scholarly journals Structural insights into integrin α5β1 opening by fibronectin ligand

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.

2021 ◽  
Author(s):  
Xiaochen Chen ◽  
Lu Wang ◽  
Zhanyu Ding ◽  
Qianqian Cui ◽  
Li Han ◽  
...  

AbstractHuman calcium-sensing receptor (CaSR) is a G-protein-coupled receptor that maintains Ca2+ homeostasis in serum. Here, we present the cryo-electron microscopy structures of the CaSR in the inactive and active states. Complemented with previously reported crystal structures of CaSR extracellular domains, it suggests that there are three distinct conformations: inactive, intermediate and active state during the activation. We used a negative allosteric nanobody to stabilize the CaSR in the fully inactive state and found a new binding site for Ca2+ ion that acts as a composite agonist with L-amino acid to stabilize the closure of active Venus flytraps. Our data shows that the agonist binding leads to the compaction of the dimer, the proximity of the cysteine-rich domains, the large-scale transitions of 7-transmembrane domains, and the inter-and intrasubunit conformational changes of 7-transmembrane domains to accommodate the downstream transducers. Our results reveal the structural basis for activation mechanisms of the CaSR.


2021 ◽  
Author(s):  
Man Pan ◽  
Yuanyuan Yu ◽  
Huasong Ai ◽  
Qingyun Zheng ◽  
Yuan Xie ◽  
...  

ABSTRACTp97, also known as valosin-containing protein (VCP), processes ubiquitinated substrates and plays a central role in cellular protein homeostasis. Mutations in human p97 are associated with multisystem proteinopathy (MSP), a dominantly inherited degenerative disorder that can affect muscle, bone and the central nervous system. It is also a drug target for cancer therapy with various inhibitors developed over the past decade. Despite significant structural insights into the fungal homologue of p97, Cdc48, little is known about how human p97 processes its substrates and how the activity is allosterically affected by inhibitors. Here, we report a series of cryo-electron microscopy (cryo-EM) structures of substrate-engaged human p97 complex with resolutions ranging from 2.9 to 3.8 Å that captured “power stroke”-like motions of both the D1 and D2 ATPase rings of p97. The structures elucidated how the unfolded substrate is engaged in the pore at atomic level. Critical conformational changes of the inter-subunit signaling (ISS) motifs were revealed, providing molecular insights into substrate translocation. Furthermore, we also determined cryo-EM structures of human p97 in complex with NMS-873, the most potent p97 inhibitor, at a resolution of 2.4 Å. The structures showed that NMS-873 binds at a cryptic groove in the D2 domain and interacts with the ISS motif, preventing its conformational change, thus blocking substrate translocation allosterically. Finally, using NMS-873 at a substoichiometric concentration, we captured a series of intermediate states, suggesting how the cofactor Npl4 coordinates with the D1 ring of p97 to initiate the translocation.


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

2021 ◽  
Vol 8 (1) ◽  
pp. 3
Author(s):  
Shelly Meron ◽  
Yulia Shenberger ◽  
Sharon Ruthstein

Electron paramagnetic resonance (EPR) spectroscopy has emerged as an ideal biophysical tool to study complex biological processes. EPR spectroscopy can follow minor conformational changes in various proteins as a function of ligand or protein binding or interactions with high resolution and sensitivity. Resolving cellular mechanisms, involving small ligand binding or metal ion transfer, is not trivial and cannot be studied using conventional biophysical tools. In recent years, our group has been using EPR spectroscopy to study the mechanism underlying copper ion transfer in eukaryotic and prokaryotic systems. This mini-review focuses on our achievements following copper metal coordination in the diamagnetic oxidation state, Cu(I), between biomolecules. We discuss the conformational changes induced in proteins upon Cu(I) binding, as well as the conformational changes induced in two proteins involved in Cu(I) transfer. We also consider how EPR spectroscopy, together with other biophysical and computational tools, can identify the Cu(I)-binding sites. This work describes the advantages of EPR spectroscopy for studying biological processes that involve small ligand binding and transfer between intracellular proteins.


Blood ◽  
2004 ◽  
Vol 104 (11) ◽  
pp. 650-650
Author(s):  
Motomu Shimaoka ◽  
Azucena Salas ◽  
Wei Yang ◽  
Gabriele Weitz-Schmidt ◽  
Timothy A. Springer

Abstract The integrin LFA-1 (αLβ2) is an αβ heterodimeric adhesion molecule critical in the effective trafficking of leukocytes and in facilitating subsequent antigen-specific inter-action. Participation of αLβ2 in multiple steps critical for T-cell-mediated immunity in vivo makes αLβ2 a valid therapeutic target for anti-inflammation therapy. Many small-molecule antagonists to αLβ2 have been developed as anti-inflammatory agents, out of which polysubstituted (S)-2-benzoylamino propionic acids, represented by XVA143 (XVA), have emerged as the most potent antagonists. αLβ2 is a large glycoprotein with a complex multi-domain organization, where a conserved von Willebrand factor-type A domain is contained in each subunit, the inserted (I) domain in the α-subunit and the I-like domain in the β subunit. The α-subunit I domain directly binds ligand, whereas the β-subunit I-like domain is thought to play a regulatory role by interacting with a part of the I domain. Thus far, it remains to be elucidated which domain the antagonists bind to and how they inhibit αLβ2 function. Here we investigate a mechanistic basis of XVA activity. XVA blocked the αLβ2-ICAM-1 interaction with EC50 of < 1 nM and suppressed mixed lymphocyte reaction as potently as cyclosporin A. XVA did not block ligand binding by αLβ2 directly, as it did not block αLβ2 containing a mutant I domain that is stabilized in the high-affinity conformation. Rather, XVA interfered with conformational changes that convert the I domain to the high-affinity state. Surface plasmon resonance analysis using an isolated I domain showed that XVA did not target the I domain. Interestingly, XVA stabilized non-covalent αβ association sufficiently to make it resistant to denaturation with SDS. Stabilization of mutant αβ complexes was utilized to test compound binding to αLβ2 mutants and locate the inhibitor-binding site. As binding of XVA was found to be metal-dependent, alanine-scanning of the metal binding sites indicated that this compound binds to the metal ion-dependent adhesion site in the I-like domain, where it disrupts the interaction of the I-like domain with the I domain. XVA inhibits αLβ2 allosterically by perturbing the inter-domain communication that is critical to relay conformational signals which induce the active I domain conformation. Furthermore, XVA stabilized a global conformation of αLβ2 in the active extended form, whereas the ligand binding I domain was left in the inactive conformation, as demonstrated by exposure of activation-dependent epitopes in αLβ2 on the cell surface and electron microscopic images of the soluble recombinant αLβ2. The results strongly suggest that XVA would serve as a mimetic for the intrinsic ligand that is involved in receptor-ligand like interaction between the I domain and I-like domain. This inhibitor revealed a crucial intersection for relaying conformational signals within the integrin αLβ2. While blocking signals in one direction (to the I domain), the antagonists induce the active conformation of the I-like domain as well as the rest of domains, and thus transmit conformational signals in the opposite direction toward the transmembrane domains.


2012 ◽  
Vol 196 (1) ◽  
pp. 131-146 ◽  
Author(s):  
Yamei Yu ◽  
Jianghai Zhu ◽  
Li-Zhi Mi ◽  
Thomas Walz ◽  
Hao Sun ◽  
...  

The lymphocyte homing receptor integrin α4β7 is unusual for its ability to mediate both rolling and firm adhesion. α4β1 and α4β7 are targeted by therapeutics approved for multiple sclerosis and Crohn’s disease. Here, we show by electron microscopy and crystallography how two therapeutic Fabs, a small molecule (RO0505376), and mucosal adhesion molecule-1 (MAdCAM-1) bind α4β7. A long binding groove at the α4–β7 interface for immunoglobulin superfamily domains differs in shape from integrin pockets that bind Arg-Gly-Asp motifs. RO0505376 mimics an Ile/Leu-Asp motif in α4 ligands, and orients differently from Arg-Gly-Asp mimics. A novel auxiliary residue at the metal ion–dependent adhesion site in α4β7 is essential for binding to MAdCAM-1 in Mg2+ yet swings away when RO0505376 binds. A novel intermediate conformation of the α4β7 headpiece binds MAdCAM-1 and supports rolling adhesion. Lack of induction of the open headpiece conformation by ligand binding enables rolling adhesion to persist until integrin activation is signaled.


2014 ◽  
Vol 111 (50) ◽  
pp. 17863-17868 ◽  
Author(s):  
Wei Xia ◽  
Timothy A. Springer

2021 ◽  
Author(s):  
Juliana Andrea Martinez Fiesco ◽  
David E Durrant ◽  
Deborah K Morrison ◽  
Ping Zhang

An unresolved issue in RAF kinase signaling is how binding of autoinhibited RAF monomers to activated RAS initiates the conformational changes required to form active RAF dimers. Here, we present cryo-electron microscopy structures of full-length BRAF complexes derived from mammalian cells: autoinhibited monomeric BRAF:14-3-32:MEK and BRAF:14-3-32 complexes and an inhibitor-bound, dimeric BRAF2:14-3-32 complex, at 3.7, 4.1, and 3.9 Å resolution, respectively. The RAS binding domain (RBD) of BRAF is resolved in the autoinhibited structures, and we find that neither MEK nor ATP binding is required to stabilize the autoinhibited complexes. Notably, the RBD was found to interact extensively with the 14-3-3 protomer bound to the BRAF C-terminal site. Moreover, through structure-guided mutational studies, our findings indicate that RAS-RAF binding is a dynamic process and that RBD residues at the 14-3-3 interface have a dual function, first stabilizing RBD orientation in the autoinhibited state and then contributing to full RAS contact.


Blood ◽  
2006 ◽  
Vol 108 (11) ◽  
pp. 144-144
Author(s):  
Robert Blue ◽  
Markéta Jiroušková ◽  
Charles Karan ◽  
Barry S. Coller

Abstract Two separate conformational changes have been proposed to accompany activation of platelet αIIbβ3: 1) leg separation leading to extension of the head region composed of the αIIb propeller and β3 βA (I-like) domains, and 2) a swing-out motion at the junction of the β3 βA (I-like) and hybrid domains. Small molecule inhibitors of αIIbβ3 competitively block the RGD ligand binding site and variably induce conformational changes in αIIbβ3 as judged by the binding of ligand-induced binding site (LIBS)-specific monoclonal antibodies. In an attempt to identify molecules that may inhibit αIIbβ3 activation without initiating the conformational changes associated with ligand binding, we screened 33,264 compounds from four different chemical libraries (Prestwick, Chembridge, Cerep and ChemDiv) for their ability to inhibit the adhesion of washed platelets in HEPES-modified Tyrode’s buffer with 1 mM Ca2+/0.5 mM Mg2+ to immobilized fibrinogen adsorbed from a 50 μg/ml solution. When tested at a final concentration of 16 μM, a total of 102 compounds (0.31%) demonstrated greater than 50% inhibition of platelet adhesion, and two of these (Figure 1) demonstrated >30% inhibition of the initial wave of ADP-induced aggregation of platelets in citrated platelet-rich plasma. IC50s for inhibition of ADP (5 μM)-induced platelet aggregation for compounds 1 and 2 were 13 ± 4.5 and 17 ± 5 μM (n=3), respectively. Compounds 1 and 2 also inhibited fibrinogen binding to platelets induced by the activating LIBS antibody AP5 with IC50s of 27 and 30 μM, and 20 and 27 μM, respectively, in two experiments. Since AP5 binds to and directly activates αIIbβ3, it is likely that the compounds’ inhibitory effects are due to direct binding to αIIbβ3 rather than inhibition of signal transduction. In two separate experiments, compound 1 at 15 - 20 μM produced variable increases in the binding of LIBS mAbs AP5, PMI-1 or LIBS1 to unactivated and ADP-activated platelets, whereas tirofiban (20 μM) consistently increased the binding of each mAb. Compound 2 did not increase the binding of any of the mAbs. Neither compound contains a negatively charged carboxyl group, which mediates the interaction of the Asp group in RGD ligands with the β3 MIDAS metal ion, but compound 1 has a carbonyl group that may potentially interact with the MIDAS metal ion. Compound 1 resembles 1,2-fused pyrimidine derivatives that have previously been demonstrated to inhibit platelet aggregation (Roma et al., Bioorg. Med. Chem. 2003, 11, 123). We conclude that high throughput screening of molecular libraries can identify novel compounds that inhibit αIIbβ3 and that one of them appears to inhibit αIIbβ3 without inducing conformational changes in the receptor. Figure Figure


eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Sandra K Schuller ◽  
Jan M Schuller ◽  
J Rajan Prabu ◽  
Marc Baumgärtner ◽  
Fabien Bonneau ◽  
...  

The yeast THO complex is recruited to active genes and interacts with the RNA-dependent ATPase Sub2 to facilitate the formation of mature export-competent messenger ribonucleoprotein particles and to prevent the co-transcriptional formation of RNA:DNA-hybrid-containing structures. How THO-containing complexes function at the mechanistic level is unclear. Here, we elucidated a 3.4 Å resolution structure of Saccharomyces cerevisiae THO-Sub2 by cryo-electron microscopy. THO subunits Tho2 and Hpr1 intertwine to form a platform that is bound by Mft1, Thp2, and Tex1. The resulting complex homodimerizes in an asymmetric fashion, with a Sub2 molecule attached to each protomer. The homodimerization interfaces serve as a fulcrum for a seesaw-like movement concomitant with conformational changes of the Sub2 ATPase. The overall structural architecture and topology suggest the molecular mechanisms of nucleic acid remodeling during mRNA biogenesis.


Sign in / Sign up

Export Citation Format

Share Document