Both experimental and theoretical structure determinations of RNAs have remained challenging due to the intrinsic dynamics of RNAs. We report here an integrated nuclear magnetic resonance/molecular dynamics (NMR/MD) structure determination approach to describe the dynamic structure of the CUUG tetraloop. We show that the tetraloop undergoes substantial dynamics, leading to averaging of the experimental data. These dynamics are particularly linked to the temperature-dependent presence of a...
[NMR paper] OCRE Domains of Splicing Factors RBM5 and RBM10: Tyrosine Ring Flip Frequencies by Integrated Use of 1H-NMR and Molecular Dynamics Simulations.
OCRE Domains of Splicing Factors RBM5 and RBM10: Tyrosine Ring Flip Frequencies by Integrated Use of 1H-NMR and Molecular Dynamics Simulations.
Related Articles OCRE Domains of Splicing Factors RBM5 and RBM10: Tyrosine Ring Flip Frequencies by Integrated Use of 1H-NMR and Molecular Dynamics Simulations.
Chembiochem. 2020 Sep 25;:
Authors: Martin BT, Malmstrom RD, Amaro RE, Wüthrich K
Abstract
* *The 55-residue OCRE domains of the splicing factors RBM5 and RBM10 contain 15 tyrosines in compact, globular folds. At 25?C all 15...
nmrlearner
Journal club
0
09-27-2020 05:47 AM
Identification of conformation-selective nanobodies against the membrane protein insertase BamA by an integrated structural biology approach
Identification of conformation-selective nanobodies against the membrane protein insertase BamA by an integrated structural biology approach
Abstract
The insertase BamA is an essential protein of the bacterial outer membrane. Its 16-stranded transmembrane β-barrel contains a lateral gate as a key functional element. This gate is formed by the C-terminal half of the last β-strand. The BamA barrel was previously found to sample different conformations in aqueous solution, as well as different gate-open, gate-closed, and collapsed conformations in...
nmrlearner
Journal club
0
05-09-2019 05:55 AM
[NMR paper] Protocol To Make Protein NMR Structures Amenable to Stable Long Time Scale Molecular Dynamics Simulations.
Protocol To Make Protein NMR Structures Amenable to Stable Long Time Scale Molecular Dynamics Simulations.
Related Articles Protocol To Make Protein NMR Structures Amenable to Stable Long Time Scale Molecular Dynamics Simulations.
J Chem Theory Comput. 2014 Apr 8;10(4):1781-7
Authors: Li DW, Brüschweiler R
Abstract
A robust protocol for the treatment of NMR protein structures is presented that makes them amenable to long time scale molecular dynamics (MD) simulations that are stable. The protocol embeds an NMR structure in a...
nmrlearner
Journal club
0
11-22-2015 01:36 AM
Integrated analysis of the conformation of a protein-linked spin label by crystallography, EPR and NMR spectroscopy
Integrated analysis of the conformation of a protein-linked spin label by crystallography, EPR and NMR spectroscopy
Abstract Long-range structural information derived from paramagnetic relaxation enhancement observed in the presence of a paramagnetic nitroxide radical is highly useful for structural characterization of globular, modular and intrinsically disordered proteins, as well as proteinâ??protein and protein-DNA complexes. Here we characterized the conformation of a spin-label attached to the homodimeric protein CylR2 using a combination of X-ray crystallography, electron...
nmrlearner
Journal club
0
01-31-2011 06:03 AM
Integrated analysis of the conformation of a protein-linked spin label by crystallography, EPR and NMR spectroscopy.
Integrated analysis of the conformation of a protein-linked spin label by crystallography, EPR and NMR spectroscopy.
Integrated analysis of the conformation of a protein-linked spin label by crystallography, EPR and NMR spectroscopy.
J Biomol NMR. 2011 Jan 28;
Authors: Gruene T, Cho MK, Karyagina I, Kim HY, Grosse C, Giller K, Zweckstetter M, Becker S
Long-range structural information derived from paramagnetic relaxation enhancement observed in the presence of a paramagnetic nitroxide radical is highly useful for structural characterization of...
nmrlearner
Journal club
0
01-29-2011 12:35 PM
[NMR paper] Extending the family of UNCG-like tetraloop motifs: NMR structure of a CACG tetraloop
Extending the family of UNCG-like tetraloop motifs: NMR structure of a CACG tetraloop from coxsackievirus B3.
Related Articles Extending the family of UNCG-like tetraloop motifs: NMR structure of a CACG tetraloop from coxsackievirus B3.
Biochemistry. 2003 Apr 22;42(15):4373-83
Authors: Du Z, Yu J, Andino R, James TL
Stable RNA tetraloop motifs are found frequently in biologically active RNAs. These motifs carry out a wide variety of functions in RNA folding, in RNA-RNA and RNA-protein interactions. A great deal of knowledge about the...
nmrlearner
Journal club
0
11-24-2010 09:01 PM
[NMR paper] Molecular dynamics-derived conformation and intramolecular interaction analysis of th
Molecular dynamics-derived conformation and intramolecular interaction analysis of the N-acetyl-9-O-acetylneuraminic acid-containing ganglioside GD1a and NMR-based analysis of its binding to a human polyclonal immunoglobulin G fraction with selectivity for O-acetylated sialic acids.
Related Articles Molecular dynamics-derived conformation and intramolecular interaction analysis of the N-acetyl-9-O-acetylneuraminic acid-containing ganglioside GD1a and NMR-based analysis of its binding to a human polyclonal immunoglobulin G fraction with selectivity for O-acetylated sialic acids.
...
nmrlearner
Journal club
0
08-22-2010 02:20 PM
[NMR paper] Conformation of parathyroid hormone antagonists by CD, NMR, and molecular dynamics si
Conformation of parathyroid hormone antagonists by CD, NMR, and molecular dynamics simulations.
Related Articles Conformation of parathyroid hormone antagonists by CD, NMR, and molecular dynamics simulations.
Biopolymers. 1995 Oct;36(4):485-95
Authors: Chorev M, Behar V, Yang Q, Rosenblatt M, Mammi S, Maretto S, Pellegrini M, Peggion E
The conformation of two highly potent parathyroid hormone (PTH) antagonists was investigated in water/2,2,2-trifluoroethanol mixtures. The two peptides are derived from the sequence (7-34) of PTH and of...
Integrated NMR/Molecular Dynamics Determination of the Ensemble Conformation of a Thermodynamically Stable CUUG RNA Tetraloop
Linear Mode
