Structure of a ligand-binding intermediate in wild-type carbonmonoxy myoglobin

Nature ◽  
2000 ◽  
Vol 403 (6772) ◽  
pp. 921-923 ◽  
Author(s):  
Kelvin Chu ◽  
Jaroslav Vojtchovský ◽  
Benjamin H. McMahon ◽  
Robert M. Sweet ◽  
Joel Berendzen ◽  
...  
Author(s):  
Hari Balaji ◽  
Selvaraj Ayyamperuma ◽  
Niladri Saha ◽  
Shyam Sundar Pottabathula ◽  
Jubie Selvaraj ◽  
...  

: Vitamin-D deficiency is a global concern. Gene mutations in the vitamin D receptor’s (VDR) ligand binding domain (LBD) variously alter the ligand binding affinity, heterodimerization with retinoid X receptor (RXR) and inhibit coactivator interactions. These LBD mutations may result in partial or total hormone unresponsiveness. A plethora of evidence report that selective long chain polyunsaturated fatty acids (PUFAs) including eicosapentaenoic acid (EPA), docosahexaenoic acid (DHA) and arachidonic acid (AA) bind to the ligand-binding domain of VDR and lead to transcriptional activation. We therefore hypothesize that selective PUFAs would modulate the dynamics and kinetics of VDRs, irrespective bioactive of vitamin-D binding. The spatial arrangements of the selected PUFAs in VDR active site were examined by in-silico docking studies. The docking results revealed that PUFAs have fatty acid structure-specific binding affinity towards VDR. The calculated EPA, DHA & AA binding energies (Cdocker energy) were lesser compared to vitamin-D in wild type of VDR (PDB id: 2ZLC). Of note, the DHA has higher binding interactions to the mutated VDR (PDB id: 3VT7) when compared to the standard Vitamin-D. Molecular dynamic simulation was utilized to confirm the stability of potential compound binding of DHA with mutated VDR complex. These findings suggest the unique roles of PUFAs in VDR activation and may offer alternate strategy to circumvent vitamin-D deficiency.


Blood ◽  
2004 ◽  
Vol 104 (13) ◽  
pp. 4226-4235 ◽  
Author(s):  
Sylvie Côté ◽  
Suzan McNamara ◽  
Daria Brambilla ◽  
Andrea Bianchini ◽  
Giovanni Rizzo ◽  
...  

Abstract Nuclear receptors are ligand-modulated transcription factors regulated by interactions with corepressors and coactivators, whose functions are not fully understood. Acute promyelocytic leukemia (APL) is characterized by a translocation, t(15;17), that produces a PML/RARα fusion oncoprotein, whose abnormal transcriptional function is successfully targeted by pharmacologic levels of all-trans-retinoic acid (ATRA). Mutations in the ligand-binding domain of PML/RARα that confer resistance to ATRA have been studied by expression in nonhematopoietic cells, such as Cos-1. Here, we show that ATRA binding and transcriptional activation by the same PML/RARα mutant differ markedly between nonhematopoietic and leukemic cell lines. Differential expression of the corepressor isoform silencing mediator for retinoid and thyroid receptors β (SMRTβ) correlates with increased ligand binding and transcription by the mutant PML/RARα. Transient and stable overexpression of SMRTβ in hematopoietic cells that only express SMRTα increased ATRA binding, ligand-induced transcription, and ATRA-induced cell differentiation. This effect may not be limited to abnormal nuclear receptors, because overexpression of SMRTβ increased ATRA-induced binding and transcriptional activation of wild-type receptors PML/RARα and RARα. Our results suggest a novel role for the SMRTβ isoform whereby its cell-specific expression may influence the binding and transcriptional capacities of nuclear receptors, thus providing new evidence of distinct functions of corepressor isoforms and adding complexity to transcriptional regulation.


2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Diogo Tavares ◽  
Artur Reimer ◽  
Shantanu Roy ◽  
Aurélie Joublin ◽  
Vladimir Sentchilo ◽  
...  

AbstractBacterial periplasmic-binding proteins have been acclaimed as general biosensing platform, but their range of natural ligands is too limited for optimal development of chemical compound detection. Computational redesign of the ligand-binding pocket of periplasmic-binding proteins may yield variants with new properties, but, despite earlier claims, genuine changes of specificity to non-natural ligands have so far not been achieved. In order to better understand the reasons of such limited success, we revisited here the Escherichia coli RbsB ribose-binding protein, aiming to achieve perceptible transition from ribose to structurally related chemical ligands 1,3-cyclohexanediol and cyclohexanol. Combinations of mutations were computationally predicted for nine residues in the RbsB binding pocket, then synthesized and tested in an E. coli reporter chassis. Two million variants were screened in a microcolony-in-bead fluorescence-assisted sorting procedure, which yielded six mutants no longer responsive to ribose but with 1.2–1.5 times induction in presence of 1 mM 1,3-cyclohexanediol, one of which responded to cyclohexanol as well. Isothermal microcalorimetry confirmed 1,3-cyclohexanediol binding, although only two mutant proteins were sufficiently stable upon purification. Circular dichroism spectroscopy indicated discernable structural differences between these two mutant proteins and wild-type RbsB. This and further quantification of periplasmic-space abundance suggested most mutants to be prone to misfolding and/or with defects in translocation compared to wild-type. Our results thus affirm that computational design and library screening can yield RbsB mutants with recognition of non-natural but structurally similar ligands. The inherent arisal of protein instability or misfolding concomitant with designed altered ligand-binding pockets should be overcome by new experimental strategies or by improved future protein design algorithms.


Blood ◽  
2006 ◽  
Vol 109 (8) ◽  
pp. 3513-3520 ◽  
Author(s):  
Vineet Gupta ◽  
Annette Gylling ◽  
José Luis Alonso ◽  
Takashi Sugimori ◽  
Petre Ianakiev ◽  
...  

Abstract Crystallographic and electron microscopy studies revealed genuflexed (bent) integrins in both unliganded (inactive) and physiologic ligandbound (active) states, suggesting that local conformational changes are sufficient for activation. Herein we have explored the role of local changes in the contact region between the membrane-proximal β-tail domain (βTD) and the ligand-binding βA domain of the bent conformation in regulating interaction of integrin CD11b/CD18 (αMβ2) with its physiologic ligand iC3b. We replaced the βTD CD loop residues D658GMD of the CD18 (β2) subunit with the equivalent D672SSG of the β3 subunit, with AGAA or with NGTD, expressed the respective heterodimeric receptors either transiently in epithelial HEK293T cells or stably in leukocytes (K562), and measured their ability to bind iC3b and to conformation-sensitive mAbs. In the presence of the physiologic divalent cations Ca2+ plus Mg2+ (at 1 mM each), the modified integrins showed increased (in HEK293) or constitutive (in K562) binding to iC3b compared with wild-type receptors. K562 expressing the βTD-modified integrins bound in Ca2+Mg2+ to the βA-directed high-affinity reporter mAb 24 but not to mAb KIM127, a reporter of the genu-straightened state. These data identify a role for the membrane proximal βTD as an allosteric modulator of integrin activation.


Blood ◽  
2006 ◽  
Vol 108 (11) ◽  
pp. 1526-1526
Author(s):  
Jun Yamanouchi ◽  
Takaaki Hato ◽  
Yoshihiro Yakushijin ◽  
Ikuya Sakai ◽  
Masaki Yasukawa

Abstract Integrin αIIbβ3 exists in a low-affinity state and requires activation for high-affinity binding with soluble ligands. αIIbβ3 activation is linked to rearrangements of the β3 I-like domain structure and the largest movement in the β3 I-like domain following ligand binding occurs in the β6-α7 loop. Although this loop does not comprise a ligand binding site, a recent mutational study has shown that introduction of disulfide bonds into the β6/α7 region to lock the β3 I-like domain in the open or closed conformation renders αIIbβ3 constitutively active or inactive, suggesting the regulatory role of this region in integrin activation. However, it remains to be determined which residues of the β6-α7 loop in the β I-like domain are critical for integrin activation. We therefore conducted alanine-scanning mutagenesis of the β6-α7 loop residues in the β3 I-like domain and tested for ligand binding to mutant β3 integrins. The β6-α7 loop is composed of residues from S334 to N339, and the region between L333 and V340 was targeted for mutagenesis. The mutant β3 cDNA was transfected into CHO cells together with wild-type αIIb cDNA. The expression of αIIbβ3 mutants on the cell surface was 56–116% that of the wild-type αIIbβ3. Then binding of an activation-dependent antibody. PAC1, to the αIIbβ3 mutants was examined in the presence or absence of the αIIbβ3-activating antibody PT25-2. As expected, wild-type αIIbβ3 showed PAC1 binding only after activation of αIIbβ3 by PT25-2. The L333A, S334A, M335A and V340A mutations had no effect on PAC1 binding. In contrast, the S337A and N339A mutations induced significant PAC1 binding in the absence of PT25-2, indicating a constitutively active state. Although the D336A and S338A mutations retained αIIbβ3 in an inactive state in the absence of PT25-2, they induced 3- and 4.5-fold as much PAC1 binding as wild-type αIIbβ3 in response to PT25-2, respectively. The S337A and N339A mutations, which rendered αIIbβ3 constitutively active, induced further PAC1 binding in the presence of PT25-2 (2.7~5.1-fold as much PAC1 binding as wild-type αIIbβ3). When soluble fibrinogen was used instead of PAC1, similar results were obtained. None of the mutations tested had any effect on PT25-2 binding. We next quantified adhesion of CHO cells stably expressing mutant or wild-type αIIbβ3 to immobilized fibrinogen. The S337A and N339A mutations enhanced cell adhesion to fibrinogen and the extent of adhesion of the mutants was comparable to that of wild-type αIIbβ3 activated by Mn2+. To determine whether the mutations of the β3 subunit responsible for αIIbβ3 activation also induce constitutive activation of αVβ3, CHO cells expressing αVβ3 mutants were tested for soluble fibrinogen binding. The surface expression of mutant αVβ3 was comparable to that of wild-type αVβ3. The αVβ3S337A and N339A mutants bound significantly more fibrinogen than wild-type αVβ3 without any stimulation, indicating that the S337A and N339A mutations also rendered another β3 integrin, αVβ3, constitutively active. These results suggest that the S337 and N339 residues in the β3 I-like domain are essential for constraining β3 integrins in a default low-affinity state and that structural rearrangement in the 336DSSN sequence of the β6-α7 loop alters the affinity state of αIIbβ3. Since the DSSN sequence is highly conserved among integrin β subunits, this motif may be a common regulatory component of integrin activation.


Blood ◽  
2008 ◽  
Vol 112 (11) ◽  
pp. 2448-2448
Author(s):  
Lan Zhou ◽  
Quanjian Yan ◽  
David Yao ◽  
Lebing W Li ◽  
Stanton L. Gerson ◽  
...  

Abstract Notch receptors are conserved cell surface molecules essential for hematopoietic cell fate determination. Activated Notch enhances self-renewal of hematopoietic stem cells and promotes T lymphopoiesis. O-linked fucose moieties attached to the EGF domains of Notch receptors and its modification by Fringe can strongly modulate Notch signaling. Our recently published results indicate that Notch-dependent signaling controls myelopoiesis both in vitro and in vivo, and identify a requirement for Notch fucosylation in the expression of Notch ligand binding activity and Notch signaling efficiency in hematopoietic progenitor cells. In the current study, we tested the hypothesis that fucosylation controlled Notch signaling regulates hematopoietic lineage homeostasis. Genetically-modified mouse embryonic stem (ES) cells deficient in Notch1 receptor (NOTCH1−/−) or pofut1 (POFUT1−/−) that controls O-fucose modification of Notch receptor EGF repeats are studied in an in vitro co-culture assay with Notch ligand-expressing OP9 cells. Activation of Notch in wild type ES cells promotes T lymphopoiesis, while exposure of NOTCH1−/− or POFUT1−/− ES cells to Notch ligand failed to generate T lymphocytes but sustained granulocytic production. When probed with recombinant Notch ligand Dll1 or Dll4, hematopoietic cells derived from wild type ES line displayed robust Notch ligand binding, but cells from NOTCH1−/− or POFUT1−/− ES lines showed completely absent or reduced Notch ligand interaction, respectively. In comparison, ES cells deficient in pofut2 (POFUT2−/−) that controls O-fucose modification on thrombospondin repeats (TSR) displayed a wild type lineage development phenotype and normal Notch ligand binding ability. When examined for their in vivo hematopoietic reconstitution, blood cells derived from NOTCH1−/− or POFUT1−/− ES lines, but not POFUT2−/− ES line, showed enhanced granulocytic but suppressed T and B lymphoid lineage development. These results are consistent with our bone marrow transplantation findings that hematopoietic reconstitution by fucosylation-deficient marrow progenitor cells exhibited increased granulocytopoiesis while wild type or fucosylation-intact marrow cells have normal lineage distribution. Our observations indicate that Notch signaling maintains blood lineage homeostasis by promoting lymphoid lineage development and suppressing overt myeloid development. O-fucose modification of EGF repeats on Notch receptor is essential for this Notch-dependent control of blood lineage homeostasis as deficiency of fucose on Notch receptor results in enhanced myeloid development.


Blood ◽  
2011 ◽  
Vol 118 (21) ◽  
pp. 3259-3259
Author(s):  
Jun Yamanouchi ◽  
Takaaki Hato ◽  
Hiroshi Fujiwara ◽  
Yoshihiro Yakushijin ◽  
Masaki Yasukawa

Abstract Abstract 3259 Integrin αIIbβ3 undergoes allosteric conformational changes in its extracellular domains, resulting in integrin activation that allows high affinity binding with soluble ligands. The crystal structure of the integrin β subunit revealed an interaction of the β-tail domain (βTD) with the βI domain containing ligand-binding sites, suggesting that βTD may be involved in allosteric mechanism for integrin activation. However, previous studies have shown conflicting results on the functional role of βTD in integrin activation. In this study, we conducted site-directed mutagenesis in the βTD domain and tested ligand binding to αIIbβ3 mutants. We produced αIIbβ3 mutants in which the β3TD loop residues (DSSG) were substituted with the corresponding β1 (NGNN) or β2TD residues (DGMD). The αIIbβ3 mutants were expressed on the surface of CHO cells by cotransfection of mutant β3 and wild-type αIIb cDNAs, and were tested for binding of PAC1, a ligand-mimetic anti-αIIbβ3 antibody. The NGNN, but not DGMD mutant bound significant PAC1 binding without any stimulation, indicating a constitutively active state. To identify the residue(s) responsible for αIIbβ3 activation in the βTD, we produced αIIbβ3 mutants in which the individual residues in the β3TD loop were substituted with the corresponding β1TD residues. Among them, only G675N bound significant PAC1 binding without any stimulation. Since G675N mutation creates a sequence known to be a consensus sequence for glycosylation (Asn-X-Ser/Thr), it is possible that the insertion of glycans into the βTD loop induces conformational changes in αIIbβ3 which allow ligand binding. To test this hypothesis, we added substitution of S677 with Thr, Ala or Asp to the G675N mutation. The resultant G675N/S677T double mutant, in which the N-glycosylation site was preserved, was constitutively active. In contrast, G675N/S677A and G675N/S677D, in which the N-glycosylation site was disrupted, were in an inactive state. These results suggest that an artificial glycan wedge between βTD and βI domains activates αIIbβ3. However, our study does not provide evidence that the βTD domain constrains wild type αIIbβ3 inactive although the separation of βTD and βI domains may be able to activate integrins. Disclosures: No relevant conflicts of interest to declare.


eLife ◽  
2016 ◽  
Vol 5 ◽  
Author(s):  
Sarvenaz Sarabipour ◽  
Kurt Ballmer-Hofer ◽  
Kalina Hristova

VEGFR-2 is the primary regulator of angiogenesis, the development of new blood vessels from pre-existing ones. VEGFR-2 has been hypothesized to be monomeric in the absence of bound ligand, and to undergo dimerization and activation only upon ligand binding. Using quantitative FRET and biochemical analysis, we show that VEGFR-2 forms dimers also in the absence of ligand when expressed at physiological levels, and that these dimers are phosphorylated. Ligand binding leads to a change in the TM domain conformation, resulting in increased kinase domain phosphorylation. Inter-receptor contacts within the extracellular and TM domains are critical for the establishment of the unliganded dimer structure, and for the transition to the ligand-bound active conformation. We further show that the pathogenic C482R VEGFR-2 mutant, linked to infantile hemangioma, promotes ligand-independent signaling by mimicking the structure of the ligand-bound wild-type VEGFR-2 dimer.


1995 ◽  
Vol 307 (2) ◽  
pp. 493-498 ◽  
Author(s):  
C Huang ◽  
H H Tai

A cDNA encoding for mouse prostaglandin E2 (PGE2) receptor EP3 subtype was cloned from a mouse kidney cDNA library by PCR using terminal primers derived from the known sequence of mouse lung EP3 receptor cDNA. The cloned cDNA was confirmed by sequencing and was expressed in Trichoplusia ni (MG1) insect cells using a baculovirus expression system. A specific protein of 60 kDa was detected by immunoblot with antibodies generated against a unique decapeptide sequence present in the second extracellular loop of the EP3 receptor. Specific binding of [3H]PGE2 with a Kd of 3 nM was also found in the membrane fraction of the insect cells. Ligand binding of the receptor was further studied by site-directed mutagenesis. Arg-309 of the receptor was separately mutated to lysine, glutamate and valine. cDNAs of the wild-type and mutant EP3 receptors were respectively expressed and studied in MG1 insect cells. Binding studies indicated that both glutamate and valine mutant EP3 receptors had no binding of [3H]PGE2. On the contrary, the lysine mutant receptor exhibited an even tighter binding (Kd = 1.3 nM) than the wild-type EP3 receptor. Immunoblot studies indicated that these receptors were expressed in a comparable amount in MG1 insect cells. These results suggest that Arg-309 of EP3 receptor may be essential in ligand binding through ionic interaction.


2010 ◽  
Vol 170 (3) ◽  
pp. 522-531 ◽  
Author(s):  
Daniela B.B. Trivella ◽  
Lucas Bleicher ◽  
Leonardo de Castro Palmieri ◽  
Helton José Wiggers ◽  
Carlos Alberto Montanari ◽  
...  

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