scholarly journals Conformational clamping by a membrane ligand activates the EphA2 receptor

2021 ◽  
Author(s):  
Justin M Westerfield ◽  
Amita Sahoo ◽  
Daiane S Alves ◽  
Brayan Grau ◽  
Alayna Cameron ◽  
...  

The EphA2 receptor is a promising drug target for cancer treatment, since EphA2 activation can inhibit metastasis and tumor progression. It has been recently described that the TYPE7 peptide activates EphA2 using a novel mechanism that involves binding to the single transmembrane domain of the receptor. TYPE7 is a conditional transmembrane (TM) ligand, which only inserts into membranes at neutral pH in the presence of the TM region of EphA2. However, how membrane interactions can activate EphA2 is not known. We systematically altered the sequence of TYPE7 to identify the binding motif used to activate EphA2. With the resulting six peptides, we performed biophysical and cell migration assays that identified a new potent peptide variant. We also performed a mutational screen that determined the helical interface that mediates dimerization of the TM domain of EphA2 in cells. These results, together with molecular dynamic simulations, allowed to elucidate the molecular mechanism that TYPE7 uses to activate EphA2, where the membrane peptide acts as a molecular clamp that wraps around the TM dimer of the receptor. We propose that this binding mode stabilizes the active conformation of EphA2. Our data, additionally, provide clues into the properties that TM ligands need to have in order to achieve activation of membrane receptors.

Blood ◽  
2006 ◽  
Vol 108 (11) ◽  
pp. 1504-1504
Author(s):  
Hang Yin ◽  
Joanna S. Slusky ◽  
Bryan W. Berger ◽  
Rustem I. Litvinov ◽  
Gaston Vilaire ◽  
...  

Abstract Integrins reside on cell surfaces in an equilibrium between inactive and active conformations. When inactive, the transmembrane (TM) domains of integrin α and β subunits interact, but the domains separate when integrins assume their active conformation. Although this conformational change has not been shown for αvβ3, we hypothesized that a peptide designed to bind to the αv TM domain might activate αvβ3 in platelets by disrupting the TM domain heterodimer of the inactive molecule. To design such a peptide, we used CHAMP (Computed Helical Anti-Membrane Protein) methodology. In the CHAMP method, the αv TM helix was scanned for motifs likely to mediate αvβ3 TM domain interactions. Next, the backbone conformation for an αv-binding peptide was selected based on known structural preferences for the motifs identified in the αv helix. Finally, the sequence for the peptide was designed computationally using a side-chain repacking algorithm. The CHAMP peptide, anti-αv, and its TM helix target, αv-TM, were synthesized by solid phase synthesis. We also synthesized anti-αvmut in which the putative anti-αv-TM binding motif, GXXXG, was mutated to LXXXL. Lys2 dipeptides and short polyethylene glycol sequences were appended to the C- and N-termini of the peptides, respectively, to facilitate their solubility and insertion into membranes. CD spectroscopy revealed that both anti-αv and αv-TM were helical in micelles and phospholipid vesicles. Measurement of Trp fluorescence intensity revealed that anti-αv rapidly inserted into unilamellar POPC/POPG vesicles. Analytical ultracentrifuge and fluorescence resonance energy transfer experiments demonstrated that anti-αv bound to the αv-TM, but not to a homologous αIIb-TM domain peptide. In addition, there was negligible interaction between αv-TM and anti-αvmut. Anti-αv also formed heteromeric complexes with the αv TM domain in bacterial membranes but not with the TM domains of αIIb, α2, β1, or β3. αvβ3 mediates the adhesion of agonist-stimulated platelets to the matrix protein osteopontin (OPN). We found that anti-αV at μM concentrations induced platelet adhesion to OPN. Adhesion was prevented by the divalent cation chelator EDTA, consistent with an integrin-mediated process, but was only minimally affected by pre-incubating the platelets with PGE1, implying that anti-αv-induced adhesion by interacting directly with the αv TM domain. Force spectroscopy using laser tweezers confirmed the specificity of the interaction of anti-αv with platelets: anti-αv induced specific rupture forces between platelets and OPN-coated beads, but not between platelets and fibrinogen-coated beads. Moreover, only non-specific rupture forces were detected between OPN-coated beads and platelets incubated with anti-αvmut. These results demonstrate the successful application of computational methods to design a soluble peptide that specifically recognizes the TM domain of αv in platelets membranes, even when a 400-fold excess of the homologous integrin subunit αIIb is present. Further, because the peptide binds to the site on the αv TM domain that interacts with the β3 TM helix and activates αvβ3, these results strongly support the hypothesis that separation of the αv and β3 TM domains regulates the function of this integrin.


Author(s):  
Chiara Luise ◽  
Dina Robaa ◽  
Wolfgang Sippl

AbstractSome of the main challenges faced in drug discovery are pocket flexibility and binding mode prediction. In this work, we explored the aromatic cage flexibility of the histone methyllysine reader protein Spindlin1 and its impact on binding mode prediction by means of in silico approaches. We first investigated the Spindlin1 aromatic cage plasticity by analyzing the available crystal structures and through molecular dynamic simulations. Then we assessed the ability of rigid docking and flexible docking to rightly reproduce the binding mode of a known ligand into Spindlin1, as an example of a reader protein displaying flexibility in the binding pocket. The ability of induced fit docking was further probed to test if the right ligand binding mode could be obtained through flexible docking regardless of the initial protein conformation. Finally, the stability of generated docking poses was verified by molecular dynamic simulations. Accurate binding mode prediction was obtained showing that the herein reported approach is a highly promising combination of in silico methods able to rightly predict the binding mode of small molecule ligands in flexible binding pockets, such as those observed in some reader proteins.


2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Agnieszka Biernatowska ◽  
Paulina Olszewska ◽  
Krzysztof Grzymajło ◽  
Dominik Drabik ◽  
Sebastian Kraszewski ◽  
...  

AbstractFlotillins are the major structural proteins in erythroid raft domains. We have shown previously that the dynamic nanoscale organization of raft domains in erythroid cells may depend on flotillin-MPP1 interactions. Here, by using molecular dynamic simulations and a surface plasmon resonance-based approach we determined that high-affinity complexes of MPP1 and flotillins are formed via a so far unidentified region within the D5 domain of MPP1. Significantly, this particular “flotillin binding motif” is of key physiological importance, as overexpression of peptides containing this motif inhibited endogenous MPP1-flotillin interaction in erythroid precursor cells, thereby causing lateral disorganization of raft domains. This was reflected by both reduction in the plasma membrane order and markedly decreased activation of signal transduction via the raft-dependent insulin receptor pathway. Our data highlight new molecular details concerning the mechanism whereby MPP1 functionally links flotillins to exert their physiological role in raft domain formation.


2021 ◽  
Vol 17 ◽  
Author(s):  
Nafiseh Karimi ◽  
Rouhollah Vahabpour Roudsari ◽  
Zahra Hajimahdi ◽  
Afshin Zarghi

Background: Integrase enzyme is a validated drug target to discover novel structures as anti-HIV-1 agents. Objective: Novel series of thioimidazolyl diketo acid derivatives characterizing various substituents at N-1 and 2-thio positions of central ring were developed as HIV-1 integrase inhibitors. Results: The obtained molecules were evaluated in the enzyme assay, displaying promising integrase inhibitory activity with IC50 values ranging from 0.9 to 7.7 M. The synthesized compounds were also tested for antiviral activity and cytotoxicity using HeLa cells infected by the single-cycle replicable HIV-1 NL4-3. Conclusion: The most potent compound was 18i with EC50=19 µM, IC50 0.9 µM and SI= 10.5. Docking studies indicated that the binding mode of the active molecule is well aligned with the known HIV-1 integrase inhibitors.


2003 ◽  
Vol 371 (2) ◽  
pp. 443-449 ◽  
Author(s):  
Frank NEUSCHÄFER-RUBE ◽  
Eva ENGEMAIER ◽  
Sina KOCH ◽  
Ulrike BÖER ◽  
Gerhard P. PÜSCHEL

Prostanoid receptors belong to the class of heptahelical plasma membrane receptors. For the five prostanoids, eight receptor subtypes have been identified. They display an overall sequence similarity of roughly 30%. Based on sequence comparison, single amino acids in different subtypes of different species have previously been identified by site-directed mutagenesis or in hybrid receptors that appear to be essential for ligand binding or G-protein coupling. Based on this information, a series of mutants of the human FP receptor was generated and characterized in ligand-binding and second-messenger-formation studies. It was found that mutation of His-81 to Ala in transmembrane domain 2 and of Arg-291 to Leu in transmembrane domain 7, which are putative interaction partners for the prostanoid's carboxyl group, abolished ligand binding. Mutants in which Ser-263 in transmembrane domain 6 or Asp-300 in transmembrane domain 7 had been replaced by Ala or Gln, respectively, no longer discriminated between prostaglandins PGF2α and PGD2. Thus distortion of the topology of transmembrane domains 6 and 7 appears to interfere with the cyclopentane ring selectivity of the receptor. PGF2α-induced inositol formation was strongly reduced in the mutant Asp-300Gln, inferring a role for this residue in agonist-induced G-protein activation.


2019 ◽  
Vol 295 (7) ◽  
pp. 1792-1814 ◽  
Author(s):  
Justin M. Westerfield ◽  
Francisco N. Barrera

Single-pass membrane receptors contain extracellular domains that respond to external stimuli and transmit information to intracellular domains through a single transmembrane (TM) α-helix. Because membrane receptors have various roles in homeostasis, signaling malfunctions of these receptors can cause disease. Despite their importance, there is still much to be understood mechanistically about how single-pass receptors are activated. In general, single-pass receptors respond to extracellular stimuli via alterations in their oligomeric state. The details of this process are still the focus of intense study, and several lines of evidence indicate that the TM domain (TMD) of the receptor plays a central role. We discuss three major mechanistic hypotheses for receptor activation: ligand-induced dimerization, ligand-induced rotation, and receptor clustering. Recent observations suggest that receptors can use a combination of these activation mechanisms and that technical limitations can bias interpretation. Short peptides derived from receptor TMDs, which can be identified by screening or rationally developed on the basis of the structure or sequence of their targets, have provided critical insights into receptor function. Here, we explore recent evidence that, depending on the target receptor, TMD peptides cannot only inhibit but also activate target receptors and can accommodate novel, bifunctional designs. Furthermore, we call for more sharing of negative results to inform the TMD peptide field, which is rapidly transforming into a suite of unique tools with the potential for future therapeutics.


Marine Drugs ◽  
2019 ◽  
Vol 17 (3) ◽  
pp. 180 ◽  
Author(s):  
Desirée Kaufmann ◽  
Alesia Tietze ◽  
Daniel Tietze

Understanding subtype specific ion channel pore blockage by natural peptide-based toxins is crucial for developing such compounds into promising drug candidates. Herein, docking and molecular dynamics simulations were employed in order to understand the dynamics and binding states of the µ-conotoxins, PIIIA, SIIIA, and GIIIA, at the voltage-gated potassium channels of the KV1 family, and they were correlated with their experimental activities recently reported by Leipold et al. Their different activities can only adequately be understood when dynamic information about the toxin-channel systems is available. For all of the channel-bound toxins investigated herein, a certain conformational flexibility was observed during the molecular dynamic simulations, which corresponds to their bioactivity. Our data suggest a similar binding mode of µ-PIIIA at KV1.6 and KV1.1, in which a plethora of hydrogen bonds are formed by the Arg and Lys residues within the α-helical core region of µ-PIIIA, with the central pore residues of the channel. Furthermore, the contribution of the K+ channel’s outer and inner pore loops with respect to the toxin binding. and how the subtype specificity is induced, were proposed.


2020 ◽  
Vol 117 (35) ◽  
pp. 21711-21722
Author(s):  
Hongkang Liu ◽  
Ping Yi ◽  
Wenjing Zhao ◽  
Yuling Wu ◽  
Francine Acher ◽  
...  

Many membrane receptors are regulated by nutrients. However, how these nutrients control a single receptor remains unknown, even in the case of the well-studied calcium-sensing receptor CaSR, which is regulated by multiple factors, including ions and amino acids. Here, we developed an innovative cell-free Förster resonance energy transfer (FRET)-based conformational CaSR biosensor to clarify the main conformational changes associated with activation. By allowing a perfect control of ambient nutrients, this assay revealed that Ca2+alone fully stabilizes the active conformation, while amino acids behave as pure positive allosteric modulators. Based on the identification of Ca2+activation sites, we propose a molecular basis for how these different ligands cooperate to control CaSR activation. Our results provide important information on CaSR function and improve our understanding of the effects of genetic mutations responsible for human diseases. They also provide insights into how a receptor can integrate signals from various nutrients to better adapt to the cell response.


Biochimie ◽  
2014 ◽  
Vol 105 ◽  
pp. 165-171 ◽  
Author(s):  
Daiming Zha ◽  
Huaidong Zhang ◽  
Houjin Zhang ◽  
Li Xu ◽  
Yunjun Yan

2016 ◽  
Vol 473 (18) ◽  
pp. 2863-2880 ◽  
Author(s):  
Jia Jia Lim ◽  
Youngjin Lee ◽  
Tue Tu Ly ◽  
Jung Youn Kang ◽  
Jung-Gyu Lee ◽  
...  

RHBDL4 is an active rhomboid that specifically recognizes and cleaves atypical, positively charged transmembrane endoplasmic reticulum-associated degradation (ERAD) substrates. Interaction of valosin-containing protein (p97/VCP) and RHBDL4 is crucial to retrotranslocate polyubiquitinated substrates for ERAD pathway. Here, we report the first complex structure of VCP-binding motif (VBM) with p97 N-terminal domain (p97N) at 1.88 Å resolution. Consistent with p97 adaptor proteins including p47-ubiquitin regulatory X (UBX), gp78-VCP-interacting motif (VIM), OTU1-UBX-like element, and FAF1-UBX, RHBDL4 VBM also binds at the interface between the two lobes of p97N. Notably, the RF residues in VBM are involved in the interaction with p97N, showing a similar interaction pattern with that of FPR signature motif in the UBX domain, although the directionality is opposite. Comparison of VBM interaction with VIM of gp78, another α-helical motif that interacts with p97N, revealed that the helix direction is inversed. Nevertheless, the conserved arginine residues in both motifs participate in the majority of the interface via extensive hydrogen bonds and ionic interactions with p97N. We identified novel VBM-binding mode to p97N that involves a combination of two types of p97–cofactor specificities observed in the UBX and VIM interactions. This highlights the induced fit model of p97N interdomain cleft upon cofactor binding to form stable p97–cofactor complexes. Our mutational and biochemical analyses in defining the specific interaction between VBM and p97N have elucidated the importance of the highly conserved VBM, applicable to other VBM-containing proteins. We also showed that RHBDL4, ubiquitins, and p97 co-operate for efficient substrate dislocation.


Sign in / Sign up

Export Citation Format

Share Document