protein cavity
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2021 ◽  
Vol 188 ◽  
pp. 109195
Author(s):  
Luiza de Carvalho Bertozo ◽  
Martyna Maszota-Zieleniak ◽  
Maytê Bolean ◽  
Pietro Ciancaglini ◽  
Sergey A. Samsonov ◽  
...  

2021 ◽  
Author(s):  
Martina Cirulli ◽  
Enrico Salvadori ◽  
Zhi-Hui Zhang ◽  
Michael Dommett ◽  
Floriana Tuna ◽  
...  

Mechanically chelating ligands have untapped potential for the engineering of metal ion properties by providing reliable control of the number, nature and geometry of donor atoms, akin to how a protein cavity controls the properties of bound metal ions. Here we demonstrate this principle in the context of Co<sup>II</sup>-based single-ion magnets. Using multi-frequency EPR, susceptibility and magnetization measurements we found that these complexes show some of the highest zero field splittings reported for five-coordinate Co<sup>II</sup> complexes to date. The predictable coordination behavior of the interlocked ligands allowed the magnetic properties of their Co<sup>II</sup> complexes to be evaluated computationally <i>a priori </i>and our combined experimental and theoretical approach enabled us to rationalize the observed trends. The predictable magnetic behavior of the rotaxane Co<sup>II</sup> complexes demonstrates that interlocked ligands offer a new strategy to design metal complexes with interesting functionality.


2021 ◽  
Author(s):  
Martina Cirulli ◽  
Enrico Salvadori ◽  
Zhi-Hui Zhang ◽  
Michael Dommett ◽  
Floriana Tuna ◽  
...  

Mechanically chelating ligands have untapped potential for the engineering of metal ion properties by providing reliable control of the number, nature and geometry of donor atoms, akin to how a protein cavity controls the properties of bound metal ions. Here we demonstrate this principle in the context of Co<sup>II</sup>-based single-ion magnets. Using multi-frequency EPR, susceptibility and magnetization measurements we found that these complexes show some of the highest zero field splittings reported for five-coordinate Co<sup>II</sup> complexes to date. The predictable coordination behavior of the interlocked ligands allowed the magnetic properties of their Co<sup>II</sup> complexes to be evaluated computationally <i>a priori </i>and our combined experimental and theoretical approach enabled us to rationalize the observed trends. The predictable magnetic behavior of the rotaxane Co<sup>II</sup> complexes demonstrates that interlocked ligands offer a new strategy to design metal complexes with interesting functionality.


Membranes ◽  
2020 ◽  
Vol 10 (11) ◽  
pp. 357
Author(s):  
Daria Melnikova ◽  
Ivan Bogdanov ◽  
Tatiana Ovchinnikova ◽  
Ekaterina Finkina

It is known that plant lipid transfer proteins (LTPs) bind a broad spectrum of ligands including fatty acids (FAs), phospho- and glycolipids, acyl-coenzyme A and secondary metabolites. In this work, we used protein−lipid overlay assays to identify new putative LTP ligands. In our experiments, the lentil lipid transfer protein Lc-LTP2 as well as LTPs from other plants were shown to bind phosphatidylinositol (4,5)-bisphosphate (PI(4,5)P2). Molecular modeling, 2-p-toluidinonaphthalene-6-sulphonate (TNS) displacement and liposome leakage experiments with Lc-LTP2 and its mutant analogs (R45A, Y80A, R45A/Y80A) were performed to investigate interactions between the protein and PI(4,5)P2. It was shown that PI(4,5)P2 initially interacted with the “bottom” entrance of the protein cavity and after complex formation the large polar head of this ligand was also oriented towards the same entrance. We also found that two highly conserved residues in plant LTPs, Arg45 and Tyr80, played an important role in protein-ligand interactions. Apparently, Arg45 is a key residue for interaction with PI(4,5)P2 during both initial contacting and holding in the protein cavity, while Tyr80 is probably a key amino acid playing an essential role in Lc-LTP2 docking to the membrane. Thus, we assumed that the ability of Lc-LTP2 to bind PI(4,5)P2 suggests the involvement of this protein in plant signal transduction.


PLoS ONE ◽  
2019 ◽  
Vol 14 (10) ◽  
pp. e0223596 ◽  
Author(s):  
Sérgio Dias ◽  
Tiago Simões ◽  
Francisco Fernandes ◽  
Ana Mafalda Martins ◽  
Alfredo Ferreira ◽  
...  

2019 ◽  
Author(s):  
T Xiao ◽  
Y Lu ◽  
J Fan ◽  
D Yang

AbstractFatty acid binding proteins (FABPs) play an important role in transportation of fatty acids. Despite intensive studies, how fatty acids enter the protein cavity for binding is still controversial. Here, a gap-closed variant of human intestinal FABP was generated by mutagenesis, in which the gap is locked by a disulfide bridge. According to its structure determined here by NMR, this variant has no obvious openings as the ligand entrance and the gap cannot be widened by internal dynamics. Nevertheless, it still uptakes fatty acids and other ligands. NMR relaxation dispersion, chemical exchange saturation transfer and hydrogen-deuterium exchange experiments show that the variant exists in a major native state, two minor native-like state, and two locally unfolded states in aqueous solution. Local unfolding of either βB–βD or helix 2 can generate an opening large enough for ligands to enter the protein cavity, but only the fast local unfolding of helix 2 is relevant to the ligand entry process.Statement of SignificanceFatty acid binding proteins transport fatty acids to specific organelles in the cell. To enable the transport, fatty acids must enter and leave the protein cavity. In spite of many studies, how fatty acids enter the protein cavity remains controversial. Using mutagenesis and biophysical techniques, we have resolved the disagreement and further showed that local unfolding of the second helix can generate a transient opening to allow ligands to enter the protein cavity. Since lipid binding proteins are highly conserved in 3D structures and ligand binding, all of them may use the same local unfolding mechanism for ligand uptake and release.


2018 ◽  
Vol 20 (48) ◽  
pp. 30159-30173 ◽  
Author(s):  
Partha Pratim Roy ◽  
Youshitoka Kato ◽  
Rei Abe-Yoshizumi ◽  
Elisa Pieri ◽  
Nicolas Ferré ◽  
...  

Photoinduced vibrational dynamics between two stereoisomers of the retinal chromophore bound inside the same protein cavity has been explored.


2016 ◽  
Vol 27 (8) ◽  
pp. 1872-1879 ◽  
Author(s):  
Yan-Syun Zeng ◽  
Ruo-Cing Gao ◽  
Ting-Wei Wu ◽  
Chien Cho ◽  
Kui-Thong Tan

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