scholarly journals Solution NMR structure of the SH3 domain of human nephrocystin and analysis of a mutation-causing juvenile nephronophthisis

2005 ◽  
Vol 59 (2) ◽  
pp. 347-355 ◽  
Author(s):  
Albane le Maire ◽  
Thomas Weber ◽  
Sophie Saunier ◽  
Isabelle Broutin ◽  
Corinne Antignac ◽  
...  
Keyword(s):  
Sh3 Domain ◽  
Nmr Structure ◽  
Solution Nmr ◽  
Juvenile Nephronophthisis

scholarly journals Solution NMR Structure of the SH3 Domain of Human Caskin1 Validates the Lack of a Typical Peptide Binding Groove and Supports a Role in Lipid Mediator Binding

Cells ◽  
2021 ◽  
Vol 10 (1) ◽  
pp. 173
Author(s):  
Orsolya Tőke ◽  
Kitti Koprivanacz ◽  
László Radnai ◽  
Balázs Merő ◽  
Tünde Juhász ◽  
...  
Keyword(s):  
Specific Binding ◽  
Sh3 Domain ◽  
Nmr Structure ◽  
Solution Nmr ◽  
Lipid Mediator ◽  
Neural Function ◽  
Cortical Actin ◽  
Sh3 Domains ◽  
Aromatic Residues ◽  
Binding Groove

SH3 domains constitute an important class of protein modules involved in a variety of cellular functions. They participate in protein-protein interactions via their canonical ligand binding interfaces composed of several evolutionarily conserved aromatic residues forming binding grooves for typical (PxxP) and atypical (PxxxPR, RxxK, RKxxY) binding motifs. The calcium/calmodulin-dependent serine protein kinase (CASK)-interacting protein 1, or Caskin1, a multidomain scaffold protein regulating the cortical actin filaments, is enriched in neural synapses in mammals. Based on its known interaction partners and knock-out animal studies, Caskin1 may play various roles in neural function and it is thought to participate in several pathological processes of the brain. Caskin1 has a single, atypical SH3 domain in which key aromatic residues are missing from the canonical binding groove. No protein interacting partner for this SH3 domain has been identified yet. Nevertheless, we have recently demonstrated the specific binding of this SH3 domain to the signaling lipid mediator lysophospatidic acid (LPA) in vitro. Here we report the solution NMR structure of the human Caskin1 SH3 domain and analyze its structural features in comparison with other SH3 domains exemplifying different strategies in target selectivity. The key differences revealed by our structural study show that the canonical binding groove found in typical SH3 domains accommodating proline-rich motifs is missing in Caskin1 SH3, most likely excluding a bona fide protein target for the domain. The LPA binding site is distinct from the altered protein binding groove. We conclude that the SH3 domain of Caskin1 might mediate the association of Caskin1 with membrane surfaces with locally elevated LPA content.

Solution NMR structure and ligand identification of human Gas7 SH3 domain reveal a typical SH3 fold but a non-canonical ligand-binding mode

2019 ◽  
Vol 516 (4) ◽  
pp. 1190-1195
Author(s):  
Yao Nie ◽  
Jiang Zhu ◽  
Theresa A. Ramelot ◽  
Michael A. Kennedy ◽  
Maili Liu ◽  
...  
Keyword(s):  
Ligand Binding ◽  
Binding Mode ◽  
Sh3 Domain ◽  
Nmr Structure ◽  
Solution Nmr ◽  
Ligand Identification

Solution NMR structure of titin N2A region Ig domain I83 and its interaction with metal ions

2021 ◽  
pp. 166977
Author(s):  
Colleen Kelly ◽  
Nicola Pace ◽  
Matthew Gage ◽  
Mark Pfuhl
Keyword(s):  
Metal Ions ◽  
Nmr Structure ◽  
Solution Nmr ◽  
Ig Domain

scholarly journals Solution NMR Structure of the Ca2+-bound N-terminal Domain of CaBP7

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

scholarly journals NMR structure of the C-terminal domain of TonB protein from Pseudomonas aeruginosa

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5412 ◽  
Author(s):  
Jesper S. Oeemig ◽  
O.H. Samuli Ollila ◽  
Hideo Iwaï
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Structural Changes ◽  
Nmr Structure ◽  
Dynamics Simulation ◽  
Solution Nmr ◽  
Gram Negative Bacteria ◽  
E Coli ◽  
Terminal Domain ◽  
Tonb Protein ◽  
Monomeric Structure

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.

scholarly journals Solution NMR structure of the N-terminal domain of the human DEK protein

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

scholarly journals Intra-locked G-quadruplex structures formed by irregular DNA G-rich motifs

2020 ◽  
Vol 48 (6) ◽  
pp. 3315-3327 ◽  
Author(s):  
Arijit Maity ◽  
Fernaldo Richtia Winnerdy ◽  
Weili Denyse Chang ◽  
Gang Chen ◽  
Anh Tuân Phan
Keyword(s):  
Human Genome ◽  
Dna Sequences ◽  
Structural Features ◽  
Nmr Structure ◽  
Solution Nmr ◽  
Structural Studies ◽  
High Propensity ◽  
G Quadruplex ◽  
High Prevalence

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.

scholarly journals Unusual Structural Features Revealed by the Solution NMR Structure of the NLRC5 Caspase Recruitment Domain

Biochemistry ◽  
2014 ◽  
Vol 53 (19) ◽  
pp. 3106-3117 ◽  
Author(s):  
Petrus G. M. Gutte ◽  
Simon Jurt ◽  
Markus G. Grütter ◽  
Oliver Zerbe
Keyword(s):  
Structural Features ◽  
Nmr Structure ◽  
Solution Nmr ◽  
Caspase Recruitment Domain

scholarly journals Solution NMR Structure Investigation for Releasing Mechanism of Neocarzinostatin Chromophore from the Holoprotein

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