Efficient localization of a native metal ion within a protein by Cu2+-based EPR distance measurements

2019 ◽  
Vol 21 (20) ◽  
pp. 10238-10243 ◽  
Author(s):  
Austin Gamble Jarvi ◽  
Timothy F. Cunningham ◽  
Sunil Saxena
Keyword(s):  
Binding Site ◽  
Long Range ◽  
Metal Binding ◽  
Metal Ion ◽  
Native Metal ◽  
Distance Measurements ◽  
Metal Binding Site ◽  
Paramagnetic Metal

A native paramagnetic metal binding site in a protein is located with less than 2 Å resolution by a combination of double histidine (dHis) based Cu2+ labeling and long range distance measurements by EPR.

scholarly journals Detailed Insight into the Interaction of Bicyclic Somatostatin Analogue with Cu(II) Ions

2020 ◽  
Vol 21 (22) ◽  
pp. 8794
Author(s):  
Aleksandra Marciniak ◽  
Weronika Witak ◽  
Giuseppina Sabatino ◽  
Anna Maria Papini ◽  
Justyna Brasuń
Keyword(s):  
Binding Site ◽  
Disulfide Bond ◽  
Metal Binding ◽  
Metal Ion ◽  
Magnetic Circular Dichroism ◽  
Intramolecular Interaction ◽  
Peptide Receptor Radionuclide Therapy ◽  
Somatostatin Analogue ◽  
Receptor Binding Site ◽  
Metal Binding Site

Somatostatin analogues are useful pharmaceuticals in peptide receptor radionuclide therapy. In previous studies, we analyzed a new bicyclic somatostatin analogue (BCS) in connection with Cu(II) ions. Two characteristic sites were present in the peptide chain: the receptor- and the metal-binding site. We have already shown that this ligand can form very stable imidazole complexes with the metal ion. In this work, our aim was to characterize the intramolecular interaction that occurs in the peptide molecule. Therefore, we analyzed the coordination abilities of two cyclic ligands, i.e., P1 only with the metal binding site and P2 with both sites, but without the disulfide bond. Furthermore, we used magnetic circular dichroism (MCD) spectroscopy to better understand the coordination process. We applied this method to analyze spectra of P1, P2, and BCS, which we have described previously. Additionally, we analyzed the MCD spectra of P3 ligand, which has only the receptor binding site in its structure. We have unequivocally shown that the presence of the Phe-Trp-Lys-Thr motif and the disulfide bond significantly increases the metal binding efficiency.

scholarly journals Hybrid QM/MM Simulations Confirm Zn(II) Coordination Sphere That Includes Four Cysteines from the P2 × 4R Head Domain

2021 ◽  
Vol 22 (14) ◽  
pp. 7288
Author(s):  
Francisco Andrés Peralta ◽  
J. Pablo Huidobro-Toro ◽  
Raúl Mera-Adasme
Keyword(s):  
Binding Site ◽  
Coordination Sphere ◽  
Metal Binding ◽  
Metal Ion ◽  
Dynamic Simulations ◽  
Metal Binding Site ◽  
Head Domain ◽  
Water Ligands ◽  
Role Of Zn

To ascertain the role of Zn(II) as an allosteric modulator on P2X4R, QM/MM molecular dynamic simulations were performed on the WT and two P2X4R mutants suggested by previous electrophysiological data to affect Zn(II) binding. The Gibbs free energy for the reduction of the putative P2X4R Zn(II) binding site by glutathione was estimated at −22 kcal/mol. Simulations of the WT P2X4R head domain revealed a flexible coordination sphere dominated by an octahedral geometry encompassing C126, N127, C132, C149, C159 and a water molecule. The C132A mutation disrupted the metal binding site, leading to a coordination sphere with a majority of water ligands, and a displacement of the metal ion towards the solvent. The C132A/C159A mutant exhibited a tendency towards WT-like stability by incorporating the R148 backbone to the coordination sphere. Thus, the computational findings agree with previous experimental data showing Zn(II) modulation for the WT and C132A/C159A variants, but not for the C132A mutant. The results provide molecular insights into the nature of the Zn(II) modulation in P2X4R, and the effect of the C132A and C132A/C159A mutations, accounting for an elusive modulation mechanism possibly occurring in other extracellular or membrane protein.

Structural analysis and insight into metal-ion activation of the iron-dependent regulator fromThermoplasma acidophilum

2014 ◽  
Vol 70 (5) ◽  
pp. 1281-1288 ◽  
Author(s):  
Hyun Ku Yeo ◽  
Young Woo Park ◽  
Jae Young Lee
Keyword(s):  
Binding Site ◽  
Metal Binding ◽  
Metal Ion ◽  
Ion Homeostasis ◽  
Binding Property ◽  
Metal Ion Binding ◽  
Mobility Shift ◽  
Iron Cluster ◽  
Metal Binding Site ◽  
Metal Ion Homeostasis

The iron-dependent regulator (IdeR) is a metal ion-activated transcriptional repressor that regulates the expression of genes encoding proteins involved in iron uptake to maintain metal-ion homeostasis. IdeR is a functional homologue of the diphtheria toxin repressor (DtxR), and both belong to the DtxR/MntR family of metalloregulators. The structure of Fe2+-bound IdeR (TA0872) fromThemoplasma acidophilumwas determined at 2.1 Å resolution by X-ray crystallography using single-wavelength anomalous diffraction. The presence of Fe2+, which is the true biological activator of IdeR, in the metal-binding site was ascertained by the use of anomalous difference electron-density maps using diffraction data collected at the Fe absorption edge. Each DtxR/IdeR subunit contains two metal ion-binding sites separated by 9 Å, labelled the primary and ancillary sites, whereas the crystal structures of IdeR fromT. acidophilumshow a binuclear iron cluster separated by 3.2 Å, which is novel toT. acidophilumIdeR. The metal-binding site analogous to the primary site in DtxR was unoccupied, and the ancillary site was occupied by binuclear clustered ions. This difference suggests thatT. acidophilumIdeR and its closely related homologues are regulated by a mechanism distinct from that of either DtxR or MntR.T. acidophilumIdeR was also shown to have a metal-dependent DNA-binding property by electrophoretic mobility shift assay.

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