Isotropically shifted NMR resonances for the proximal histidyl imidazole NH protons in cobalt hemoglobin and iron-cobalt hybrid hemoglobins. Binding of the proximal histidine toward porphyrin metal ion in the intermediate state of cooperative ligand binding

Biochemistry ◽  
1983 ◽  
Vol 22 (12) ◽  
pp. 2904-2907 ◽  
Author(s):  
Toshiro Inubushi ◽  
Masao Ikeda-Saito ◽  
Takeshi Yonetani
2009 ◽  
Vol 87 (10) ◽  
pp. 1480-1484 ◽  
Author(s):  
Jian Li ◽  
Charles. H. Reynolds

Linear-scaling quantum mechanical method was applied to calculate binding affinities of six stromelysin-1 (MMP-3) inhibitors with two different zinc binding groups (ZBGs). The entire protein and ligand–protein complexes were calculated using PM5 Hamiltonian, which enables the treatment of metal ion coordination, bond forming/breaking, and proton/charge transfers associated with the ligand binding process by the self-consistent field method. The calculated binding energies reproduce the binding-affinity trend observed experimentally.


2006 ◽  
Vol 393 (3) ◽  
pp. 749-755 ◽  
Author(s):  
Takuma Shiraki ◽  
Takashi S. Kodama ◽  
Sayaka Shiki ◽  
Tatsuo Nakagawa ◽  
Hisato Jingami

PPARγ (peroxisome proliferator-activated receptor γ) is a nuclear receptor that is activated by natural lipid metabolites, including 15d-PGJ2 (15-deoxy-Δ12,14-prostaglandin J2). We previously reported that several oxidized lipid metabolites covalently bind to PPARγ through a Michael-addition to activate transcription. To separate the ligand-entering (dock) and covalent-binding (lock) steps in PPARγ activation, we investigated the binding kinetics of 15d-PGJ2 to the PPARγ LBD (ligand-binding domain) by stopped-flow spectroscopy. We analysed the spectral changes of 15d-PGJ2 by multi-wavelength global fitting based on a two-step chemical reaction model, in which an intermediate state represents the 15d-PGJ2–PPARγ complex without covalent binding. The extracted spectrum of the intermediate state in wild-type PPARγ was quite similar to the observed spectrum of 15d-PGJ2 in the C285S mutant, which cannot be activated by 15d-PGJ2, indicating that the complex remains in the inactive, intermediate state in the mutant. Thus ‘lock’ rather than ‘dock’ is one of the critical steps in PPARγ activation by 15d-PGJ2.


2019 ◽  
Vol 20 (S3) ◽  
Author(s):  
Shan Wang ◽  
Xiuzhen Hu ◽  
Zhenxing Feng ◽  
Xiaojin Zhang ◽  
Liu Liu ◽  
...  

Abstract Background In many important life activities, the execution of protein function depends on the interaction between proteins and ligands. As an important protein binding ligand, the identification of the binding site of the ion ligands plays an important role in the study of the protein function. Results In this study, four acid radical ion ligands (NO2−,CO32−,SO42−,PO43−) and ten metal ion ligands (Zn2+,Cu2+,Fe2+,Fe3+,Ca2+,Mg2+,Mn2+,Na+,K+,Co2+) are selected as the research object, and the Sequential minimal optimization (SMO) algorithm based on sequence information was proposed, better prediction results were obtained by 5-fold cross validation. Conclusions An efficient method for predicting ion ligand binding sites was presented.


Blood ◽  
2006 ◽  
Vol 108 (11) ◽  
pp. 143-143
Author(s):  
Marketa Jirouskova ◽  
Marta Murcia ◽  
JiHong Li ◽  
Marta Filizola ◽  
Barry S. Coller

Abstract The role of the β3 MIDAS in αIIbβ3 ligand binding is well established, but the role of the nearby ADMIDAS is less well defined. Thus, we studied HEK293 cells expressing normal αIIbβ3 (normal cells) or the ADMIDAS mutants β3 D126A and D127A (mutant cells). Both mutant cells adhered as well or better than normal cells to immobilized fibrinogen under static conditions in the presence of either Ca2+/Mg2+ or Mn2+. Under low shear flow conditions (0.15 dyne/cm2), adhesion of normal cells and D126A mutant cells to fibrinogen was similar in the presence of either Ca2+/Mg2+ or Mn2+. Adherent D126A mutant cells, however, demonstrated greater resistance to detachment at increasing shear rates in the presence of Ca2+/Mg2+ (e.g., at 20.4 dynes/cm2, only 40 ± 10% of normal cells remained vs 85 ± 8% of D126A mutant cells; mean ± SD; p<0.001). Substituting Mn2+ for Ca2+/Mg2+ increased the resistance to detachment of the normal cells (60 ± 20% remaining at 20.4 dynes/cm2; p=0.01), but the value was still less than the mutant cells in the presence of either Ca2+/Mg2+ (see above; p<0.01) or Mn2+ (84 ± 4%; p<0.01). The increased strength of adhesion we observed in the αIIbβ3 ADMIDAS mutant cells is similar to that found in α4β7 ADMIDAS mutant cells (Chen et al, JBC 2004) and is consistent with the findings in isolated β3 βA (I-like) domains (Pesho et al. JBC 2006). The binding of 7E3, whose epitope is near the ADMIDAS, to the D126 mutant cells was similar to its binding to the normal cells, but 7E3 binding to the D127A mutant cells was reduced by 89 ± 7% (n = 4; p<0.001). 7E3 decreased adhesion of normal cells to fibrinogen by 88 ± 4%, but it only decreased adhesion of D126A mutant cells by 3 ± 9%, and it did not inhibit adhesion of D127A cells at all. To provide a structural context for the role of the ADMIDAS in ligand binding to αIIbβ3, we compared results from nanosecond time-scale molecular dynamics (MD) simulations of the cyclic peptide ligand eptifibatide in complex with either the fully hydrated normal αIIbβ3 or the D126A mutant in the presence of Ca2+/Mg2+. Calculations were carried out using the OPLS all-atom force-field of the GROMACS simulation package. With respect to normal αIIbβ3, the mutant receptor demonstrated reduced fluctuations in the β3 207–210 and 335 regions and increased fluctuations in the β3 282–284 region. In addition, the ADMIDAS metal ion moved ~3 Å away from the MIDAS and became more solvent exposed. Rearrangements of the coordination of the ADMIDAS involving S123, D251, and D127 were also observed in the D126A mutant compared to normal αIIbβ3. Steered MD simulations were used to investigate the unbinding of eptifibatide from its binding site. The unbinding force for the D126A mutant was similar to that for the normal αIIbβ3. Quantitative estimations of the binding energies of eptifibatide to normal and D126A mutant αIIbβ3 from Molecular Mechanics/Poisson Boltzman Surface Area analysis of the MD trajectories also yielded similar results. Thus, the much greater resistance of D126A mutant cells to detachment from fibrinogen at increasing shear rates does not appear to be explained by differences in fibrinogen-αIIbβ3 interactions at the sites involved in the binding of eptifibatide. Potential alternative mechanisms involve differences in fibrinogen’s access to the binding site, interactions with other sites, or changes in fibrinogen avidity due to receptor clustering.


Blood ◽  
2011 ◽  
Vol 118 (21) ◽  
pp. 3255-3255
Author(s):  
Jieqing Zhu ◽  
Won-Seok Choi ◽  
Joshua G. McCoy ◽  
Ana Negri ◽  
Jianghai Zhu ◽  
...  

Abstract Abstract 3255 The platelet αIIbβ3 integrin receptor plays a central role in hemostasis and thrombosis. Small molecule inhibitors of αIIbβ3 based on the RGD cell recognition sequence block ligand binding by interacting with αIIb D224 via their positively-charged (R-like) group and coordinating the Mg2+ ion in the metal ion adhesion site (MIDAS) via their carboxyl (D-like) group. We recently reported a novel inhibitor of αIIbβ3 (RUC-1) that binds exclusively to αIIb and we now report the structure-based design and synthesis of RUC-2 [2-amino-N-(3-(5-oxo-7-(piperazin-1-yl)-5H-[1,3,4]thiadiazolo[3,2-a]pyrimidin-2-yl)phenyl)acetamide; MW 385], a RUC-1 derivative with ∼100-fold higher affinity and an IC50= ∼90 nM for ADP-induced platelet aggregation. RUC-2, like RUC-1 shows specificity for αIIbβ3 compared to αVβ3 and produces much less exposure of the β3 LIBS1 epitope than does eptifibatide (eptifibatide=100%, untreated platelets=22±3 %; RUC-2=21±3%). RUC-2 also produces less of a global conformational change in αIIbβ3 compared to eptifibatide as measured by dynamic light scattering, gel permeation chromatography, and electron microscopic imaging of αIIbβ3 in nanodiscs. X-ray crystallography of RUC-2 soaked into the αIIbβ3 headpiece in 1 mM Ca2+ and 5 mM Mg2+ at 2.6 Å revealed that RUC-2 binds to αIIb much the way RUC-1 does, but in addition it binds to one of the sidechain carboxyl oxygens of the β3 MIDAS residue Glu-220, thus displacing Mg2+ from the MIDAS. When RUC-2 was soaked into the crystal in the presence of 20 mM Mg2+, however, the Mg2+ was identified in the MIDAS and RUC-2 was absent from the pocket. Molecular dynamics simulations were in accord with the X-ray crystallographic data. Support for competition between RUC-2 and Mg2+ for binding to the MIDAS came from studies showing that increasing the Mg2+ concentration significantly decreased RUC-2's ability to inhibit PAC-1 binding to CHO cells expressing αIIbβ3, platelet adhesion to fibrinogen, and thrombin receptor activating peptide-induced platelet aggregation. We conclude that RUC-2 inhibits ligand binding with high affinity and specificity by a novel mechanism in which it competes with Mg2+ for Glu-220, and as such may offer advantages as a therapeutic agent. The binding pocket of RUC-2 in the closed αIIbβ3 headpiece crystal structure. αIIb and β3 are shown as solvent accessible surfaces. Ca2+ ions of SyMBS or ADMIDAS (yellow) are shown as spheres. RUC-2 and selected αIIbβ3 sidechain and backbone atoms are shown as sticks with green (RUC-2), light blue (αIIb), or wheat carbons (β3), red oxygens, blue nitrogens, and yellow sulphurs. Water molecules are small red spheres. Hydrogen and metal coordination bonds are shown as dashed blue lines. Disclosures: Coller: Centocor/Accumetrics/Rockefeller University: Royalty interests in abciximab/VerifyNow assays/RUC-1 and RUC-2.


2020 ◽  
Vol 45 (5) ◽  
Author(s):  
Emeka Chima Ogoko ◽  
Ajayi Olayinka Sylvester

Surface water may constitute public health issues if the water is contaminated. Consequent upon this assertion, the physicochemical parameters and tr ace metal concentration of Jabi Lake surface water were analysed and compared with WHO standards. Sixteen water samples were taken for analysis from Jabi Lake within Abuja in Nigeria. Official Methods of Analysis of the Association of Official Analytical Chemists (AOAC) were adopted in the analysis of the physicochemical parameters while heavy metals ions determination was performed using Atomic Absorption Spectrophotometer. The results obtained revealed marked differences in the levels of some physicochemical properties and trace metal ion concentration in the surface water samples when compared with WHO standards. Though most physicochemical parameters were within acceptable and safe limits, but with nitrate having higher concentrations. The concentrations of manganese, iron, cobalt, lead and chromium were well above the WHO maximum permissible limits for surface water. The pollution index of manganese, iron, cobalt, lead and chromium were above unity (1.0), indicating very high level of pollution. The results of the physicochemical and trace metal analysis when compared with WHO suggest that the water samples from Jabi Lake was not suitable for drinking while the concentrations of the metal ions were found decreasing in this order; Pb ˃Fe˃Cr˃Mn˃Co˃Zn.


PLoS ONE ◽  
2013 ◽  
Vol 8 (10) ◽  
pp. e76793 ◽  
Author(s):  
Joel Raborn ◽  
Ting Fu ◽  
Xue Wu ◽  
Zhilong Xiu ◽  
Guohui Li ◽  
...  

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