News:

  • 2018/07/19:

    Our paper on MALDI chips suitable for detection of transferrin variants is now in Clinical Chemistry. So now we can detect who has serious problem with alcohol...

  • 2018/07/13:

    FEBS Congress 2018 in Prague is over. Thanks all who represented our lab at this event (one oral, one speed talk and four posters).

  • 2018/07/12:

    Joint paper with Veverka's group is now in PNAS.

  • 2018/06/25:

    Unique possibility to learn about FT-ICR MS opens to anyone through Summer school funded by EU FT-ICR MS Horizon project. Details available here. Number of places is limited, expenses are covered!

  • 2018/06/14:

    Prof. Dan Fabris from the University at Albany has just joined our group for half a year. Together we will work on DNA/RNA structure and interactions.

  • 2018/06/09:

    We returned from California where our lab presented three posters at the 66th ASMS Conference on Mass Spectrometry and Allied Topics

Important:

  • 2018/07/13:

    Our lab is a part of Horizon 2020 project EU FT-ICR MS (reg. no 731077). Through this project you can access our expertise as well as other participating FT-ICR labs. Check Trans-National Acess web section for more details. Also, various FT-ICR focused courses and schools are organized by the labs participating in the project.

  • 2018/06/25:

    Bachelor and master theses are available in the lab. Areas of structrual biology, cutting edge mass spectrometry and cell signalling are awaiting new students. Check the tab Teaching.

Publications

2018

2017

  • Vališ K, Grobárová V, Hernychová L, Bugáňová M, Kavan D, Kalous M, Černý J, Stodůlková E, Kuzma M, Flieger M, Černý J, Novák P.
    Reprogramming of leukemic cell metabolism through the naphthoquinonic compound Quambalarine B.
    Oncotarget. 2017 Oct 7;8(61): 103137-103153.
    doi:10.18632/oncotarget.21663, PMID:29262552

  • Tarbouriech N, Ducournau C, Hutin S, Mas PJ, Man P, Forest E, Hart DJ, Peyrefitte CN, Burmeister WP, Iseni F
    High-resolution structure of E9, the vaccinia virus DNA polymerase: Insight into the structural organization of the holoenzyme.
    Nat Commun 2017 Nov 13; 8(1): 1455
    doi:10.1038/s41467-017-01542-z, PMID:29129932

  • Gupta K, Watson AA, Scheer E, Köhler Ch, Zou J, Obong-Ebong I, Kandiah E, Temblador A, Round A, Forest E, Man P, Bieniossek C, Laue ED, Lemke EA, Rappsilber J, Robinson CV, Tora L, Berger I
    Architecture of TAF11/TAF13/TBP complex suggests novel regulation properties of general transcription factor TFIID.
    eLife 2017 Nov 7; 6. pii: e30395
    doi:10.7554/eLife.30395, PMID:29111974

  • Bláha J, Kalousková B, Skořepa O, Pažický S, Novák P, Vaněk O.
    High-level expression and purification of soluble form of human natural killer cell receptor NKR-P1 in HEK293S GnTI- cells.
    Protein Expr Purif. 2017 Dec;140: 36-43.
    doi:10.1016/j.pep.2017.07.016, PMID:28757467

  • Stranava M, Man P, Skalova T, Kolenko P, Blaha J, Fojtikova V, Martinek V, Dohnalek J, Lengalova A, Rosulek M, Shimizu T, Martinkova M
    Coordination and redox state-dependent structural changes of the heme-based oxygen sensor AfGcHK associated with intraprotein signal transduction.
    J Biol Chem 2017, in press
    doi: 10.1074/jbc.M117.817023, PMID:29092908

  • Kalabova D, Smidova A, Petrvalska O, Alblova M, Kosek D, Man P, Obsil T, Obsilova V.
    Human procaspase-2 phosphorylation at both S139 and S164 is required for 14-3-3 binding.
    Biochem Biophys Res Commun. 2017 Nov 18;493(2):940-945.
    doi:10.1016/j.bbrc.2017.09.116, PMID:28943433

  • Masin J, Roderova J, Osickova A, Novak P, Bumba L, Fiser R, Sebo P, Osicka R.
    The conserved tyrosine residue 940 plays a key structural role in membrane interaction of Bordetella adenylate cyclase toxin.
    Sci Rep. 2017 Aug;7(1):9330.
    doi:10.1038/s41598-017-09575-6, PMID:28839199

  • Giladi M, van Dijk L, Refaeli B, Almagor L, Hiller R, Man P, Forest E, Khananshvili D.
    Dynamic distinctions in the sodium-calcium exchanger adopting the inward- and outward-facing conformational states.
    J Biol Chem. 2017 Jul 21; 292(29):12311-12323.
    doi:10.1074/jbc.M117.787168, PMID:28572509

  • Schräder CU, Lee L, Rey M, Sarpe V, Man P, Sharma S, Zabrouskov V, Larsen B, Schriemer DC.
    Neprosin, a Selective Prolyl Endoprotease for Bottom-up Proteomics and Histone Mapping.
    Mol Cell Proteomics. 2017 Jun;16(6):1162-1171.
    doi:10.1074/mcp.M116.066803, PMID:28404794

  • A community proposal to integrate proteomics activities in ELIXIR.
    Vizcaíno JA, Walzer M, Jiménez RC, Bittremieux W, Bouyssié D, Carapito C, Corrales F, Ferro M, Heck AJR, Horvatovich P, Hubalek M, Lane L, Laukens K, Levander F, Lisacek F, Novak P, Palmblad M, Piovesan D, Pühler A, Schwämmle V, Valkenborg D, van Rijswijk M, Vondrasek J, Eisenacher M, Martens L, Kohlbacher O.
    F1000Res. 2017 Jun;6. pii: ELIXIR-875.
    doi:10.12688/f1000research.11751.1, PMID:28713550

  • Kacirova M, Novacek J, Man P, Obsilova V, Obsil T.
    Structural Basis for the 14-3-3 Protein-Dependent Inhibition of Phosducin Function.
    Biophys J. 2017 Apr 11;112(7):1339-1349.
    doi:10.1016/j.bpj.2017.02.036, PMID:28402877

  • Voráčová K, Hájek J, Mareš J, Urajová P, Kuzma M, Cheel J, Villunger A, Kapuscik A, Bally M, Novák P, Kabeláč M, Krumschnabel G, Lukeš M, Voloshko L, Kopecký J, Hrouzek P.
    The cyanobacterial metabolite nocuolin a is a natural oxadiazine that triggers apoptosis in human cancer cells.
    PLoS One. 2017 Mar 2;12(3):e0172850.
    doi:10.1371/journal.pone.0172850, PMID:28253280

  • Kadek A, Kavan D, Marcoux J, Stojko J, Felice AK, Cianférani S, Ludwig R, Halada P, Man P. Interdomain electron transfer in cellobiose dehydrogenase is governed by surface electrostatics. Biochim Biophys Acta. 2017 Feb;1861(2):157-167.
    doi:10.1016/j.bbagen.2016.11.016, PMID:27851982

  • Darebna P, Novak P, Kucera R, Topolcan O, Sanda M, Goldman R, Pompach P.
    Changes in the expression of N- and O-glycopeptides in patients with colorectal cancer and hepatocellular carcinoma quantified by full-MS scan FT-ICR and multiple reaction monitoring.
    J Proteomics. 2016 Feb 5;153:44-52.
    doi:10.1016/j.jprot.2016.09.004, PMID:27646713

  • Sviridova E, Rezacova P, Bondar A, Veverka V, Novak P, Schenk G, Svergun DI, Kuta Smatanova I, Bumba L.
    Structural basis of the interaction between the putative adhesion-involved and iron-regulated FrpD and FrpC proteins of Neisseria meningitidis.
    Sci Rep. 2017 Jan 13;7:40408.
    doi:10.1038/srep40408, PMID:28084396

  • Horníková L, Fraiberk M, Man P, Janovec V, Forstová J.
    VP1, the major capsid protein of the mouse polyomavirus, binds microtubules, promotes their acetylation and blocks the host cell cycle.
    FEBS J. 2017 Jan;284(2):301-323.
    doi:10.1111/febs.13977, PMID:27885808

2016

  • Vališ K, Talacko P, Grobárová V, Černý J, Novák P.
    Shikonin regulates C-MYC and GLUT1 expression through the MST1-YAP1-TEAD1 axis.
    Exp Cell Res. 2016 Dec 10;349(2):273-281.
    doi:10.1016/j.yexcr.2016.10.018, PMID:27793648

  • Hnízda A, Škerlová J, Fábry M, Pachl P, Šinalová M, Vrzal L, Man P, Novák P, Řezáčová P, Veverka V.
    Oligomeric interface modulation causes misregulation of purine 5´-nucleotidase in relapsed leukemia.
    BMC Biol. 2016 Oct 19;14(1):91.
    doi:10.1186/s12915-016-0313-y, PMID:27756303

  • Stranava M, Martínek V, Man P, Fojtikova V, Kavan D, Vaněk O, Shimizu T, Martinkova M.
    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.
    Proteins. 2016 Oct;84(10):1375-89.
    doi:10.1002/prot.25083, PMID:27273553

  • Kylarova S, Kosek D, Petrvalska O, Psenakova K, Man P, Vecer J, Herman P, Obsilova V, Obsil T.
    Cysteine residues mediate high-affinity binding of thioredoxin to ASK1.
    FEBS J. 2016 Oct;283(20):3821-3838.
    doi:10.1111/febs.13893, PMID:27588831

  • Grobárová V, Vališ K, Talacko P, Pavlů B, Hernychová L, Nováková J, Stodůlková E, Flieger M, Novák P, Černý J.
    Quambalarine B, a Secondary Metabolite from Quambalaria cyanescens with Potential Anticancer Properties.
    J Nat Prod. 2016 Sep 23;79(9):2304-14.
    doi:10.1021/acs.jnatprod.6b00362, PMID:27571379

  • Petrvalska O, Kosek D, Kukacka Z, Tosner Z, Man P, Vecer J, Herman P, Obsilova V, Obsil T.
    Structural Insight into the 14-3-3 Protein-dependent Inhibition of Protein Kinase ASK1 (Apoptosis Signal-regulating kinase 1).
    J Biol Chem. 2016 Sep 23;291(39):20753-65.
    doi:10.1074/jbc.M116.724310, PMID:27514745

  • Rozbeský D, Adámek D, Pospíšilová E, Novák P, Chmelík J.
    Solution structure of the lymphocyte receptor Nkrp1a reveals a distinct conformation of the long loop region as compared to in the crystal structure.
    Proteins. 2016 Sep;84(9):1304-11.
    doi:10.1002/prot.25078, PMID:27238500

  • Pompach P, Benada O, Rosůlek M, Darebná P, Hausner J, Růžička V, Volný M, Novák P.
    Protein Chips Compatible with MALDI Mass Spectrometry Prepared by Ambient Ion Landing.
    Anal Chem. 2016 Sep 6;88(17):8526-34.
    doi:10.1021/acs.analchem.6b01366, PMID:27478994

  • Flieger M, Bandouchova H, Cerny J, Chudíčková M, Kolarik M, Kovacova V, Martínková N, Novák P, Šebesta O, Stodůlková E, Pikula J.
    Vitamin B2 as a virulence factor in Pseudogymnoascus destructans skin infection.
    Sci Rep. 2016 Sep 13;6:33200.
    doi:10.1038/srep33200, PMID:27620349

  • Forest E, Man P.
    Conformational Dynamics and Interactions of Membrane Proteins by Hydrogen/Deuterium Mass Spectrometry.
    Methods Mol Biol. 2016 Aug 3;1432:269-79.
    doi:10.1007/978-1-4939-3637-3_17, PMID:27485342

  • Rey M, Yang M, Lee L, Zhang Y, Sheff JG, Sensen CW, Mrazek H, Halada P, Man P, McCarville JL, Verdu EF, Schriemer DC.
    Addressing proteolytic efficiency in enzymatic degradation therapy for celiac disease.
    Sci Rep. 2016 Aug 2;6:30980.
    doi:10.1038/srep30980, PMID:27481162

  • Fojtikova V, Bartosova M, Man P, Stranava M, Shimizu T, Martinkova M.
    Effects of hydrogen sulfide on the heme coordination structure and catalytic activity of the globin-coupled oxygen sensor AfGcHK.
    Biometals. 2016 Jul 9;29(4):715-29.
    doi:10.1007/s10534-016-9947-z , PMID:27395436

  • Durech M, Trcka F, Man P, Blackburn EA, Hernychova L, Dvorakova P, Coufalova D, Kavan D, Vojtesek B, Muller P.
    Novel Entropically Driven Conformation-specific Interactions with Tomm34 Protein Modulate Hsp70 Protein Folding and ATPase Activities.
    Mol Cell Proteomics. 2016 May;15(5):1710-27.
    doi:10.1074/mcp.M116.058131, PMID:26944342

  • Pospíšilová E, Kavan D, Novák P, Chmelík J.
    1H, 13C and 15N resonance assignments of human DCL-1 (CD302) extracellular domain.
    Biomol NMR Assign. 2016 Apr;10(1):189-92.
    doi:10.1007/s12104-015-9664-5, PMID:26725057

  • Marková E, Kotik M, Křenková A, Man P, Haudecoeur R, Boumendjel A, Hardré R, Mekmouche Y, Courvoisier-Dezord E, Réglier M, Martínková L.
    Recombinant Tyrosinase from Polyporus arcularius: Overproduction in Escherichia coli, Characterization, and Use in a Study of Aurones as Tyrosinase Effectors.
    J Agric Food Chem. 2016 Apr 13;64(14):2925-31.
    doi:10.1021/acs.jafc.6b00286, PMID:26961852

  • 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.
    Structural insights and in vitro reconstitution of membrane targeting and activation of human PI4KB by the ACBD3 protein.
    Sci Rep. 2016 Mar 24;6:23641.
    doi:10.1038/srep23641, PMID:27009356

  • Vit O, Man P, Kadek A, Hausner J, Sklenar J, Harant K, Novak P, Scigelova M, Woffendin G, Petrak J.
    Large-scale identification of membrane proteins based on analysis of trypsin-protected transmembrane segments.
    J Proteomics. 2016 Oct 21;149:15-22.
    doi:10.1016/j.jprot.2016.03.016, PMID:26975722

  • Giladi M, Almagor L, van Dijk L, Hiller R, Man P, Forest E, Khananshvili D.
    Asymmetric Preorganization of Inverted Pair Residues in the Sodium-Calcium Exchanger.
    Sci Rep. 2016 Feb 15;6:20753.
    doi:10.1038/srep20753, PMID:26876271

  • Hermanova I, Arruabarrena-Aristorena A, Valis K, Nuskova H, Alberich-Jorda M, Fiser K, Fernandez-Ruiz S, Kavan D, Pecinova A, Niso-Santano M, Zaliova M, Novak P, Houstek J, Mracek T, Kroemer G, Carracedo A, Trka J, Starkova J.
    Pharmacological inhibition of fatty-acid oxidation synergistically enhances the effect of l-asparaginase in childhood ALL cells.
    Leukemia. 2016 Jan;30(1):209-18.
    doi:10.1038/leu.2015.213, PMID:26239197

  • Pompach P, Nováková J, Kavan D, Benada O, Růžička V, Volný M, Novák P.
    Planar Functionalized Surfaces for Direct Immunoaffinity Desorption/Ionization Mass Spectrometry.
    Clin Chem. 2016 Jan;62(1):270-8.
    doi:10.1373/clinchem.2015.244004, PMID:26482160

  • Fejfarová K, Kádek A, Mrázek H, Hausner J, Tretyachenko V, Koval‘ T, Man P, Hašek J, Dohnálek J.
    Crystallization of nepenthesin I using a low-pH crystallization screen.
    Acta Crystallogr F Struct Biol Commun. 2016 Jan;72(Pt 1):24-8.
    doi:10.1107/S2053230X15022323, PMID:26750480

  • Pospíšilová E, Kavan D, Novák P, Chmelík J.
    1H, 13C and 15N resonance assignments of human DCL-1 (CD302) extracellular domain.
    Biomol NMR Assign. 2016 Apr;10(1):189-92.
    doi:10.1007/s12104-015-9664-5, PMID:26725057

2015

  • Capkova J, Margaryan H, Kubatova A, Novak P, Peknicova J.
    Target antigens for Hs-14 monoclonal antibody and their various expression in normozoospermic and asthenozoospermic men.
    Basic Clin Androl. 2015 Nov 6;25:11.
    doi: 10.1186/s12610-015-0025-0, PMID:26550480

  • Kukacka Z, Rosulek M, Strohalm M, Kavan D, Novak P.
    Mapping protein structural changes by quantitative cross-linking.
    Methods. 2015 Nov 1;89:112-20
    doi:10.1016/j.ymeth.2015.05.027, PMID:26048481

  • Drobek A, Kralova J, Skopcova T, Kucova M, Novák P, Angelisová P, Otahal P, Alberich-Jorda M, Brdicka T.
    PSTPIP2, a Protein Associated with Autoinflammatory Disease, Interacts with Inhibitory Enzymes SHIP1 and Csk.
    J Immunol. 2015 Oct 1;195(7):3416-26.
    doi:10.4049/jimmunol.1401494, PMID:26304991

  • Lennartz F, Bengtsson A, Olsen RW, Joergensen L, Brown A, Remy L, Man P, Forest E, Barfod LK, Adams Y, Higgins MK, Jensen AT.
    Mapping the Binding Site of a Cross-Reactive Plasmodium falciparum PfEMP1 Monoclonal Antibody Inhibitory of ICAM-1 Binding.
    J Immunol. 2015 Oct 1;195(7):3273-83.
    doi:10.4049/jimmunol.1501404, PMID:26320251

  • Vimberg V, Kuzma M, Stodůlková E, Novák P, Bednárová L, Šulc M, Gažák R.
    Hydnocarpin-Type Flavonolignans: Semisynthesis and Inhibitory Effects on Staphylococcus aureus Biofilm Formation.
    J Nat Prod. 2015 Aug 28;78(8):2095-103.
    doi:10.1021/acs.jnatprod.5b00430, PMID:26273725

  • Marášek P, Dzijak R, Studenyak I, Fišerová J, Uličná L, Novák P, Hozák P.
    Paxillin-dependent regulation of IGF2 and H19 gene cluster expression.
    J Cell Sci. 2015 Aug 15;128(16):3106-16.
    doi:10.1242/jcs.170985, PMID:26116569

  • Yan F, Fojtikova V, Man P, Stranava M, Martínková M, Du Y, Huang D, Shimizu T.
    Catalytic enhancement of the heme-based oxygen-sensing phosphodiesterase EcDOS by hydrogen sulfide is caused by changes in heme coordination structure.
    Biometals. 2015 Aug;28(4):637-52.
    doi:10.1007/s10534-015-9847-7, PMID:25804428

  • Hernychová L, Mrázek H, Ivanova L, Kukačka Z, Chmelík J, Novák P.
    Recombinant expression, in vitro refolding and characterizing disulfide bonds of a mouse inhibitory C-type lectin-like receptor Nkrp1b.
    Physiol Res. 2015 Jul 16;64 Suppl 1:S85-93. PMID:.
    Fulltext:Physiological research, PMID:26447598

  • Yang M, Hoeppner M, Rey M, Kadek A, Man P, Schriemer DC.
    Recombinant Nepenthesin II for Hydrogen/Deuterium Exchange Mass Spectrometry.
    Anal Chem. 2015 Jul 7;87(13):6681-7.
    doi:10.1021/acs.analchem.5b00831, PMID:25993527

  • Krásný L, Pompach P, Strnadová M, Hynek R, Vališ K, Havlíček V, Novák P, Volný M.
    High-throughput workflow for identification of phosphorylated peptides by LC-MALDI-TOF/TOF-MS coupled to in situ enrichment on MALDI plates functionalized by ion landing.
    J Mass Spectrom. 2015 Jun;50(6):802-11.
    doi:10.1002/jms.3586, PMID:26169134

  • Kacirova M, Kosek D, Kadek A, Man P, Vecer J, Herman P, Obsilova V, Obsil T.
    Structural Characterization of Phosducin and Its Complex with the 14-3-3 Protein.
    J Biol Chem. 2015 Jun 26;290(26):16246-60.
    doi:10.1074/jbc.M115.636563, PMID:25971962

  • Bláha J, Pachl P, Novák P, Vaněk O.
    Expression and purification of soluble and stable ectodomain of natural killer cell receptor LLT1 through high-density transfection of suspension adapted HEK293S GnTI(-) cells.
    Protein Expr Purif. 2015 May;109:7-13.
    doi:10.1016/j.pep.2015.01.006, PMID:25623399

  • Stodůlková E, Man P, Kuzma M, Černý J, Císařová I, Kubátová A, Chudíčková M, Kolařík M, Flieger M.
    A highly diverse spectrum of naphthoquinone derivatives produced by the endophytic fungus Biatriospora sp. CCF 4378.
    Folia Microbiol (Praha). 2015 May;60(3):259-67.
    doi:10.1007/s12223-014-0366-7, PMID:25416512

  • Kadek A, Kavan D, Felice AK, Ludwig R, Halada P, Man P.
    Structural insight into the calcium ion modulated interdomain electron transfer in cellobiose dehydrogenase.
    FEBS Lett. 2015 May 8;589(11):1194-9.
    doi:10.1016/j.febslet.2015.03.029, PMID:25862501

  • Janata J, Kadlcik S, Koberska M, Ulanova D, Kamenik Z, Novak P, Kopecky J, Novotna J, Radojevic B, Plhackova K, Gazak R, Najmanova L.
    Lincosamide synthetase–a unique condensation system combining elements of nonribosomal peptide synthetase and mycothiol metabolism.
    PLoS One. 2015 Mar 5;10(3):e0118850.
    doi:10.1371/journal.pone.0118850, PMID:25741696

  • Stodůlková E, Císařová I, Kolařík M, Chudíčková M, Novák P, Man P, Kuzma M, Pavlů B, Černý J, Flieger M.
    Biologically active metabolites produced by the basidiomycete Quambalaria cyanescens.
    PLoS One. 2015 Feb 27;10(2):e0118913.
    doi:10.1371/journal.pone.0118913, PMID:25723150

  • Rozbeský D, Ivanova L, Hernychová L, Grobárová V, Novák P, Černý J.
    Nkrp1 family, from lectins to protein interacting molecules.
    Molecules. 2015 Feb 17;20(2):3463-78.
    doi:10.3390/molecules20023463, PMID:25690298

  • Tomek P, Hrouzek P, Kuzma M, Sýkora J, Fiser R, Cerný J, Novák P, Bártová S, Simek P, Hof M, Kavan D, Kopecký J.
    Cytotoxic Lipopeptide Muscotoxin A, Isolated from Soil Cyanobacterium Desmonostoc muscorum, Permeabilizes Phospholipid Membranes by Reducing Their Fluidity.
    Chem Res Toxicol. 2015 Feb 16;28(2):216-24.
    doi:10.1021/tx500382b, PMID:25621379

  • Hasan S, Osickova A, Bumba L, Novák P, Sebo P, Osicka R.
    Interaction of Bordetella adenylate cyclase toxin with complement receptor 3 involves multivalent glycan binding.
    FEBS Lett. 2015 Jan 30;589(3):374-9.
    doi:10.1016/j.febslet.2014.12.023, PMID:25554420