DeutEx

Publications

List of bublications where DeutEx was used for HDX-MS data processing.

List of publications

• A conserved tryptophan in the acylated segment of RTX toxins controls their β2-integrin-independent cell penetration
  Osickova A, Knoblochova S, Bumba L, Man P, Kalaninova Z, Lepesheva A, Jurnecka D, Cizkova M, Biedermannova L, Goldsmith JA, Maynard JA, McLellan, JS, Osicka R, Sebo P, Masin J
  J. Biol. Chem. in press
• Hydrogen/Deuterium Exchange Mass Spectrometry of Heme-Based Oxygen Sensor Proteins. Vávra J, Sergunin A, Stráňava M, Kádek A, Shimizu T, Man P, Martínková M
  Methods Mol Biol. 2023;2648:99-122.DOI: 10.1007/978-1-0716-3080-8_8
• Counterintuitive structural and functional effects due to naturally-occurring mutations targeting the active site of the disease-associated NQO1 enzyme.
  Pacheco-Garcia JL, Anoz-Carbonell E, Loginov DS, Kavan D, Salido E, Man P, Medina M, Pey AL
  FEBS J 2023 Apr; 290(7):1855-1873. DOI: 10.1111/febs.16677
• Loss of stability and unfolding cooperativity in hPGK1 upon gradual structural perturbation of its N-terminal domain hydrophobic core.
  Pacheco-Garcia JL, Loginov DS, Naganathan AN, Vankova P, Cano-Munoz M, Man P, Pey AL
  Sci. Rep. 2022 Oct 13; 12:17200. DOI: 10.1038/s41598-022-22088-1
• Different phenotypic outcome due to site-specific phosphorylation in the cancer-associated NQO1 enzyme studied by phosphomimetic mutations.
  Pacheco-Garcia JL, Anoz-Carbonell E, Loginov DS, Vankova P, Salido E, Man P, Medina M, Palomino-Morales R, Pey AL
  Arch. Biochem. Biophys. 2022 Sep 9; 109392. DOI: 10.1016/j.abb.2022.109392
• TTYH family members form tetrameric complexes at the cell membrane.
  Melvin E, Kalaninova Z, Slush E, Man P, Giladi M, Haitin Y.
  Commun. Biol. 2022 Aug 30;5:886. DOI: 10.1038/s42003-022-03862-3
• Allosteric communication in the multifunctional and redox NQO1 protein studied by cavity-making mutations.
  Pacheco-Garcia JL, Loginov DS, Anoz-Carbonell E, Vankova P, Palomino-Morales R, Salido E, Man P, Medina M, Naganathan AN, Pey AL
  Antioxidants 2022 Jun 2; 11(6); 1110. DOI: 10.3390/antiox11061110
• Giladi M, Lisnyansky Bar-El M, Vaňková P, Ferofontov A, Melvin E, Alkaderi S, Kavan D, Redko B, Haimov E, Wiener R, Man P, Haitin Y.
  Structural basis for long-chain isoprenoid synthesis by cis-prenyltransferases.
  Sci Adv. 2022 May 20;8(20):eabn1171. DOI: 10.1126/sciadv.abn1171
• A single evolutionarily divergent mutation determines the different FAD-binding affinities of human and rat NQO1 due to site-specific phosphorylation.
  Pacheco-Garcia JL, Loginov D, Rizzuti B, Vankova P, Neira JL, Kavan D, Mesa-Torres N, Guzzi R, Man P, Pey AL.
  FEBS Lett. 2022 Jan;596(1):29-41. doi: 10.1002/1873-3468.14238
• Structural basis of the pleiotropic and specific phenotypic consequences of missense mutations in the multifunctional NAD(P)H:quinone oxidoreductase 1 and their pharmacological rescue.
  Pacheco-Garcia JL, Anoz-Carbonell E, Vankova P, Kannan A, Palomino-Morales R, Mesa-Torres N, Salido E, Man P, Medina M, Naganathan AN, Pey AL.
  Redox Biol. 2021 Oct;46:102112. doi: 10.1016/j.redox.2021.102112
• An Integrative Structural Biology Analysis of Von Willebrand Factor Binding and Processing by ADAMTS-13 in Solution.
  Del Amo-Maestro L, Sagar A, Pompach P, Goulas T, Scavenius C, Ferrero DS, Castrillo-Briceño M, Taulés M, Enghild JJ, Bernadó P, Gomis-Rüth FX.
  J Mol Biol. 2021 Jun 25;433(13):166954. doi: 10.1016/j.jmb.2021.166954
• Motif orientation matters: Structural characterization of TEAD1 recognition of genomic DNA.
  Filandrová R, Vališ K, Černý J, Chmelík J, Slavata L, Fiala J, Rosůlek M, Kavan D, Man P, Chum T, Cebecauer M, Fabris D, Novák P.
  Structure. 2021 Apr 1;29(4):345-356.e8. doi: 10.1016/j.str.2020.11.018
• Chimeric Cellobiose Dehydrogenases Reveal the Function of Cytochrome Domain Mobility for the Electron Transfer to Lytic Polysaccharide Monooxygenase.
  Felice AKG, Schuster C, Kadek A, Filandr F, Laurent CVFP, Scheiblbrandner S, Schwaiger L, Schachinger F, Kracher D, Sygmund C, Man P, Halada P, Oostenbrink C, Ludwig R.
  ACS Catal. 2021 Jan 15;11(2):517-532. doi: 10.1021/acscatal.0c05294
• Studying Protein-DNA Interactions by Hydrogen/Deuterium Exchange Mass Spectrometry.
  Filandrova R, Kavan D, Kadek A, Novak P, Man P.
  Methods Mol Biol. 2021;2247:193-219. doi: 10.1007/978-1-0716-1126-5_11
• Structural basis of heterotetrameric assembly and disease mutations in the human cis-prenyltransferase complex.
  Bar-El ML, Vaňková P, Yeheskel A, Simhaev L, Engel H, Man P, Haitin Y, Giladi M.
  Nat Commun. 2020 Oct 19;11(1):5273. doi: 10.1038/s41467-020-18970-z
• Conserved cysteine dioxidation enhances membrane interaction of human Cl- intracellular channel 5.
  Ferofontov A, Vankova P, Man P, Giladi M, Haitin Y.
  FASEB J. 2020 Aug;34(8):9925-9940. doi: 10.1096/fj.202000399R
• The interaction of the mitochondrial protein importer TOMM34 with HSP70 is regulated by TOMM34 phosphorylation and binding to 14-3-3 adaptors.
  Trcka F, Durech M, Vankova P, Vandova V, Simoncik O, Kavan D, Vojtesek B, Muller P, Man P.
  J Biol Chem. 2020 Jul 3;295(27):8928-8944. doi: 10.1074/jbc.RA120.012624
• On the mechanism of calcium-dependent activation of NADPH oxidase 5 (NOX5).
  Millana Fañanás E, Todesca S, Sicorello A, Masino L, Pompach P, Magnani F, Pastore A, Mattevi A.
  FEBS J. 2020 Jun;287(12):2486-2503. doi: 10.1111/febs.15160
• Structural Dynamics of Lytic Polysaccharide Monooxygenase during Catalysis.
  Filandr F, Kavan D, Kracher D, Laurent CVFP, Ludwig R, Man P, Halada P.
  Biomolecules. 2020 Feb 5;10(2):242. doi: 10.3390/biom10020242
• 14-3-3 protein binding blocks the dimerization interface of caspase-2.
  Kalabova D, Filandr F, Alblova M, Petrvalska O, Horvath M, Man P, Obsil T, Obsilova V.
  FEBS J. 2020 Aug;287(16):3494-3510. doi: 10.1111/febs.15215
• HSPA1A conformational mutants reveal a conserved structural unit in Hsp70 proteins.
  Vandova V, Vankova P, Durech M, Houser J, Kavan D, Man P, Muller P, Trcka F.
  Biochim Biophys Acta Gen Subj. 2020 Jan;1864(1):129458. doi: 10.1016/j.bbagen.2019.129458
• A Dynamic Core in Human NQO1 Controls the Functional and Stability Effects of Ligand Binding and Their Communication across the Enzyme Dimer.
  Vankova P, Salido E, Timson DJ, Man P, Pey AL.
  Biomolecules. 2019 Nov 12;9(11):728. doi: 10.3390/biom9110728
• MS-Based Approaches Enable the Structural Characterization of Transcription Factor/DNA Response Element Complex.
  Slavata L, Chmelík J, Kavan D, Filandrová R, Fiala J, Rosůlek M, Mrázek H, Kukačka Z, Vališ K, Man P, Miller M, McIntyre W, Fabris D, Novák P.
  Biomolecules. 2019 Sep 26;9(10):535. doi: 10.3390/biom9100535
• Thiopurine intolerance-causing mutations in NUDT15 induce temperature-dependent destabilization of the catalytic site.
  Man P, Fábry M, Sieglová I, Kavan D, Novák P, Hnízda A.
  Biochim Biophys Acta Proteins Proteom. 2019 Apr;1867(4):376-381. doi: 10.1016/j.bbapap.2019.01.006
• Human Stress-inducible Hsp70 Has a High Propensity to Form ATP-dependent Antiparallel Dimers That Are Differentially Regulated by Cochaperone Binding.
  Trcka F, Durech M, Vankova P, Chmelik J, Martinkova V, Hausner J, Kadek A, Marcoux J, Klumpler T, Vojtesek B, Muller P, Man P.
  Mol Cell Proteomics. 2019 Feb;18(2):320-337. doi: 10.1074/mcp.RA118.001044
• Coordination and redox state-dependent structural changes of the heme-based oxygen sensor AfGcHK associated with intraprotein signal transduction.
  Stranava M, Man P, Skálová T, Kolenko P, Blaha J, Fojtikova V, Martínek V, Dohnálek J, Lengalova A, Rosůlek M, Shimizu T, Martínková M.
  J Biol Chem. 2017 Dec 22;292(51):20921-20935. doi: 10.1074/jbc.M117.817023
• Interdomain electron transfer in cellobiose dehydrogenase is governed by surface electrostatics.
  Kadek A, Kavan D, Marcoux J, Stojko J, Felice AK, Cianférani S, Ludwig R, Halada P, Man P. Biochim Biophys Acta Gen Subj. 2017 Feb;1861(2):157-167. doi: 10.1016/j.bbagen.2016.11.016
• Oligomeric interface modulation causes misregulation of purine 5´-nucleotidase in relapsed leukemia.
  Hnízda A, Škerlová J, Fábry M, Pachl P, Šinalová M, Vrzal L, Man P, Novák P, Řezáčová P, Veverka V.
  BMC Biol. 2016 Oct 19;14(1):91. doi: 10.1186/s12915-016-0313-y
• Structural characterization of the heme-based oxygen sensor, AfGcHK, its interactions with the cognate response regulator, and their combined mechanism of action in a bacterial two-component signaling system.
  Stranava M, Martínek V, Man P, Fojtikova V, Kavan D, Vaněk O, Shimizu T, Martinkova M.
  Proteins. 2016 Oct;84(10):1375-89. doi: 10.1002/prot.25083
• Structural insights and in vitro reconstitution of membrane targeting and activation of human PI4KB by the ACBD3 protein.
  Klima M, Tóth DJ, Hexnerova R, Baumlova A, Chalupska D, Tykvart J, Rezabkova L, Sengupta N, Man P, Dubankova A, Humpolickova J, Nencka R, Veverka V, Balla T, Boura E.
  Sci Rep. 2016 Mar 24;6:23641. doi: 10.1038/srep23641
• Novel Entropically Driven Conformation-specific Interactions with Tomm34 Protein Modulate Hsp70 Protein Folding and ATPase Activities.
  Durech M, Trcka F, Man P, Blackburn EA, Hernychova L, Dvorakova P, Coufalova D, Kavan D, Vojtesek B, Muller P.
  Mol Cell Proteomics. 2016 May;15(5):1710-27. doi: 10.1074/mcp.M116.058131
• Structural Characterization of Phosducin and Its Complex with the 14-3-3 Protein.
  Kacirova M, Kosek D, Kadek A, Man P, Vecer J, Herman P, Obsilova V, Obsil T.
  J Biol Chem. 2015 Jun 26;290(26):16246-60. doi: 10.1074/jbc.M115.636563
• Structural insight into the calcium ion modulated interdomain electron transfer in cellobiose dehydrogenase.
  Kadek A, Kavan D, Felice AK, Ludwig R, Halada P, Man P.
  FEBS Lett. 2015 May 8;589(11):1194-9. doi: 10.1016/j.febslet.2015.03.029
• Role of the EF-hand-like motif in the 14-3-3 protein-mediated activation of yeast neutral trehalase Nth1.
  Kopecka M, Kosek D, Kukacka Z, Rezabkova L, Man P, Novak P, Obsil T, Obsilova V.
  J Biol Chem. 2014 May 16;289(20):13948-61. doi: 10.1074/jbc.M113.544551
• The assembly and intermolecular properties of the Hsp70-Tomm34-Hsp90 molecular chaperone complex.
  Trcka F, Durech M, Man P, Hernychova L, Muller P, Vojtesek B.
  J Biol Chem. 2014 Apr 4;289(14):9887-901. doi: 10.1074/jbc.M113.526046
• Identification of a second Nutlin-3 responsive interaction site in the N-terminal domain of MDM2 using hydrogen/deuterium exchange mass spectrometry.
  Hernychova L, Man P, Verma C, Nicholson J, Sharma CA, Ruckova E, Teo JY, Ball K, Vojtesek B, Hupp TR.
  Proteomics. 2013 Aug;13(16):2512-25. doi: 10.1002/pmic.201300029
• Structural basis of the 14-3-3 protein-dependent activation of yeast neutral trehalase Nth1.
  Macakova E, Kopecka M, Kukacka Z, Veisova D, Novak P, Man P, Obsil T, Obsilova V.
  Biochim Biophys Acta. 2013 Oct;1830(10):4491-9. doi: 10.1016/j.bbagen.2013.05.025
• The combination of hydrogen/deuterium exchange or chemical cross-linking techniques with mass spectrometry: mapping of human 14-3-3ζ homodimer interface.
  Haladová K, Mrázek H, Ječmen T, Halada P, Man P, Novák P, Chmelík J, Obšil T, Šulc M.
  J Struct Biol. 2012 Jul;179(1):10-7. doi: 10.1016/j.jsb.2012.04.016