Faculty Opinions recommendation of RNA helical packing in solution: NMR structure of a 30 kDa GAAA tetraloop-receptor complex.

Author(s):  
Eric Westhof
2005 ◽  
Vol 351 (2) ◽  
pp. 371-382 ◽  
Author(s):  
Jared H. Davis ◽  
Marco Tonelli ◽  
Lincoln G. Scott ◽  
Luc Jaeger ◽  
James R. Williamson ◽  
...  

2006 ◽  
Vol 360 (3) ◽  
pp. 742 ◽  
Author(s):  
Jared H. Davis ◽  
Marco Tonelli ◽  
Lincoln G. Scott ◽  
Luc Jaeger ◽  
James R. Williamson ◽  
...  

2021 ◽  
pp. 166977
Author(s):  
Colleen Kelly ◽  
Nicola Pace ◽  
Matthew Gage ◽  
Mark Pfuhl

2012 ◽  
Vol 287 (45) ◽  
pp. 38231-38243 ◽  
Author(s):  
Hannah V. McCue ◽  
Pryank Patel ◽  
Andrew P. Herbert ◽  
Lu-Yun Lian ◽  
Robert D. Burgoyne ◽  
...  

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5412 ◽  
Author(s):  
Jesper S. Oeemig ◽  
O.H. Samuli Ollila ◽  
Hideo Iwaï

The TonB protein plays an essential role in the energy transduction system to drive active transport across the outer membrane (OM) using the proton-motive force of the cytoplasmic membrane of Gram-negative bacteria. The C-terminal domain (CTD) of TonB protein is known to interact with the conserved TonB box motif of TonB-dependent OM transporters, which likely induces structural changes in the OM transporters. Several distinct conformations of differently dissected CTDs of Escherichia coli TonB have been previously reported. Here we determined the solution NMR structure of a 96-residue fragment of Pseudomonas aeruginosa TonB (PaTonB-96). The structure shows a monomeric structure with the flexible C-terminal region (residues 338–342), different from the NMR structure of E. coli TonB (EcTonB-137). The extended and flexible C-terminal residues are confirmed by 15N relaxation analysis and molecular dynamics simulation. We created models for the PaTonB-96/TonB box interaction and propose that the internal fluctuations of PaTonB-96 makes it more accessible for the interactions with the TonB box and possibly plays a role in disrupting the plug domain of the TonB-dependent OM transporters.


2008 ◽  
Vol 17 (2) ◽  
pp. 205-215 ◽  
Author(s):  
Matthew Devany ◽  
Ferdinand Kappes ◽  
Kuan-Ming Chen ◽  
David M. Markovitz ◽  
Hiroshi Matsuo

2020 ◽  
Vol 48 (6) ◽  
pp. 3315-3327 ◽  
Author(s):  
Arijit Maity ◽  
Fernaldo Richtia Winnerdy ◽  
Weili Denyse Chang ◽  
Gang Chen ◽  
Anh Tuân Phan

Abstract G-rich DNA sequences with tracts of three or more continuous guanines (G≥3) are known to have high propensity to adopt stable G-quadruplex (G4) structures. Bioinformatic analyses suggest high prevalence of G-rich sequences with short G-tracts (G≤2) in the human genome. However, due to limited structural studies, the folding principles of such sequences remain largely unexplored and hence poorly understood. Here, we present the solution NMR structure of a sequence named AT26 consisting of irregularly spaced G2 tracts and two isolated single guanines. The structure is a four-layered G4 featuring two bi-layered blocks, locked between themselves in an unprecedented fashion making it a stable scaffold. In addition to edgewise and propeller-type loops, AT26 also harbors two V-shaped loops: a 2-nt V-shaped loop spanning two G-tetrad layers and a 0-nt V-shaped loop spanning three G-tetrad layers, which are named as VS- and VR-loop respectively, based on their distinct structural features. The intra-lock motif can be a basis for extending the G-tetrad core and a very stable intra-locked G4 can be formed by a sequence with G-tracts of various lengths including several G2 tracts. Findings from this study will aid in understanding the folding of G4 topologies from sequences containing irregularly spaced multiple short G-tracts.


2017 ◽  
Vol 114 (28) ◽  
pp. E5645-E5654 ◽  
Author(s):  
Alfonso Blázquez-Moreno ◽  
Soohyung Park ◽  
Wonpil Im ◽  
Melissa J. Call ◽  
Matthew E. Call ◽  
...  

Many activating immunoreceptors associate with signaling adaptor molecules like FcεR1γ or CD247. FcεR1γ and CD247 share high sequence homology and form disulphide-linked homodimers that contain a pair of acidic aspartic acid residues in their transmembrane (TM) domains that mediate assembly, via interaction with an arginine residue at a similar register to these aspartic acids, with the activating immunoreceptors. However, this model cannot hold true for receptors like CD16A, whose TM domains do not contain basic residues. We have carried out an extensive site-directed mutagenesis analysis of the CD16A receptor complex and now report that the association of receptor with the signaling adaptor depends on a network of polar and aromatic residues along the length of the TM domain. Molecular modeling indicates that CD16A TM residues F202, D205, and T206 form the core of the membrane-embedded trimeric interface by establishing highly favorable contacts to the signaling modules through rearrangement of a hydrogen bond network previously identified in the CD247 TM dimer solution NMR structure. Strikingly, the amino acid D205 also regulates the turnover and surface expression of CD16A in the absence of FcεR1γ or CD247. Modeling studies indicate that similar features underlie the association of other activating immune receptors, including CD64 and FcεR1α, with signaling adaptor molecules, and we confirm experimentally that equivalent F, D, and T residues in the TM domain of FcεR1α markedly influence the biology of this receptor and its association with FcεR1γ.


Biochemistry ◽  
2014 ◽  
Vol 53 (19) ◽  
pp. 3106-3117 ◽  
Author(s):  
Petrus G. M. Gutte ◽  
Simon Jurt ◽  
Markus G. Grütter ◽  
Oliver Zerbe

2005 ◽  
Vol 280 (12) ◽  
pp. 11340-11346 ◽  
Author(s):  
Hiroyuki Takashima ◽  
Takuya Yoshida ◽  
Tetsuya Ishino ◽  
Katsumi Hasuda ◽  
Tadayasu Ohkubo ◽  
...  

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