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81
المؤلفون: Justin T Seffernick, Daniel R Marzolf, Steffen Lindert
المصدر: Journal of Chemical Theory and Computation. 17:2619-2629
مصطلحات موضوعية: Models, Molecular, Measure (data warehouse), Binding Sites, 010304 chemical physics, Protein Conformation, Computer science, Model selection, Ab initio, Deuterium Exchange Measurement, Proteins, Protein structure prediction, ENCODE, Amides, 01 natural sciences, Computer Science Applications, Protein structure, 0103 physical sciences, Benchmark (computing), Hydrogen–deuterium exchange, Physical and Theoretical Chemistry, Biological system, Nuclear Magnetic Resonance, Biomolecular
الوصف: Amide hydrogen-deuterium exchange (HDX) has long been used to determine regional flexibility and binding sites in proteins; however, the data are too sparse for full structural characterization. Experiments that measure HDX rates, such as HDX-NMR, have far higher throughput compared to structure determination via X-ray crystallography, cryo-EM, or a full suite of NMR experiments. Data from HDX-NMR experiments encode information on the protein structure, making HDX a prime candidate to be supplemented by computational algorithms for protein structure prediction. We have developed a methodology to incorporate HDX-NMR data into ab initio protein structure prediction using the Rosetta software framework to predict structures based on experimental agreement. To demonstrate the efficacy of our algorithm, we examined 38 proteins with HDX-NMR data available, comparing the predicted model with and without the incorporation of HDX data into scoring. The root-mean-square deviation (rmsd, a measure of the average atomic distance between superimposed models) of the predicted model improved by 1.42 A on average after incorporating the HDX-NMR data into scoring. The average rmsd improvement for the proteins where the selected model rmsd changed after incorporating HDX data was 3.63 A, including one improvement of more than 11 A and seven proteins improving by greater than 4 A, with 12/15 proteins improving overall. Additionally, for independent verification, two proteins that were not part of the original benchmark were scored including HDX data, with a dramatic improvement of the selected model rmsd of nearly 9 A for one of the proteins. Moreover, we have developed a confidence metric allowing us to successfully identify near-native models in the absence of a native structure. Improvement in model selection with a strong confidence measure demonstrates that protein structure prediction with HDX-NMR is a powerful tool which can be performed with minimal additional computational strain and expense.
الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::fe132e4d78cbff915d234acb3eaa4f02Test
https://doi.org/10.1021/acs.jctc.1c00077Test -
82
المؤلفون: Miklos Guttman, Rick Harkewicz, Kimberly M. Alonge
المصدر: Curr Mol Med
مصطلحات موضوعية: Spectrometry, Mass, Electrospray Ionization, Ion-mobility spectrometry, Chondroitin Sulfates, Disaccharide, Deuterium Exchange Measurement, General Medicine, Mass spectrometry, Biochemistry, Article, chemistry.chemical_compound, Sulfation, chemistry, Deuterium, Computational chemistry, Humans, Molecular Medicine, Hydrogen–deuterium exchange, Chondroitin sulfate, Sulfate, Molecular Biology
الوصف: Chondroitin sulfate (CS)-glycosaminoglycans (GAGs) are linear, negatively charged polysaccharides attached to CS proteoglycans that make up a major component of biological matrices throughout both central and peripheral tissues. The position of their attached sulfate groups to the CS disaccharide is predicted to influence protein-glycan interactions and biological function. Although traditional immunohistochemical analysis of CS-GAGs in biological tissues has provided information regarding changes in GAG abundance during developmental and disease states, quantitative analysis of their specific sulfation patterns is limited due to the inherent complexity of separating CS isomers. While methods have been developed to analyze and quantify sulfation isomers using liquid phase separation, new techniques are still needed to elucidate the full biology of CS-GAGs. Here, we examine ion mobility spectrometry and gas-phase hydrogen-deuterium exchange to resolve positional sulfation isomers in the most common sulfated 4S- and 6S-CS disaccharides. The mobilities for these two isomers are highly similar and could not be resolved effectively with any drift gas tested. In contrast, gas-phase hydrogen-deuterium exchange showed very different rates of deuterium uptake with several deuterium exchange reagents, thereby presenting a promising novel and rapid approach for resolving CS isomers.
الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::19e46484e92eefadf3dfb7957fc278ddTest
https://doi.org/10.2174/1566524020666200915110707Test -
83دورية أكاديمية
المؤلفون: Canul-Tec, Juan, Assal, Reda, Cirri, Erica, Legrand, Pierre, Brier, Sébastien, Chamot-Rooke, Julia, Reyes, Nicolas
المساهمون: Mécanismes moléculaires du transport membranaire - Molecular mechanisms of membrane transport, Institut Pasteur Paris (IP)-Centre National de la Recherche Scientifique (CNRS), Synchrotron SOLEIL (SSOLEIL), Centre National de la Recherche Scientifique (CNRS), Spectrométrie de Masse pour la Biologie – Mass Spectrometry for Biology (UTechS MSBio), Institut Pasteur Paris (IP)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), The work was funded by the ERC Starting grant 309657 (N.R.). Further support from G5 Institut Pasteur funds (N.R.), CACSICE grant (ANR-11-EQPX-008), and CNRS UMR3528 (N.R., J.C.-R.) is acknowledged., We thank O. Boudker for comments on the manuscript and discussion on consensus mutagenesis, P. V. Krasteva for comments on the manuscript, A. Haouz and the staff at the crystallogenesis core facility of the Institut Pasteur for assistance with crystallization screens, Staff at Synchrotron SOLEIL and the European Synchrotron Radiation Facility for assistance with data collection, D. O’Brien for discussion of HDX results., ANR-11-EQPX-0008,CACSICE,Centre d'analyse de systèmes complexes dans les environnements complexes(2011), European Project: 309657,EC:FP7:ERC,ERC-2012-StG_20111109,HEAATS(2012)
المصدر: ISSN: 0028-0836.
مصطلحات موضوعية: Membrane proteins, Molecular neuroscience, Permeation and transport, MESH: Allosteric Regulation, MESH: Allosteric Site, MESH: Crystallization, MESH: Crystallography, X-Ray, MESH: Deuterium Exchange Measurement, MESH: Excitatory Amino Acid Transporter 1, MESH: Humans, MESH: Mass Spectrometry, MESH: Models, Molecular, MESH: Protein Domains, [SDV.BBM.BP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics
الوصف: International audience ; Human members of the solute carrier 1 (SLC1) family of transporters take up excitatory neurotransmitters in the brain and amino acids in peripheral organs. Dysregulation of the function of SLC1 transporters is associated with neurodegenerative disorders and cancer. Here we present crystal structures of a thermostabilized human SLC1 transporter, the excitatory amino acid transporter 1 (EAAT1), with and without allosteric and competitive inhibitors bound. The structures reveal architectural features of the human transporters, such as intra- and extracellular domains that have potential roles in transport function, regulation by lipids and post-translational modifications. The coordination of the allosteric inhibitor in the structures and the change in the transporter dynamics measured by hydrogen-deuterium exchange mass spectrometry reveal a mechanism of inhibition, in which the transporter is locked in the outward-facing states of the transport cycle. Our results provide insights into the molecular mechanisms underlying the function and pharmacology of human SLC1 transporters.
العلاقة: info:eu-repo/semantics/altIdentifier/pmid/28424515; info:eu-repo/grantAgreement/EC/FP7/309657/EU/Molecular bases of human excitatory neurotransmitter transport across the plasma membrane/HEAATS; pasteur-01655604; https://hal-pasteur.archives-ouvertes.fr/pasteur-01655604Test; https://hal-pasteur.archives-ouvertes.fr/pasteur-01655604/documentTest; https://hal-pasteur.archives-ouvertes.fr/pasteur-01655604/file/Canul-Tech-etal_nature_accepted_HAL.pdfTest; PUBMED: 28424515; PUBMEDCENTRAL: PMC5410168
الإتاحة: https://doi.org/10.1038/nature22064Test
https://hal-pasteur.archives-ouvertes.fr/pasteur-01655604Test
https://hal-pasteur.archives-ouvertes.fr/pasteur-01655604/documentTest
https://hal-pasteur.archives-ouvertes.fr/pasteur-01655604/file/Canul-Tech-etal_nature_accepted_HAL.pdfTest -
84دورية أكاديمية
المؤلفون: Reading, Eamonn, Hall, Zoe, Martens, Chloé, Haghighi, Tabasom, Findlay, Heather, Ahdash, Zainab, Politis, Argyris, Booth, P. S L
المصدر: Angewandte Chemie, 56 (49
مصطلحات موضوعية: Sciences bio-médicales et agricoles, DNA-Binding Proteins -- metabolism, Deuterium Exchange Measurement, Endopeptidases -- metabolism, Escherichia coli Proteins -- metabolism, Lipids -- chemistry, Mass Spectrometry, Membrane Proteins -- chemistry -- metabolism, Protein Conformation, lipids, membrane nanodiscs, membrane proteins, structural biology
الوصف: The interplay between membrane proteins and the lipids of the membrane is important for cellular function, however, tools enabling the interrogation of protein dynamics within native lipid environments are scarce and often invasive. We show that the styrene-maleic acid lipid particle (SMALP) technology can be coupled with hydrogen-deuterium exchange mass spectrometry (HDX-MS) to investigate membrane protein conformational dynamics within native lipid bilayers. We demonstrate changes in accessibility and dynamics of the rhomboid protease GlpG, captured within three different native lipid compositions, and identify protein regions sensitive to changes in the native lipid environment. Our results illuminate the value of this approach for distinguishing the putative role(s) of the native lipid composition in modulating membrane protein conformational dynamics. ; info:eu-repo/semantics/published
وصف الملف: 1 full-text file(s): application/pdf
العلاقة: uri/info:doi/10.1002/anie.201709657; uri/info:pmid/29049865; https://dipot.ulb.ac.be/dspace/bitstream/2013/310048/3/Reading_et_al2017Angewandte_Chemie.pdfTest; http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/310048Test
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85دورية أكاديمية
المؤلفون: Zheng, J., Chang, M., Stites, R., Wang, Y., Bruning, J., Pascal, B., Novick, S., Garcia-Ordonez, R., Stayrook, K., Chalmers, M., Dodge, J., Griffin, P.
مصطلحات موضوعية: Humans, Hydrogen, Vitamin D, Osteocalcin, Retinoid X Receptors, Receptors, Calcitriol, DNA, Ligands, Deuterium Exchange Measurement, Protein Binding, Dimerization, Mass Spectrometry
الوصف: The vitamin D receptor/retinoid X receptor-α heterodimer (VDRRXRα) regulates bone mineralization via transcriptional control of osteocalcin (BGLAP) gene and is the receptor for 1α,25-dihydroxyvitamin D3 (1,25D3). However, supra-physiological levels of 1,25D3 activates the calcium-regulating gene TRPV6 leading to hypercalcemia. An approach to attenuate this adverse effect is to develop selective VDR modulators (VDRMs) that differentially activate BGLAP but not TRPV6. Here we present structural insight for the action of a VDRM compared with agonists by employing hydrogen/deuterium exchange. Agonist binding directs crosstalk between co-receptors upon DNA binding, stabilizing the activation function 2 (AF2) surfaces of both receptors driving steroid receptor co-activator-1 (SRC1) interaction. In contrast, AF2 of VDR within VDRM:BGLAP bound heterodimer is more vulnerable for large stabilization upon SRC1 interaction compared with VDRM:TRPV6 bound heterodimer. These results reveal that the combination of ligand structure and DNA sequence tailor the transcriptional activity of VDR toward specific target genes.The vitamin D receptor/retinoid X receptor-α heterodimer (VDRRXRα) regulates bone mineralization. Here the authors employ hydrogen/deuterium exchange (HDX) mass spectrometry to study the conformational dynamics of VDRRXRα and give mechanistic insights into how VDRRXRα controls the transcriptional activity of specific genes. ; Jie Zheng, Mi Ra Chang, Ryan E. Stites, Yong Wang, John B. Bruning, Bruce D. Pascal, Scott J. Novick, Ruben D. Garcia-Ordonez, Keith R. Stayrook, Michael J. Chalmers, Jeffrey A. Dodge & Patrick R. Griffin
وصف الملف: application/pdf
العلاقة: Nature Communications, 2017; 8(1):923-1-923-13; http://hdl.handle.net/2440/118929Test; Bruning, J. [0000-0002-6919-1824]
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86دورية أكاديمية
المؤلفون: Jensen, Pernille Foged, Schoch, Angela, Larraillet, Vincent, Hilger, Maximiliane, Schlothauer, Tilman, Emrich, Thomas, Rand, Kasper Dyrberg
المصدر: Jensen , P F , Schoch , A , Larraillet , V , Hilger , M , Schlothauer , T , Emrich , T & Rand , K D 2017 , ' A Two-pronged Binding Mechanism of IgG to the Neonatal Fc Receptor Controls Complex Stability and IgG Serum Half-life ' , Molecular and Cellular Proteomics , vol. 16 , no. 3 , pp. 451-456 . https://doi.org/10.1074/mcp.M116.064675Test
مصطلحات موضوعية: Antibodies, Monoclonal/chemistry, Binding Sites, Deuterium Exchange Measurement/methods, Half-Life, Histocompatibility Antigens Class I/metabolism, Humans, Hydrogen-Ion Concentration, Immunoglobulin G/chemistry, Mass Spectrometry/methods, Models, Molecular, Protein Binding, Protein Stability, Receptors, Fc/metabolism
الوصف: The success of recombinant monoclonal immunoglobulins (IgG) is rooted in their ability to target distinct antigens with high affinity combined with an extraordinarily long serum half-life, typically around 3 weeks. The pharmacokinetics of IgGs is intimately linked to the recycling mechanism of the neonatal Fc receptor (FcRn). For long serum half-life of therapeutic IgGs, the highly pH-dependent interaction with FcRn needs to be balanced to allow efficient FcRn binding and release at slightly acidic pH and physiological pH, respectively. Some IgGs, like the antibody briakinumab has an unusually short half-life of ∼8 days. Here we dissect the molecular origins of excessive FcRn binding in therapeutic IgGs using a combination of hydrogen/deuterium exchange mass spectrometry and FcRn affinity chromatography. We provide experimental evidence for a two-pronged IgG-FcRn binding mechanism involving direct FcRn interactions with both the Fc region and the Fab regions of briakinumab, and correlate the occurrence of excessive FcRn binding to an unusually strong Fab-FcRn interaction.
وصف الملف: application/pdf
الإتاحة: https://doi.org/10.1074/mcp.M116.064675Test
https://curis.ku.dk/portal/da/publications/a-twopronged-binding-mechanism-of-igg-to-the-neonatal-fc-receptor-controls-complex-stability-and-igg-serum-halflifeTest(17c9172d-f7ef-40e1-8929-838b76eb8e52).html
https://curis.ku.dk/ws/files/196136206/451.full.pdfTest -
87
المساهمون: Chimie et Biologie des Membranes et des Nanoobjets (CBMN), Université de Bordeaux (UB)-École Nationale d'Ingénieurs des Travaux Agricoles - Bordeaux (ENITAB)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), European Project: H2020 MSCA-60 ITN
المصدر: Biophysical Chemistry
Biophysical Chemistry, 2022, 289, ⟨10.1016/j.bpc.2022.106861⟩مصطلحات موضوعية: Lead, Protein Conformation, Organic Chemistry, Paint, Biophysics, Deuterium Exchange Measurement, Proteins, Hydrogen Deuterium Exchange-Mass Spectrometry, [CHIM.MATE]Chemical Sciences/Material chemistry, Deuterium, Biochemistry
الوصف: Little is known about structural alterations of proteins within the polymeric films of paints. For the first time, hydrogen‑deuterium exchange mass spectrometry (HDX-MS) was implemented to explore the conformational alterations of proteins resulting from their interaction with inorganic pigments within the early stages of the paint film formation. Intact protein analysis and bottom-up electrospray-ionisation mass spectrometry strategies combined with progressively increasing deuterium incubation times were used to compare the protein structures of the model protein hen egg-white lysozyme (HEWL) extracted from newly dried non-pigmented films and newly dried films made from a freshly made mixture of HEWL with lead white pigment (2PbCO3 Pb(OH)2). The action of other pigments was also investigated, expanding the HDX study with a global approach to paint models of HEWL mixed with zinc white (ZnO), cinnabar (HgS) and red lead (Pb3O4) pigments. The results show structural modifications of HEWL induced by the interaction with the pigment metal ions during the paint formulation after drying and prior to ageing. Both the charge distribution of HEWL proteoforms, its oxidation rate and its deuterium absorption rate, were influenced by the pigment type, providing the first insights into the correlation of pigment type/metal cation to specific chemistries related to protein stability.
الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::4af0aab181eaef42b346c4a2403f93deTest
https://pubmed.ncbi.nlm.nih.gov/35940022Test -
88
المصدر: Cellular and Molecular Life Sciences. 79
مصطلحات موضوعية: Pharmacology, Ubiquitin-Protein Ligases, Serine Endopeptidases, Deuterium Exchange Measurement, Cell Biology, Dengue Virus, Viral Nonstructural Proteins, Mass Spectrometry, Dengue, Tripartite Motif Proteins, Cellular and Molecular Neuroscience, Humans, Molecular Medicine, Molecular Biology
الوصف: Tripartite motif (TRIM) E3 ligases target specific substrates, including viral proteins, for proteasomal degradation, and are thus essential regulators of the innate antiviral response. TRIM69 ubiquitinates the non-structural NS3 protein of Dengue virus for its degradation by the host machinery. This antiviral strategy abrogates the immunosuppression mediated by the NS2B-NS3 protease complex. To understand how this host-driven antiviral response against Dengue virus, we sought to define the mode of interaction between human TRIM69 and Dengue NS2B-NS3 and the subsequent polyubiquitination of the protease by the E3 ligase. We show that NS2B-NS3Δpro is sufficient as a substrate for ubiquitination by TRIM69 using ELISA and in vitro assays. Using hydrogen-deuterium exchange mass spectrometry (HDXMS), we mapped the interface of the interaction between TRIM69 and NS2B-NS3Δpro, and propose a rationale for the binding and subsequent ubiquitination process. Furthermore, through sequence analysis, we showed that the regions targeted by TRIM69 on the DENV-2 NS3 protease (NS3Δpro) are well conserved across DENV serotypes and other flaviviruses, including Zika virus, West Nile virus, and Japanese encephalitis virus. Our results show the direct interactions of TRIM69 with viral proteins, provide mechanistic insights at a molecular level, and highlight the functional relevance of TRIM69 interacting with the Dengue viral protein. Collectively, our findings suggest that TRIM69 may act as a pan-antiflaviviral restriction factor.
الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::ccf5efa5fbfb62a1201424dcf6002443Test
https://doi.org/10.1007/s00018-022-04245-xTest -
89
المؤلفون: Andrew P. Hinck
المصدر: Archives of biochemistry and biophysics. 726
مصطلحات موضوعية: Biophysics, Deuterium Exchange Measurement, Proteins, Deuterium, Peptides, Molecular Biology, Biochemistry, Hydrogen
الوصف: This commentary highlights the landmark manuscript published in 1957 by Arieh Berger and K. Linderstrøm-Lang that describes the measurement and analysis of hydrogen exchange rates. This highly referenced manuscript is recognized because the impact hydrogen exchange has had on characterizing the structure and dynamics of natively folded proteins and folding intermediates.
الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::76810b32e772040b2689a2c294d5fc85Test
https://pubmed.ncbi.nlm.nih.gov/35321824Test -
90
المؤلفون: Alice R Eddershaw, Karl Syson, Paul R. J. Davey, Gregory Hamm, Christopher D. Stubbs, Paul Clarkson, Elizabeth Underwood, Lucy V Edwardes
المصدر: Biochemistry. 59:4775-4786
مصطلحات موضوعية: Models, Molecular, Protein-Arginine N-Methyltransferases, Methyltransferase, Arginine, In Vitro Techniques, Biochemistry, Mass Spectrometry, Substrate Specificity, 03 medical and health sciences, Protein structure, Catalytic Domain, Humans, Protein Interaction Domains and Motifs, Amino Acid Sequence, Enzyme Inhibitors, Protein Structure, Quaternary, Ternary complex, Adaptor Proteins, Signal Transducing, 0303 health sciences, Chemistry, Protein arginine methyltransferase 5, 030302 biochemistry & molecular biology, Deuterium Exchange Measurement, Recombinant Proteins, Kinetics, Biophysics, Hydrogen–deuterium exchange, Steady state (chemistry)
الوصف: Protein arginine methyltransferases (PRMTs) are of great interest for the development of therapeutics due to their involvement in a number of malignancies, such as lung and colon cancer. PRMT5 catalyzes the formation of symmetrical dimethylarginine of a wide variety of substrates and is responsible for the majority of this mark within cells. To gain insight into the mechanism of PRMT5 inhibition, we co-expressed the human PRMT5:MEP50 complex (hPRMT5:MEP50) in insect cells for a detailed mechanistic study. In this report, we carry out steady state, product, and dead-end inhibitor studies that show hPRMT5:MEP50 uses a rapid equilibrium random order mechanism with EAP and EBQ dead-end complexes. We also provide evidence of ternary complex formation in solution using hydrogen/deuterium exchange mass spectrometry. Isotope exchange and intact protein mass spectrometry further rule out ping-pong as a potential enzyme mechanism, and finally, we show that PRMT5 exhibits a pre-steady state burst that corresponds to an initial slow turnover with all four active sites of the hetero-octamer being catalytically active.
الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::e0c63875119c271f482688a035fe6bfcTest
https://doi.org/10.1021/acs.biochem.0c00554Test
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