scholarly journals Metal ion and ligand binding of integrin α5β1

2014 ◽  
Vol 111 (50) ◽  
pp. 17863-17868 ◽  
Author(s):  
Wei Xia ◽  
Timothy A. Springer
2021 ◽  
Vol 7 (19) ◽  
pp. eabe9716
Author(s):  
Stephanie Schumacher ◽  
Dirk Dedden ◽  
Roberto Vazquez Nunez ◽  
Kyoko Matoba ◽  
Junichi Takagi ◽  
...  

Integrin α5β1 is a major fibronectin receptor critical for cell migration. Upon complex formation, fibronectin and α5β1 undergo conformational changes. While this is key for cell-tissue connections, its mechanism is unknown. Here, we report cryo–electron microscopy structures of native human α5β1 with fibronectin to 3.1-angstrom resolution, and in its resting state to 4.6-angstrom resolution. The α5β1-fibronectin complex revealed simultaneous interactions at the arginine-glycine-aspartate loop, the synergy site, and a newly identified binding site proximal to adjacent to metal ion–dependent adhesion site, inducing the translocation of helix α1 to secure integrin opening. Resting α5β1 adopts an incompletely bent conformation, challenging the model of integrin sharp bending inhibiting ligand binding. Our biochemical and structural analyses showed that affinity of α5β1 for fibronectin is increased with manganese ions (Mn2+) while adopting the half-bent conformation, indicating that ligand-binding affinity does not depend on conformation, and α5β1 opening is induced by ligand-binding.


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.


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.


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

Sign in / Sign up

Export Citation Format

Share Document