scholarly journals Conformational maps of human 20S proteasomes reveal PA28- and immuno-dependent inter-ring crosstalks

2020 ◽  
Author(s):  
Jean Lesne ◽  
Marie Locard-Paulet ◽  
Julien Parra ◽  
Dušan Zivković ◽  
Marie-Pierre Bousquet ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Protein Complexes ◽  
3D Visualization ◽  
Solvent Accessibility ◽  
Proof Of Concept ◽  
Bioinformatic Pipeline ◽  
Hydrogen Deuterium ◽  
Hdx Ms ◽  
First Time ◽  
Structural Insights

AbstractHere, we used for the first time Hydrogen-Deuterium eXchange coupled to Mass Spectrometry (HDX-MS) to investigate conformational differences between the human standard 20S (std20S) and immuno 20S (i20s) proteasomes alone or in complex with PA28αβ or PA28γ activators. Their solvent accessibility was analyzed through a dedicated bioinformatic pipeline including stringent statistical analysis and 3D visualization. These data confirmed the existence of allosteric differences between the std20S and i20S at the surface of the α-ring triggered from inside the catalytic β-ring. Additionally, binding of the PA28 regulators to the 20S proteasomes modified solvent accessibility due to conformational changes of the β-rings. This work is not only a proof-of-concept that HDX-MS can be used to get structural insights on large multi-protein complexes in solution, it also demonstrates that the binding of the std20S or i20S subtype to any of its PA28 activator triggers allosteric changes that are specific to this 20S/PA28 pair.

scholarly journals Conformational maps of human 20S proteasomes reveal PA28- and immuno-dependent inter-ring crosstalks

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Jean Lesne ◽  
Marie Locard-Paulet ◽  
Julien Parra ◽  
Dušan Zivković ◽  
Thomas Menneteau ◽  
...  
Keyword(s):  
Structural Biology ◽  
Conformational Changes ◽  
Protein Complexes ◽  
3D Visualization ◽  
Solvent Accessibility ◽  
Proof Of Concept ◽  
Bioinformatic Pipeline ◽  
Hydrogen Deuterium ◽  
Hdx Ms ◽  
Structural Insights

AbstractHydrogen-Deuterium eXchange coupled to Mass Spectrometry (HDX-MS) is now common practice in structural biology. However, it is most of the time applied to rather small oligomeric complexes. Here, we report on the use of HDX-MS to investigate conformational differences between the human standard 20S (std20S) and immuno 20S (i20s) proteasomes alone or in complex with PA28αβ or PA28γ activators. Their solvent accessibility is analyzed through a dedicated bioinformatic pipeline including stringent statistical analysis and 3D visualization. These data confirm the existence of allosteric differences between the std20S and i20S at the surface of the α-ring triggered from inside the catalytic β-ring. Additionally, binding of the PA28 regulators to the 20S proteasomes modify solvent accessibility due to conformational changes of the β-rings. This work is not only a proof-of-concept that HDX-MS can be used to get structural insights on large multi-protein complexes in solution, it also demonstrates that the binding of the std20S or i20S subtype to any of its PA28 activator triggers allosteric changes that are specific to this 20S/PA28 pair.

scholarly journals Structure and nucleotide-induced conformational dynamics of the Chlorobium tepidum Roco protein

2019 ◽  
Vol 476 (1) ◽  
pp. 51-66 ◽  
Author(s):  
Egon Deyaert ◽  
Margaux Leemans ◽  
Ranjan Kumar Singh ◽  
Rodrigo Gallardo ◽  
Jan Steyaert ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Bound States ◽  
Conformational Dynamics ◽  
Bound State ◽  
Chlorobium Tepidum ◽  
Leucine Rich Repeat ◽  
Hydrogen Deuterium ◽  
Gtpase Cycle ◽  
Hdx Ms ◽  
First Time

Abstract The LRR (leucine-rich repeat)–Roc (Ras of complex proteins)–COR (C-terminal of Roc) domains are central to the action of nearly all Roco proteins, including the Parkinson's disease-associated protein LRRK2 (leucine-rich repeat kinase 2). We previously demonstrated that the Roco protein from Chlorobium tepidum (CtRoco) undergoes a dimer–monomer cycle during the GTPase reaction, with the protein being mainly dimeric in the nucleotide-free and GDP (guanosine-5′-diphosphate)-bound states and monomeric in the GTP (guanosine-5′-triphosphate)-bound state. Here, we report a crystal structure of CtRoco in the nucleotide-free state showing for the first time the arrangement of the LRR–Roc–COR. This structure reveals a compact dimeric arrangement and shows an unanticipated intimate interaction between the Roc GTPase domains in the dimer interface, involving residues from the P-loop, the switch II loop, the G4 region and a loop which we named the ‘Roc dimerization loop’. Hydrogen–deuterium exchange coupled to mass spectrometry (HDX-MS) is subsequently used to highlight structural alterations induced by individual steps along the GTPase cycle. The structure and HDX-MS data propose a pathway linking nucleotide binding to monomerization and relaying the conformational changes via the Roc switch II to the LRR and COR domains. Together, this work provides important new insights in the regulation of the Roco proteins.

scholarly journals Activation of GCN2 by the ribosomal P-stalk

2019 ◽  
Vol 116 (11) ◽  
pp. 4946-4954 ◽  
Author(s):  
Alison J. Inglis ◽  
Glenn R. Masson ◽  
Sichen Shao ◽  
Olga Perisic ◽  
Stephen H. McLaughlin ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Principal Component ◽  
Protein Translation ◽  
Translation Initiation Factor ◽  
Initiation Factor ◽  
Exchange Mass Spectrometry ◽  
Hydrogen Deuterium ◽  
Hdx Ms ◽  
Ribosomal P

Cells dynamically adjust their protein translation profile to maintain homeostasis in changing environments. During nutrient stress, the kinase general control nonderepressible 2 (GCN2) phosphorylates translation initiation factor eIF2α, initiating the integrated stress response (ISR). To examine the mechanism of GCN2 activation, we have reconstituted this process in vitro, using purified components. We find that recombinant human GCN2 is potently stimulated by ribosomes and, to a lesser extent, by tRNA. Hydrogen/deuterium exchange–mass spectrometry (HDX-MS) mapped GCN2–ribosome interactions to domain II of the uL10 subunit of the ribosomal P-stalk. Using recombinant, purified P-stalk, we showed that this domain of uL10 is the principal component of binding to GCN2; however, the conserved 14-residue C-terminal tails (CTTs) in the P1 and P2 P-stalk proteins are also essential for GCN2 activation. The HisRS-like and kinase domains of GCN2 show conformational changes upon binding recombinant P-stalk complex. Given that the ribosomal P-stalk stimulates the GTPase activity of elongation factors during translation, we propose that the P-stalk could link GCN2 activation to translational stress, leading to initiation of ISR.

scholarly journals Modulation of PTH1R signaling by an ECD binding antibody results in inhibition of β-arrestin 2 coupling

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Kaushik Sarkar ◽  
Lisa Joedicke ◽  
Marta Westwood ◽  
Rebecca Burnley ◽  
Michael Wright ◽  
...  
Keyword(s):  
Parathyroid Hormone ◽  
Conformational Changes ◽  
Transmembrane Domain ◽  
Receptor Activation ◽  
Parathyroid Hormone Receptor ◽  
Exchange Mass Spectrometry ◽  
Gpcr Activation ◽  
Hydrogen Deuterium ◽  
Binding Antibody ◽  
Hdx Ms

Abstract Parathyroid hormone receptor 1 (PTH1R) belongs to the secretin class of G protein coupled receptors (GPCRs) and natively binds parathyroid hormone (PTH) and parathyroid hormone related peptide (PTHrP). Ligand binding to PTH1R involves binding to the large extracellular domain (ECD) and the orthosteric pocket, inducing conformational changes in the transmembrane domain and receptor activation. PTH1R regulates bone metabolism, signaling mainly through Gs and Gq/11 G-proteins. Here, we used phage display to generate PTH1R ECD-specific antibodies with the aim of modulating receptor functionality. We identified ECD-scFvhFc, which exhibited high affinity binding to both the isolated ECD and to the full-length receptor in styrene-maleic acid (SMA) lipid particles. Epitope mapping using hydrogen-deuterium exchange mass spectrometry (HDX-MS) indicates that the α1 helix of the ECD is ECD-scFvhFc’s epitope which may partially overlap with the known PTH (1–34) binding site. However, PTH (1–34)-mediated Gs activation is Undisturbed by ECD-scFvhFc binding. In contrast, ECD-scFvhFc potently inhibits β-arrestin-2 recruitment after PTH (1–34)-driven receptor activation and thus represents the first monoclonal antibody to selectively inhibit distinct PTH1R signaling pathways. Given the complexity of PTH1R signaling and the emerging importance of biased GPCR activation in drug development, ECD-scFvhFc could be a valuable tool to study PTH1R signaling bias.

scholarly journals Structural insights into SETD3-mediated histidine methylation on β-actin

2018 ◽  
Author(s):  
Qiong Guo ◽  
Shanhui Liao ◽  
Sebastian Kwiatkowski ◽  
Weronika Tomaka ◽  
Huijuan Yu ◽  
...  
Keyword(s):  
Pulmonary Hypertension ◽  
Enzyme Activity ◽  
Small Molecule ◽  
Conformational Changes ◽  
Catalytic Mechanism ◽  
Site Directed Mutagenesis ◽  
Directed Mutagenesis ◽  
Domain Protein ◽  
First Time ◽  
Structural Insights

SETD3 is a member of SET (Su(var)3-9, Enhancer of zeste, and Trithorax) domain protein superfamily and plays important roles in hypoxic pulmonary hypertension, muscle differentiation, and carcinogenesis. Recently, we have identified SETD3 as the actin-specific methyltransferase that methylates the N3 of His73 on β-actin. Here we present two structures of S-adenosyl-L-homocysteine-bound SETD3 in complex with either an unmodified β-actin peptide or its His-methylated variant. Structural analyses supported by the site-directed mutagenesis experiments and the enzyme activity assays indicated that the recognition and methylation of β-actin by SETD3 is highly sequence specific, and both SETD3 and β-actin adopt pronounce conformational changes upon binding to each other. In conclusion, the data show for the first time a catalytic mechanism of SETD3-mediated histidine methylation in β-actin, which not only throws light on protein histidine methylation phenomenon, but also facilitates the design of small molecule inhibitors of SETD3.

scholarly journals A p.Arg127Gln variant in GPIbα LRR5 allosterically enhances affinity for VWF: a novel form of platelet-type VWD

2021 ◽  
Author(s):  
Loredana Bury ◽  
Emanuela Falcinelli ◽  
Haripriya Kuchi Bhotla ◽  
Anna Maria Mezzasoma ◽  
Giuseppe Guglielmini ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Conformational Dynamics ◽  
Von Willebrand Disease ◽  
High Affinity ◽  
Laboratory Test Results ◽  
Hydrogen Deuterium ◽  
Von Willebrand ◽  
The Impact ◽  
First Time ◽  
Willebrand Factor

Gain-of-function (GoF) variants in GP1BA cause platelet-type von Willebrand disease (PT-VWD), a rare inherited autosomal dominant bleeding disorder characterized by enhanced platelet GPIbα-von Willebrand factor (VWF) interaction and thrombocytopenia. To date, only 6 variants causing PT-VWD have been described, 5 in the C-terminal disulfide loop of the VWF-binding domain of GPIbα and 1 in the macroglycopeptide. GoF GP1BA variants generate a high affinity conformation of the C-terminal disulfide loop with a consequent allosteric conformational change on another region of GPIbα, the leucine-rich-repeat (LRR) domain. We identified a novel GP1BA variant (p.Arg127Gln) affecting the LRR5 domain of GPIbα in a boy with easy bruising and laboratory test results suggestive of PT-VWD. We thus aimed to investigate the impact of the p.Arg127Gln variant on GPIbα affinity for VWF and on GPIbα structure. CHO cells expressing p.Arg127Gln GPIbα showed increased binding of VWF induced by ristocetin and enhanced tethering on immobilized VWF as compared with cells expressing wild-type (WT) GPIbα. Surface plasmon resonance confirmed that p.Arg127Gln enhances the binding affinity of GPIbα for VWF. Hydrogen-deuterium exchange mass spectrometryshowed that p.Arg127Gln of LRR, while having little effect on the dynamics of the LRR locally, enhances the conformational dynamics of the GPIbα C-terminal disulfide loop structure. Our data demonstrate for the first time that GoF variants outside the GPIbα C-terminal disulfide loop may be pathogenic and that aminoacidic changes in the LRR may cause allosterically conformational changes in the C-terminal disulfide loop of GPIbα inducing a conformation with high affinity for VWF.

scholarly journals Conformational heterogeneity of Savinase from NMR, HDX-MS and X-ray diffraction analysis

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9408
Author(s):  
Shanshan Wu ◽  
Tam T.T.N. Nguyen ◽  
Olga V. Moroz ◽  
Johan P. Turkenburg ◽  
Jens E. Nielsen ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Solvent Accessibility ◽  
Conformational Dynamics ◽  
Structural Heterogeneity ◽  
Catalytic Process ◽  
Conformational Heterogeneity ◽  
X Ray ◽  
Exchange Mass Spectrometry ◽  
Bacillus Lentus ◽  
Hdx Ms

Background Several examples have emerged of enzymes where slow conformational changes are of key importance for function and where low populated conformations in the resting enzyme resemble the conformations of intermediate states in the catalytic process. Previous work on the subtilisin protease, Savinase, from Bacillus lentus by NMR spectroscopy suggested that this enzyme undergoes slow conformational dynamics around the substrate binding site. However, the functional importance of such dynamics is unknown. Methods Here we have probed the conformational heterogeneity in Savinase by following the temperature dependent chemical shift changes. In addition, we have measured changes in the local stability of the enzyme when the inhibitor phenylmethylsulfonyl fluoride is bound using hydrogen-deuterium exchange mass spectrometry (HDX-MS). Finally, we have used X-ray crystallography to compare electron densities collected at cryogenic and ambient temperatures and searched for possible low populated alternative conformations in the crystals. Results The NMR temperature titration shows that Savinase is most flexible around the active site, but no distinct alternative states could be identified. The HDX shows that modification of Savinase with inhibitor has very little impact on the stability of hydrogen bonds and solvent accessibility of the backbone. The most pronounced structural heterogeneities detected in the diffraction data are limited to alternative side-chain rotamers and a short peptide segment that has an alternative main-chain conformation in the crystal at cryo conditions. Collectively, our data show that there is very little structural heterogeneity in the resting state of Savinase and hence that Savinase does not rely on conformational selection to drive the catalytic process.

scholarly journals HDX-Viewer: interactive 3D visualization of hydrogen–deuterium exchange data

2019 ◽  
Vol 35 (24) ◽  
pp. 5331-5333 ◽  
Author(s):  
David Bouyssié ◽  
Jean Lesne ◽  
Marie Locard-Paulet ◽  
Renaud Albigot ◽  
Odile Burlet-Schiltz ◽  
...  
Keyword(s):  
Web Application ◽  
3D Visualization ◽  
3D Structure ◽  
Academic Research ◽  
Data Interpretation ◽  
Deuterium Exchange ◽  
Hydrogen Deuterium Exchange ◽  
Biological Interpretation ◽  
Hydrogen Deuterium ◽  
Hdx Ms

Abstract Summary With the advent of fully automated sample preparation robots for Hydrogen–Deuterium eXchange coupled to Mass Spectrometry (HDX-MS), this method has become paramount for ligand binding or epitope mapping screening, both in academic research and biopharmaceutical industries. However, bridging the gap between commercial HDX-MS software (for raw data interpretation) and molecular viewers (to map experiment results onto a 3D structure for biological interpretation) remains laborious and requires simple but sometimes limiting coding skills. We solved this bottleneck by developing HDX-Viewer, an open-source web-based application that facilitates and quickens HDX-MS data analysis. This user-friendly application automatically incorporates HDX-MS data from a custom template or commercial HDX-MS software in PDB files, and uploads them to an online 3D molecular viewer, thereby facilitating their visualization and biological interpretation. Availability and implementation The HDX-Viewer web application is released under the CeCILL (http://www.cecill.info) and GNU LGPL licenses and can be found at https://masstools.ipbs.fr/hdx-viewer. The source code is available at https://github.com/david-bouyssie/hdx-viewer.

scholarly journals CryoDRGN: Reconstruction of heterogeneous structures from cryo-electron micrographs using neural networks

2020 ◽  
Author(s):  
Ellen D. Zhong ◽  
Tristan Bepler ◽  
Bonnie Berger ◽  
Joseph H. Davis
Keyword(s):  
Neural Networks ◽  
Conformational Changes ◽  
Deep Neural Networks ◽  
Protein Complexes ◽  
Structural Heterogeneity ◽  
Particle Analysis ◽  
Single Particle Analysis ◽  
Current Analysis ◽  
Heterogeneous Structures ◽  
First Time

AbstractCryo-EM single-particle analysis has proven powerful in determining the structures of rigid macromolecules. However, many protein complexes are flexible and can change conformation and composition as a result of functionally-associated dynamics. Such dynamics are poorly captured by current analysis methods. Here, we present cryoDRGN, an algorithm that for the first time leverages the representation power of deep neural networks to efficiently reconstruct highly heterogeneous complexes and continuous trajectories of protein motion. We apply this tool to two synthetic and three publicly available cryo-EM datasets, and we show that cryoDRGN provides an interpretable representation of structural heterogeneity that can be used to identify discrete states as well as continuous conformational changes. This ability enables cryoDRGN to discover previously overlooked structural states and to visualize molecules in motion.

scholarly journals HDX-MS reveals nucleotide-dependent, anti-correlated opening and closure of SecA and SecY channels of the bacterial translocon

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Zainab Ahdash ◽  
Euan Pyle ◽  
William John Allen ◽  
Robin A Corey ◽  
Ian Collinson ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Opposite Effect ◽  
Protein Transport ◽  
Protein Translocation ◽  
Brownian Ratchet ◽  
Exchange Mass Spectrometry ◽  
Hydrogen Deuterium ◽  
Deuterium Exchange Mass Spectrometry ◽  
Dependent Transport ◽  
Hdx Ms

The bacterial Sec translocon is a multi-protein complex responsible for translocating diverse proteins across the plasma membrane. For post-translational protein translocation, the Sec-channel – SecYEG – associates with the motor protein SecA to mediate the ATP-dependent transport of pre-proteins across the membrane. Previously, a diffusional-based Brownian ratchet mechanism for protein secretion has been proposed; the structural dynamics required to facilitate this mechanism remain unknown. Here, we employ hydrogen-deuterium exchange mass spectrometry (HDX-MS) to reveal striking nucleotide-dependent conformational changes in the Sec protein-channel from Escherichia coli. In addition to the ATP-dependent opening of SecY, reported previously, we observe a counteracting, and ATP-dependent, constriction of SecA around the pre-protein. ATP binding causes SecY to open and SecA to close; while, ADP produced by hydrolysis, has the opposite effect. This alternating behaviour could help impose the directionality of the Brownian ratchet for protein transport through the Sec machinery.

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