscopy.
Warhaut S; Mertinkus KR; Höllthaler P; Fürtig B; Heilemann M; Hengesbach M; Schwalbe H
Nucleic Acids Res; 2017 May; 45(9):5512-5522. PubMed ID: 28204648
[TBL] [Abstract][Full Text] [Related]
10. Ligand-Induced Stabilization of a Duplex-like Architecture Is Crucial for the Switching Mechanism of the SAM-III Riboswitch.
Suresh G; Srinivasan H; Nanda S; Priyakumar UD
Biochemistry; 2016 Jun; 55(24):3349-60. PubMed ID: 27249101
[TBL] [Abstract][Full Text] [Related]
11. Ligand Selectivity Mechanism and Conformational Changes in Guanine Riboswitch by Molecular Dynamics Simulations and Free Energy Calculations.
Hu G; Ma A; Wang J
J Chem Inf Model; 2017 Apr; 57(4):918-928. PubMed ID: 28345904
[TBL] [Abstract][Full Text] [Related]
12. Approach to the unfolding and folding dynamics of add A-riboswitch upon adenine dissociation using a coarse-grained elastic network model.
Li C; Lv D; Zhang L; Yang F; Wang C; Su J; Zhang Y
J Chem Phys; 2016 Jul; 145(1):014104. PubMed ID: 27394096
[TBL] [Abstract][Full Text] [Related]
13. Atomic-scale characterization of conformational changes in the preQ₁ riboswitch aptamer upon ligand binding.
Petrone PM; Dewhurst J; Tommasi R; Whitehead L; Pomerantz AK
J Mol Graph Model; 2011 Sep; 30():179-85. PubMed ID: 21831681
[TBL] [Abstract][Full Text] [Related]
14. Ligand Binding Mechanism and Its Relationship with Conformational Changes in Adenine Riboswitch.
Hu G; Li H; Xu S; Wang J
Int J Mol Sci; 2020 Mar; 21(6):. PubMed ID: 32168940
[TBL] [Abstract][Full Text] [Related]
15. Single-molecule conformational dynamics of a biologically functional hydroxocobalamin riboswitch.
Holmstrom ED; Polaski JT; Batey RT; Nesbitt DJ
J Am Chem Soc; 2014 Dec; 136(48):16832-43. PubMed ID: 25325398
[TBL] [Abstract][Full Text] [Related]
16. Molecular mechanism for preQ1-II riboswitch function revealed by molecular dynamics.
Aytenfisu AH; Liberman JA; Wedekind JE; Mathews DH
RNA; 2015 Nov; 21(11):1898-907. PubMed ID: 26370581
[TBL] [Abstract][Full Text] [Related]
17. Conformational Ensemble of
Ma B; Bai G; Nussinov R; Ding J; Wang YX
J Phys Chem B; 2021 Mar; 125(10):2589-2596. PubMed ID: 33683130
[TBL] [Abstract][Full Text] [Related]
18. Comparative study between transcriptionally- and translationally-acting adenine riboswitches reveals key differences in riboswitch regulatory mechanisms.
Lemay JF; Desnoyers G; Blouin S; Heppell B; Bastet L; St-Pierre P; Massé E; Lafontaine DA
PLoS Genet; 2011 Jan; 7(1):e1001278. PubMed ID: 21283784
[TBL] [Abstract][Full Text] [Related]
19. Exploring the Binding Process of Cognate Ligand to Add Adenine Riboswitch Aptamer by Using Explicit Solvent Molecular Dynamics (MD) Simulation.
Bao L; Xiao Y
Methods Mol Biol; 2023; 2568():103-122. PubMed ID: 36227564
[TBL] [Abstract][Full Text] [Related]
20. MD simulations of ligand-bound and ligand-free aptamer: molecular level insights into the binding and switching mechanism of the add A-riboswitch.
Sharma M; Bulusu G; Mitra A
RNA; 2009 Sep; 15(9):1673-92. PubMed ID: 19625387
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]