Laboratory of Structural Biology and Cell Signaling

Publications

2024

• Giladi M, Fojtik L, Strauss T, Da'adoosh B, Hiller R, Man P, Khananshvili D.
  Structural dynamics of Na+ and Ca2+ interactions with full-size mammalian NCX.
  Commun Biol 2024 Apr 16; 7:463. DOI 10.1038/s42003-024-06159-9. (PDF) (PRIDE)
• Felčíková K, Hovan A, Polák M, Loginov DS, Holotová V, Díaz C, Kožár T, Lee OS, Varhač R, Novák P, Bánó G, Sedlák E.
  Design of AsLOV2 domain as a carrier of light-induced dissociable FMN photosensitizer.
  Protein Sci. 2024 Apr;33(4):e4921. DOI 10.1002/pro.4921.
• Smirnova AM, Hronová V, Mohammad MP, Herrmannová A, Gunišová S, Petráčková D, Halada P, Coufal Š, Świrski M, Rendleman J, Jendruchová K, Hatzoglou M, Beznosková P, Vogel C, Valášek LS.
  Stem-loop-induced ribosome queuing in the uORF2/ATF4 overlap fine-tunes stress-induced human ATF4 translational control.
  Cell Rep. 2024 Mar 19;43(4):113976. DOI 10.1016/j.celrep.2024.113976.
• Manori B, Vaknin A, Vaňková P, Nitzan A, Zaidel-Bar R, Man P, Giladi M, Haitin Y.
  Chloride intracellular channel (CLIC) proteins function as fusogens.
  Nat Commun. 2024 Mar 7;15(1):2085. DOI 10.1038/s41467-024-46301-z. (PDF) (PRIDE)
• Shaliutina-Loginova A, Loginov DS
  Transferrin maintains the motility rate, ATP content, and DNA integrity of common carp spermatozoa during short-term storage.
  Anim Reprod Sci. 2024 Feb 13;263:107437. DOI 10.1016/j.anireprosci.2024.107437. (PDF)
• Matoušková Z, Orsághová K, Srb P, Pytelková J, Kukačka Z, Buša M, Hajdušek O, Šíma R, Fábry M, Novák P, Horn M, Kopáček P, Mareš M.
  An Unusual Two-Domain Thyropin from Tick Saliva: NMR Solution Structure and Highly Selective Inhibition of Cysteine Cathepsins Modulated by Glycosaminoglycans.
  Int J Mol Sci. 2024 Feb 13;25(4):2240. DOI 10.3390/ijms25042240. (PDF)
• Hausnerová VV, Shoman M, Kumar D, Schwarz M, Modrák M, Matějčková JJ, Mikesková E, Neva S, Herrmannová A, Šiková M, Halada P, Novotná I, Pajer P, Valášek LS, Převorovský M, Krásný L, Hnilicová J.
  RIP-seq reveals RNAs that interact with RNA polymerase and primary sigma factors in bacteria.
  Nucleic Acids Res. 2024 Feb 13:gkae081. DOI 10.1093/nar/gkae081. (PDF)
• Dhillon A, Persson BD, Volkov AN, Sülzen H, Kádek A, Pompach P, Kereïche S, Lepšík M, Danskog K, Uetrecht C, Arnberg N, Zoll S.
  Structural insights into the interaction between adenovirus C5 hexon and human lactoferrin.
  J Virol. 2024 Feb 7:e0157623. DOI 10.1128/jvi.01576-23. (PDF)
• Vankova P, Pacheco-Garcia JL, Loginov DS, Gomez-Mulas A, Kadek A, Martin-Garcia JM, Salido E, Man P and Pey AL
  Insights into PH1 disease mechanisms from the analyses of the structural stability and dynamics of AGT variants.
  FEBS Lett. 2024 Feb;598(4):485-499. DOI: 10.1002/1873-3468.14800. (PRIDE)
• Polak M, Cerny J, Novak P
  Isotopic Depletion Increases the Spatial Resolution of FPOP Top-Down Mass Spectrometry Analysis.
  Anal Chem. 2024 Jan 30;96(4):1478-1487. DOI: 10.1021/acs.analchem.3c03759. (PDF) (PRIDE)
• Zakopcanik M, Kavan D, Novak P, Loginov DS
  Quantifying the Impact of the Peptide Identification Framework on the Results of Fast Photochemical Oxidation of Protein Analysis.
  J Proteome Res. 2024 Feb 2;23(2):609-617. DOI: 10.1021/acs.jproteome.3c00390. (PDF)

2023

• Kmochová T, Kidd KO, Orr A, Hnízda A, Hartmannová H, Hodaňová K, Vyleťal P, Naušová K, Brinsa V, Trešlová H, Sovová J, Barešová V, Svojšová K, Vrbacká A, Stránecký V, Robins VC, Taylor A, Martin L, Rivas-Chavez A, Payne R, Bleyer HA, Williams A, Rennke HG, Weins A, Short PJ, Agrawal V, Storsley LJ, Waikar SS, McPhail ED, Dasari S, Leung N, Hewlett T, Yorke J, Gaston D, Geldenhuys L, Samuels M, Levine AP, West M, Hůlková H, Pompach P, Novák P, Weinberg RB, Bedard K, Živná M, Sikora J, Bleyer AJ Sr, Kmoch S.
  Autosomal dominant ApoA4 mutations present as tubulointerstitial kidney disease with medullary amyloidosis.
  Kidney Int. 2023 Dec 12:S0085-2538(23)00859-1. DOI: 10.1016/j.kint.2023.11.021.
• Polák M, Palasser M, Kádek A, Kavan D, Wootton CA, Delsuc MA, Breuker K, Novák P, van Agthoven MA.
  Top-Down Proteoform Analysis by 2D MS with Quadrupolar Detection.
  Anal Chem. 2023 Nov 7;95(44):16123-16130. DOI: 10.1021/acs.analchem.3c02225. (PDF)
• Simke F, Fischer P, Damjanovic T, Kadek A, Kierspel T, Lorenzen K, Uetrecht C, Schweikhard L..
  Commissioning the digital mass-filter/ion-trap module for the MS SPIDOC prototype.
  JINST 2023; 18:P10021. DOI: 10.1088/1748-0221/18/10/P10021. (PDF)
• Lambert T, Gramlich M, Stutzke L, Smith L, Deng D, Kaiser PD, Rothbauer U, Benesch JLP, Wagner C, Koenig M, Pompach P, Novak P, Zeck A, Rand KD.
  Development of a PNGase Rc Column for Online Deglycosylation of Complex Glycoproteins during HDX-MS.
  J Am Soc Mass Spectrom. 2023 Nov 1;34(11):2556-2566. DOI: 10.1021/jasms.3c00268. (PDF)
• Kalaninová Z, Fojtík L, Chmelík J, Novák P, Volný M, Man P.
  Probing Antibody Structures by Hydrogen/Deuterium Exchange Mass Spectrometry.
  Methods Mol Biol. 2023;2718:303-334. DOI: 10.1007/978-1-0716-3457-8_17
• Koutná E, Lux V, Kouba T, Škerlová J, Nováček J, Srb P, Hexnerová R, Šváchová H, Kukačka Z, Novák P, Fábry M, Poepsel S, Veverka V.
  Multivalency of nucleosome recognition by LEDGF.
  Nucleic Acids Res. 2023 Aug 24:gkad674. DOI: 10.1093/nar/gkad674 (PDF)
• 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.
  A conserved tryptophan in the acylated segment of RTX toxins controls their β2- integrin-independent cell penetration.
  J. Biol. Chem. 2023 Jun 28:104978. DOI: 10.1016/j.jbc.2023.104978 (PDF) (PRIDE-1) (PRIDE-2)
• Vermeire PJ, Lilina AV, Hashim HM, Dlabolová L, Fiala J, Beelen S, Kukačka Z, Harvey JN, Novák P, Strelkov SV.
  Molecular structure of soluble vimentin tetramers.
  Sci Rep. 2023 May 31;13(1):8841. DOI: 10.1038/s41598-023-34814-4 (PDF)
• Dvorak J, Novakova J, Kraftova L, Studentova V, Matejovic M, Radej J, Karvunidis T, Horak J, Kralovcova M, Hrabak J, Kalaninova Z, Volny M, Novak P, Pompach P
  The rapid detection of procalcitonin in septic serum using immunoaffinity MALDI chips.
  Clin Proteomics. 2023 May 11;20(1):20. DOI: 10.1186/s12014-023-09410-3 (PDF) (PRIDE)
• Heames B, Buchel F, Aubel M, Tretyachenko V, Loginov D, Novák P, Lange A, Bornberg-Bauer E, Hlouchová K
  Experimental characterization of de novo proteins and their unevolved random-sequence counterparts.
  Nat Ecol Evol. 2023 Apr 6. DOI: 10.1038/s41559-023-02010-2
• Vávra J, Sergunin A, Stráňava M, Kádek A, Shimizu T, Man P, Martínková M
  Hydrogen/Deuterium Exchange Mass Spectrometry of Heme-Based Oxygen Sensor Proteins.
  Methods Mol Biol. 2023;2648:99-122. DOI: 10.1007/978-1-0716-3080-8_8
• Kierspel T, Kadek A, Barran P, Bellina B, Bijedic A, Brodmerkel MN, Commandeur J, Caleman C, Damjanović T, Dawod I, De Santis E, Lekkas A, Lorenzen K, Morillo LL, Mandl T, Marklund EG, Papanastasiou D, Ramakers LAI, Schweikhard L, Simke F, Sinelnikova A, Smyrnakis A, Timneanu N, Uetrecht C; MS SPIDOC Consortium
  Coherent diffractive imaging of proteins and viral capsids: simulating MS SPIDOC.
  Anal Bioanal Chem. 2023 Apr 4. DOI: 10.1007/s00216-023-04658-y
• Pacheco-Garcia JL, Anoz-Carbonell E, Loginov DS, Kavan D, Salido E, Man P, Medina M, Pey AL
  Counterintuitive structural and functional effects due to naturally-occurring mutations targeting the active site of the disease-associated NQO1 enzyme.
  FEBS J 2023 Apr; 290(7):1855-1873. DOI: 10.1111/febs.16677 (PDF) (PRIDE)
• Shaliutina-Loginova A, Loginov DS
  Oxidative stress and DNA fragmentation in frozen/thawed common Carp Cyprinus carpio sperm with and without supplemental proteins.
  Anim Reprod Sci. 2023 Mar 14;251:107213. DOI: 10.1016/j.anireprosci.2023.107213
• Křístková B, Rädisch R, Kulik N, Horvat M, Rucká L, Grulich M, Rudroff F, Kádek A, Pátek M, Winkler M, Martínková L.
  Scanning aldoxime dehydratase sequence space and characterization of a new aldoxime dehydratase from Fusarium vanettenii.
  Enzyme Microb Technol. 2023 Mar;164:110187 DOI: 10.1016/j.enzmictec.2022.110187

2022

• Studentova V, Sudova V, Bitar I, Paskova V, Moravec J, Pompach P, Volny M, Novak P, Hrabak J
  Preferred β-lactone synthesis can explain high rate of false-negative results in the detection of OXA-48-like carbapenemases.
  Sci Rep. 2022 Dec 23;12(1):22235. DOI: 10.1038/s41598-022-26735-5 (PDF)
• Alquezar-Artieda N, Kuzilkova D, Roberts J, Hlozkova K, Pecinova A, Pecina P, Zwyrtkova M, Potuckova E, Kavan D, Hermanova I, Zaliova M, Novak P, Mracek T, Sramkova L, Tennant DA, Trka J, Starkova J.
  Restored biosynthetic pathways induced by MSCs serve as rescue mechanism in leukemia cells after L-asparaginase therapy.
  Blood Adv. 2023 May 23;7(10):2228-2236. DOI: 10.1182/bloodadvances.2021006431
• Pacheco-Garcia JL, Loginov DS, Naganathan AN, Vankova P, Cano-Munoz M, Man P, Pey AL
  Loss of stability and unfolding cooperativity in hPGK1 upon gradual structural perturbation of its N-terminal domain hydrophobic core.
  Sci. Rep. 2022 Oct 13; 12:17200. DOI: 10.1038/s41598-022-22088-1 (PDF)
• Pacheco-Garcia JL, Anoz-Carbonell E, Loginov DS, Vankova P, Salido E, Man P, Medina M, Palomino-Morales R, Pey AL
  Different phenotypic outcome due to site-specific phosphorylation in the cancer-associated NQO1 enzyme studied by phosphomimetic mutations.
  Arch. Biochem. Biophys. 2022 Sep 9; 109392. DOI: 10.1016/j.abb.2022.109392 (PDF) (PRIDE)
• Melvin E, Kalaninova Z, Slush E, Man P, Giladi M, Haitin Y.
  TTYH family members form tetrameric complexes at the cell membrane.
  Commun. Biol. 2022 Aug 30;5:886. DOI: 10.1038/s42003-022-03862-3 (PDF) (PRIDE)
• Nikitushkin V, Shleeva M, Loginov D, Dyčka F F, Sterba J, Kaprelyants A.
  Shotgun proteomic profiling of dormant, 'non-culturable' Mycobacterium tuberculosis.
  PLoS One. 2022 Aug 9;17(8):e0269847. DOI: 10.1371/journal.pone.0269847 (PDF)
• Yassaghi G, Kukačka Z, Fiala J, Kavan D, Halada P, Volný M, Novák P.
  Top-Down Detection of Oxidative Protein Footprinting by Collision-Induced Dissociation, Electron-Transfer Dissociation, and Electron-Capture Dissociation.
  Anal Chem. 2022 Jul 19;94(28):9993-10002. DOI: 10.1021/acs.analchem.1c05476. (PDF)
• Vaňková Hausnerová V, Marvalová O, Šiková M, Shoman M, Havelková J, Kambová M, Janoušková M, Kumar D, Halada P, Schwarz M, Krásný L, Hnilicová J, Pánek J
  Ms1 RNA Interacts With the RNA Polymerase Core in Streptomyces coelicolor and Was Identified in Majority of Actinobacteria Using a Linguistic Gene Synteny Search.
  Front Microbiol. 2022 May 11;13:848536. DOI: 10.3389/fmicb.2022.848536 (PDF)
• Pacheco-Garcia JL, Loginov DS, Anoz-Carbonell E, Vankova P, Palomino-Morales R, Salido E, Man P, Medina M, Naganathan AN, Pey AL
  Allosteric communication in the multifunctional and redox NQO1 protein studied by cavity-making mutations.
  Antioxidants 2022 Jun 2; 11(6); 1110. DOI: 10.3390/antiox11061110 (PDF)
• 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 (PDF)
• Messahel NE, Benallal KE, Halada P, Lafri I, Manseur H, Hakem A, Houali K, Harrat Z, Volf P, Dvorak V.
  Identification of blood source preferences and Leishmania infection in sand flies (Diptera: Psychodidae) in north-eastern Algeria.
  Vet Parasitol Reg Stud Reports. 2022 Jun;31:100729. DOI: 10.1016/j.vprsr.2022.100729
• Polák M, Yassaghi G, Kavan D, Filandr F, Fiala J, Kukačka Z, Halada P, Loginov DS, Novák P..
  Utilization of Fast Photochemical Oxidation of Proteins and Both Bottom-up and Top-down Mass Spectrometry for Structural Characterization of a Transcription Factor-dsDNA Complex.
  Anal Chem. 2022 Feb 22;94(7):3203-3210. DOI: 10.1021/acs.analchem.1c04746
• Giacobelli VG, Fujishima K, Lepšík M, Tretyachenko V, Kadavá T, Makarov M, Bednárová L, Novák P, Hlouchová K.
  In vitro evolution reveals non-cationic protein-RNA interaction mediated by metal ions.
  Mol Biol Evol. 2022 Mar 2; 39(3):msac032. DOI: 10.1093/molbev/msac032 (PDF)
• Loginov DS, Fiala J, Brechlin P, Kruppa G, Novak P.
  Hydroxyl radical footprinting analysis of a human haptoglobin-hemoglobin complex.
  Biochim Biophys Acta Proteins Proteom. 2022;1870(2):140735. DOI: 10.1016/j.bbapap.2021.140735 (PDF)
• Pacheco-Garcia JL,Loginov DS, Rizzuti B, Vankova P, Neira JL, Kavan D, Mesa-Torres N, Guzzi R, Man P, Pey AL.
  A single evolutionarily divergent mutation determines the different FAD binding affinity of human and rat NQO1 due to site-specific phosphorylation.
  FEBS Lett 2022; 596:29-41. DOI: 10.1002/1873-3468.14238 (PDF)

2021

• Fojtík L, Fiala J, Pompach P, Chmelík J, Matoušek V, Beier P, Kukačka Z, Novák P.
  Fast Fluoroalkylation of Proteins Uncovers the Structure and Dynamics of Biological Macromolecules.
  J Am Chem Soc. 2021 Dec 15;143(49):20670-20679. DOI: 10.1021/jacs.1c07771.
• Dadras H, Policar T, Loginov DS, Boryshpolets S, Loginova Y, Sampels S, Sotnikov A, Kholodnyy V, Sterba J, Xin M, Dzyuba B.
  Relationship of Motility Activation to Lipid Composition, Protein Profile, and Swelling Rate of Burbot Lota lota Spermatozoon Following Change of Temperature and Osmolality.
  Front. Mar. Sci. 2021 Oct 21. DOI: 10.3389/fmars.2021.736087 (PDF)
• Dohnálek J, Dušková J, Tishchenko G, Kolenko P, Skálová T, Novak P, Fejfarová K, Šimůnek J.
  Chitinase Chit62J4 Essential for Chitin Processing by Human Microbiome Bacterium Clostridium paraputrificum J4.
  Molecules 2021 Oct 2; 26(19):5978. DOI: 10.3390/molecules26195978 (PDF)
• Kanderova V, Svobodova T, Borna S, Fejtkova M, Martinu V, Paderova J, Svaton M, Kralova J, Fronkova E, Klocperk A, Pruhova S, Lee-Kirsch MA, Hornofova L, Koblizek M, Novak P, Zimmermannova O, Parackova Z, Sediva A, Kalina T, Janda A, Kayserova J, Dvorakova M, Macek M, Pohunek P, Sedlacek P, Poh A, Ernst M, Brdicka T, Hrusak O, Lebl J.
  Early-onset pulmonary and cutaneous vasculitis driven by constitutively active SRC-family kinase HCK.
  J Allergy Clin Immunol. 2021 Sep 15; S0091-6749(21)01395-6. DOI: 10.1016/j.jaci.2021.07.046
• Vermeire P-J, Stalmans G, Lilina AV, Fiala J, Novak P, Herrmann H, Strelkov SV.
  Molecular Interactions Driving Intermediate Filament Assembly.
  Cells 2021 Sep17; 10(9):2457. DOI: 10.3390/cells10092457 (PDF)
• 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.
  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.
  Redox Biol. 2021 Aug 18; 102112. DOI: 10.1016/j.redox.2021.102112 (PDF)
• Șuleșco T, Erisoz Kasap O, Halada P, Oğuz G, Rusnac D, Gresova M, Alten B, Volf P, Dvorak V.
  Phlebotomine sand fly survey in the Republic of Moldova: species composition, distribution and host preferences.
  Parasit Vectors. 2021 Jul 21;14(1):371. DOI: 10.1186/s13071-021-04858-4 (PDF)
• Rusanov AL, Kozhin PM, Tikhonova OV, Zgoda VG, Loginov DS, Chlastáková A, Selinger M, Sterba J, Grubhoffer L, Luzgina NG.
  Proteome Profiling of PMJ2-R and Primary Peritoneal Macrophages.
  Int J Mol Sci 2021 Jun 12; 22(12):6323. DOI: 10.3390/ijms22126323 (PDF)
• Kniha E, Milchram M, Dvořák V, Halada P, Obwaller AG, Poeppl W, Mooseder G, Volf P, Walochnik J.
  Ecology, seasonality and host preferences of Austrian Phlebotomus (Transphlebotomus) mascittii Grassi, 1908, populations.
  Parasit Vectors 2021 May 29; 14(1):291. DOI: 10.1186/s13071-021-04787-2
• Bousova K, Bednarova L, Zouharova M, Vetyskova V, Postulkova K, Hofbauerová K, Petrvalska O, Vanek O, Tripsianes K, Vondrasek J.
  The order of PDZ3 and TrpCage in fusion chimeras determines their properties - a biophysical characterization.
  Protein Sci. 2021 May 10; 30(8):1653-1666. DOI: 10.1002/pro.4107
• Csarman F, Obermann T, Zanjko MC, Man P, Halada P, Seiboth B,Ludwig R.
  Functional expression and characterization of two laccases from the brown rot Fomitopsis pinicola.
  Enzyme Microb Technol 2021 Apr 20; 148:109801. DOI: 10.1016/j.enzmictec.2021.109801 (PDF)
• Loginov DS, Fiala J, Chmelik J, Brechlin P, Kruppa G, Novak P.
  Benefits of Ion Mobility Separation and Parallel Accumulation–Serial Fragmentation Technology on timsTOF Pro for the Needs of Fast Photochemical Oxidation of Protein Analysis.
  ACS Omega 2021 Apr 8; 6(15):10352-10361. DOI: 10.1021/acsomega.1c00732 (PDF)
• Knoppová J, Yu J, Janouškovec J, Halada P, Nixon PJ, Whitelegge JP, Komenda J.
  The Photosystem II Assembly Factor Ycf48 from the Cyanobacterium Synechocystis sp. PCC 6803 Is Lipidated Using an Atypical Lipobox Sequence.
  Int J Mol Sci. 2021 Apr 2;22(7):3733. DOI: 10.3390/ijms22073733 (PDF)
• 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.
  An Integrative Structural Biology Analysis of Von Willebrand Factor Binding and Processing by ADAMTS-13 in Solution.
  J Mol Biol. 2021 Mar 24;433(13):166954. DOI: 10.1016/j.jmb.2021.166954
• Mhaidi I, Ait Kbaich M, El Kacem S, Daoui O, Akarid K, Spitzova T, Halada P, Dvorak V, Lemrani M.
  Entomological study in an anthroponotic cutaneous leishmaniasis focus in Morocco: Fauna survey, Leishmania infection screening, molecular characterization and MALDI-TOF MS protein profiling of relevant Phlebotomus species.
  Transbound Emerg Dis. 2021 Mar 8,in press. DOI: 10.1111/tbed.14064
• Kukacka Z, Rosulek M, , Jelinek J, Slavata L, Kavan D, Novak P.
  LinX: A Software Tool for Uncommon Cross-Linking Chemistry.
  J. Prot. Res. 2021 Apr 2;20(4):2021-2027. DOI: 10.1021/acs.jproteome.0c00858
• Tomaskova N, Novak P, Kozar T, Petrencakova M, Jancura D, Yassaghi G, Man P,, Sedlak E.
  Early modification of cytochrome c by hydrogen peroxide triggers its fast degradation.
  Int. J. Biol. Macromol. 2021 Jan 30, 174:413-423. DOI: 10.1016/j.ijbiomac.2021.01.189
• Hnízda A, Tesina P, Nguyen TB, Kukačka Z, Kater L, Chaplin A, Beckmann R, Ascher DB, Novák P, Blundell TL.
  SAP domain forms a flexible part of DNA aperture in Ku70/80.
  FEBS J. 2021 Jul;288(14):4382-4393. DOI: 10.1111/febs.15732
• Felice AK, Schuster C, Kadek A, Filandr F, Laurent CVFP, Scheiblbrandner S, Schwaiger L, Schachinger F, Kracher D, Sygmud C, Man P, Halada P, Oostenbrink C and Ludwig R.
  Chimeric Cellobiose Dehydrogenases Reveal the Function of Cytochrome Domain Mobility for the Electron Transfer to Lytic Polysaccharide Monooxygenase.
  ACS Catal. 2021; 11:517-532. DOI: 10.1021/acscatal.0c05294
• 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.
  Motif orientation matters: structural characterization of TEAD1 recognition of genomic DNA.
  Structure 2021, Apr 1;29(4):345-356.e8. DOI: 10.1016/j.str.2020.11.018 (PDF)
• Filandrova R, Kavan D, Kadek A, Novak P, Man P.
  Studying Protein-DNA Interactions by Hydrogen/Deuterium Exchange Mass Spectrometry.
  Methods Mol Biol. 2021;2247:193-219. DOI: 10.1007/978-1-0716-1126-5_11

2020

• Kouba T, Koval’ T, Sudzinová P, Pospíšil J, Brezovská B, Hnilicová J, Šanderová H, Janoušková M, Šiková M,Halada P, Sýkora M, Barvík I, Nováček J, Trundová M, Dušková J, Skálová T, URee Chon UR, Murakami KS, Dohnálek J, Krásný L.
  Mycobacterial HelD is a nucleic acids-clearing factor for RNA polymerase.
  Nat Commun. 2020 Dec 18;11, 6419. DOI: 10.1038/s41467-020-20158-4 (PDF).
• Kniha E, Dvořák V, Halada P, Milchram M, Obwaller AG, Kuhls K, Schlegel S, Köhsler M, Poeppl W, Bakran-Lebl K, Fuehrer HP, Volfová V, Mooseder G, Ivovic V, Volf P, Walochnik J.
  Integrative Approach to Phlebotomus mascittii Grassi, 1908: First Record in Vienna with New Morphological and Molecular Insights.
  Pathogens. 2020 Dec 9;9(12):E1032. DOI: 10.3390/pathogens9121032 (PDF).
• Lux V, Brouns T, Cermakova K, Srb P, Fabry M, Madlikova M, Horejsi M, Kukacka Z, Novak P, Kugler M, Brynda J, DeRijck J, Christ F, Debyser Z, Debyser Z
  Molecular Mechanism of LEDGF/p75 Dimerization.
  Structure. 2020 Dec 1;28(12):1288-1299.e7. DOI: 10.1016/j.str.2020.08.012
• Pareyn M, Dvorak V, Halada P, Van Houtte N, Girma N, de Kesel W, Merdekios B, Massebo F, Leirs H, Volf P.
  An integrative approach to identify sand fly vectors of leishmaniasis in Ethiopia by morphological and molecular techniques.
  Parasit Vectors. 2020 Nov 17;13(1):580. DOI: 10.1186/s13071-020-04450-2
• Dvořák V, Tsirigotakis N, Pavlou C, Dokianakis E, Akhoundi M, Halada P, Volf P, Depaquit J, Antoniou M.
  Sand fly fauna of Crete and the description of Phlebotomus (Adlerius) creticus n. sp. (Diptera: Psychodidae).
  Parasit Vectors. 2020 Nov 4;13(1):547. DOI: 10.1186/s13071-020-04358-x
• Pavlikova N, Sramek J, Jelinek M, Halada P, Kovar J.
  Markers of acute toxicity of DDT exposure in pancreatic beta-cells determined by a proteomic approach.
  PLoS One. 2020 Oct 26;15(10):e0229430. DOI: 10.1371/journal.pone.0229430 (PDF)
• Lisnyansky Bar-El M, Vaňková P, Yeheskel A, Simhaev L, Engel H, Man P, Haitin Y, Giladi M
  Structural basis of heterotetrameric assembly and disease mutations in the human cis-prenyltransferase complex.
  Nat Commun. 2020; 11:5273. DOI: 10.1038/s41467-020-18970-z (PDF)
• Leitner A, Bonvin AMJJ, Borchers CH, Chalkley RJ, Chamot-Rooke J, Combe CW, Cox J, Dong MQ, Fischer L, Götze M, Gozzo FC, Heck AJR, Hoopmann MR, Huang L, Ishihama Y, Jones AR, Kalisman N, Kohlbacher O, Mechtler K, Moritz RL, Netz E, Novak P, Petrotchenko E, Sali A, Scheltema RA, Schmidt C, Schriemer D, Sinz A, Sobott F, Stengel F, Thalassinos K, Urlaub H, Viner R, Vizcaíno JA, Wilkins MR, Rappsilber J.
  Toward Increased Reliability, Transparency, and Accessibility in Cross-linking Mass Spectrometry.
  Structure. 2020 Nov 3;28(11):1259-1268. DOI: 10.1016/j.str.2020.09.011 (PDF)
• Fialova J, Hrabak J, Studentova V, Kavan D, Pompach P, Novak P
  Three-Dimensional Printed Target Plates for Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry.
  Anal Chem. 2020 Oct 6;92(19):12783-12788. DOI: 10.1021/acs.analchem.0c01737
• Rucká L, Kulik N, Novotný P, Sedova A, Petrásková L, Příhodová R, Křístková B, Halada P, Pátek M, Martínková L
  Plant Nitrilase Homologues in Fungi: Phylogenetic and Functional Analysis with Focus on Nitrilases in Trametes versicolor and Agaricus bisporus.
  Molecules. 2020 Aug 25;25(17):E3861. DOI: 10.3390/molecules25173861 (PDF)
• Skořepa O, Pazicky S, Kalousková B, Bláha J, Abreu C, Ječmen T, Rosůlek M, Fish A, Sedivy A, Harlos K, Dohnálek J, Skálová T, Vaněk O.
  Natural Killer Cell Activation Receptor NKp30 Oligomerization Depends on Its N-Glycosylation.
  Cancers (Basel). 2020 Jul 21;12(7):1998. DOI: 10.3390/cancers12071998 (PDF)
• Ferofontov A, Vankova P, Man P, Giladi M, Haitin Y
  Conserved cysteine dioxidation enhances membrane interaction of human Cl- intracellular channel 5.
  FASEB J. 2020 Jun 17; 34(8): 9925-9940. DOI: 10.1096/fj.202000399R (PDF)
• Stalmans G, Lilina AV, Vermeire PJ, Fiala J, Novák P, Strelkov SV.
  Addressing the Molecular Mechanism of Longitudinal Lamin Assembly Using Chimeric Fusions.
  Cells. 2020 Jul 7;9(7):E1633. DOI: 10.3390/cells9071633 (PDF)
• Bousova K, Barvik I, Herman P, Hofbauerová K, Monincova L, Majer P, Zouharova M, Vetyskova V, Postulkova K, Vondrasek J.
  Mapping of CaM, S100A1 and PIP2-Binding Epitopes in the Intracellular N- and C-Termini of TRPM4.
  Int J Mol Sci. 2020 Jun 17;21(12):E4323. DOI: 10.3390/ijms21124323 (PDF)
• Trcka F, Durech M, Vankova P, Vandova V, Simoncik O, Kavan D, Vojtesek B, Muller P, Man P
  The interaction of the mitochondrial protein importer TOMM34 with HSP70 is regulated by TOMM34 phosphorylation and binding to 14-3-3 adaptors.
  J. Biol Chem 2020 Jul 3;295(27):8928-8944. DOI: 10.1074/jbc.RA120.012624
• Vališ K, Novák P
  Targeting ERK-Hippo Interplay in Cancer Therapy.
  Int J Mol Sci 2020 May 3; 21(9):E3236. DOI: 10.3390/ijms21093236
• Fiala, J, Kukacka, Z, Novak, P.
  Influence of cross-linker polarity on selectivity towards lysine side chains.
  J. Proteomics 2020 Feb 20; 218: 103716. DOI: 10.1016/j.jprot.2020.103716
• Petrenčáková M, Filandr F, Hovan A, Yassaghi G, Man P, Kožár T, Schwer M, Jancura D, Plückthun A, Novák P, Miškovský P, Bánó G, Sedlák E
  Photoinduced damage of AsLOV2 domain is accompanied by increased singlet oxygen production due to flavin dissociation.
  Sci. Rep 2020; 10:4119. DOI: 10.1038/s41598-020-60861-2 (PDF)
• Filandr F, Man P, Halada P, Chang H, Ludwig R, Kracher D
  The H₂O₂-dependent activity of a fungal lytic polysaccharide monooxygenase investigated with a turbidimetric assay.
  Biotechnol Biofules 2020 Mar 5; 13: 37. DOI: 10.1186/s13068-020-01673-4 (PDF)
• Filandr F, Kavan D, Kracher D, Laurent CVFP, Ludwig R, Man P, Halada P
  Structural investigation of lytic polysaccharide monooxygenase during catalysis.
  Biomolecules 2020 Feb 5; 10(2): 242. DOI: 10.3390/biom10020242 (PDF)
• Kalabova D, Filandr F, Alblova M, Petrvalska O, Horvath M, Man P, Obsil T, Obsilova V
  14-3-3 protein binding blocks the dimerization interface of caspase-2.
  FEBS J 2020 Jan 21; 287(16):3494-3510. DOI: 10.1111/febs.15215
• Steiningerova L, Kamenik Z, Gazak R, Kadlcik S, Bashiri G, Man P, Kuzma M, Pavlikova M, Janata J
  Different Reaction Specificities of F₄₂₀H₂-Dependent Reductases Facilitate Pyrrolobenzodiazepines and Lincomycin to Fit Their Biological Targets.
  J Am Chem Soc 2020 Feb 19;142(7):3440-3448. DOI: 10.1021/jacs.9b11234
• Main P, Hata T, Loo TS, Man P, Novak P, Havlíček V, Norris GE, Patchett ML
  Bacteriocin ASM1 is an O/S-diglycosylated, plasmid-encoded homologue of glycocin F.
  FEBS Lett 2020 Apr14; 594(7): 1196-1206. DOI: 10.1002/1873-3468.13708
• Millana-Fañanas E, Todesca S, Siccorello A, Masino L, Pompach P, Magnani F, Pastore A, Mattevi A.
  On the mechanism of calcium-dependent activation of NADPH oxidase 5 (NOX5).
  FEBS J 2020; 287(12):2486-2503. DOI: 10.1111/febs.15160
• Vandova V, Vankova P,, Durech M, Houser J, Kavan D, Man P, Muller P, Trcka F
  HSPA1A conformational mutants reveal a conserved structural unit in Hsp70 proteins.
  Biochim Biophys Acta: Gen Subjects 2020; 1864(1):129458.
  DOI: 10.1016/j.bbagen.2019.129458

2019

• Vankova P, Salido E, Timson DJ, Man P, Pey AL
  A dynamic core in human NQO1 controls the functional and stability effects of ligand binding and their communication across the enzyme dimer.
  Biomolecules 2019 Nov 12; 9(11): E728. DOI: 10.3390/biom9110728 (PDF)
• Pavlíková N, Daniel P, Šrámek J, Jelínek M, Šrámková V, Němcová V, Balušíková K, Halada P, Kovář J
  Upregulation of vitamin D-binding protein is associated with changes in insulin production in pancreatic beta-cells exposed to p,p'-DDT and p,p'-DDE.
  Sci Rep. 2019 Dec 2; 9(1):18026. DOI: 10.1038/s41598-019-54579-z (PDF)
• Vaněk O, Celadova P, Skořepa O, Bláha J, Kalousková B, Dvorská A, Poláchová E, Pucholtová H, Kavan D, Pompach P, Hofbauerová K, Kopecký V, Mesci A, Voigt S, Carlyle JR
  Production of recombinant soluble dimeric C-type lectin-like receptors of rat natural killer cells.
  Sci Rep. 2019 Nov 28; 9(1):17836. DOI: 10.1038/s41598-019-52114-8 (PDF)
• Weiz G, Mazzaferro LS, Kotik M, Neher BD, Halada P, Křen V, Breccia JD
  The flavonoid degrading fungus Acremonium sp. DSM 24697 produces two diglycosidases with different specificities.
  Appl Microbiol Biotechnol. 2019 Nov 8; 103(23-24):9493-9504.
  DOI: 10.1007/s00253-019-10180-y
• Pompach P, Viola CM, Radosavljević J, Lin J, Jiráček J, Brzozowski AM, Selicharová I.
  Cross-Linking/Mass Spectrometry Uncovers Details of Insulin-Like Growth Factor Interaction With Insect Insulin Binding Protein Imp-L2.
  Front Endocrinol (Lausanne) 2019 Oct 9; 10:695. DOI: 10.3389/fendo.2019.00695
• Rosulek M, Darebna P, Pompach P, Slavata L, Novak P
  Proteases Immobilization for In Situ Time-Limited Proteolysis on MALDI Chips.
  Catalyst 2019 Oct 3; 9(10): 833. DOI: 10.3390/catal9100833 (PDF)
• Slavata L, Chmelik J, Kavan D, Filandrova R, Fiala J, Rosulek M, Mrazek H, Kukacka Z, Valis K, Man P, Miller M, McIntyre W, Fabris D, Novak P
  MS-Based Approaches Enable the Structural Characterization of Transcription Factor / DNA Response Element Complex.
  Biomolecules 2019 Sep 26; 9(10): 535. DOI: 10.3390/biom9100535 (PDF)
• Rahimidashaghoul K, Klimánková I, Hubálek M, Korecký M, Chvojka M, Pokorný D, Matoušek V, Fojtík L, Kavan D, Kukačka Z, Novák P, Beier P.
  Reductant-Induced Free Radical Fluoroalkylation of Nitrogen Heterocycles and Innate Aromatic Amino Acid Residues in Peptides and Proteins.
  Chemistry 2019 Dec10; 25(69): 15779-15785. DOI: 10.1002/chem.201902944
• Hlavackova K, Dvorak V, Chaskopoulou A, Volf P, Halada P.
  A novel MALDI-TOF MS-based method for blood meal identification in insect vectors: A proof of concept study on phlebotomine sand flies.
  PLoS Negl Trop Dis. 2019 Sep 9;13(9):e0007669. DOI: 10.1371/journal.pntd.0007669
• Zouharova M, Herman P, Hofbauerová K, Vondrasek J, Bousova K.
  TRPM6 N-Terminal CaM- and S100A1-Binding Domains.
  Int J Mol Sci. 2019 Sep 9; 20(18):E4430. DOI: 10.3390/ijms20184430
• Vaselek S, Dvorak V, Hlavackova K, Ayhan N, Halada P, Oguz G, Ivović V, Ozbel Y, Charrel RN, Alten B, Petrić D.
  A survey of sand flies (Diptera, Phlebotominae) along recurrent transit routes in Serbia.
  Acta Trop. 2019 Sep; 197:105063. DOI: 10.1016/j.actatropica.2019.105063
• Kiss É, Knoppová J, Aznar GP, Pilný J, Yu J, Halada P, Nixon PJ, Sobotka R, Komenda J.
  A Photosynthesis-Specific Rubredoxin-Like Protein Is Required for Efficient Association of the D1 and D2 Proteins during the Initial Steps of Photosystem II Assembly.
  Plant Cell. 2019 Sep;31(9):2241-2258. DOI: 10.1105/tpc.19.00155
• Vit O, Harant K, Klener P, Man P, Petrak J.
  A three-pronged 'Pitchfork' strategy enables an extensive description of the human membrane proteome and the identification of missing proteins.
  J Proteomics. 2019 Jul 30;204:103411. DOI: 10.1016/j.jprot.2019.103411
• Flieger M, Stodulkova E, Wyka SA, Cerny J, Grobarova V, Pichova K, Novak P, Man P, Kuzma M, Cvak L, Broders KD, Kolarik M
  Ergochromes: Heretofore Neglected Side of Ergot Toxicity
  Toxins 2019 Jul 25, 11(8), 439 DOI: 10.3390/toxins11080439 (PDF)
• Zeman J, Itoh Y, Kukačka Z, Rosůlek M, Kavan D, Kouba T, Jansen ME, Mohammad MP, Novák P, Valášek LS.
  Binding of eIF3 in complex with eIF5 and eIF1 to the 40S ribosomal subunit is accompanied by dramatic structural changes.
  Nucleic Acids Res. 2019 Jul 10. pii: gkz570. DOI: 10.1093/nar/gkz570
• Masson GR, Burke JE, Ahn NG, Anand GS, Borchers C, Brier S, Bou-Assaf GM, Engen JR, Englander SW, Faber J, Garlish R, Griffin PR, Gross ML, Guttman M, Hamuro Y, Heck AJR, Houde D, Iacob RE, Jørgensen TJD, Kaltashov IA, Klinman JP, Konermann L, Man P, Mayne L, Pascal BD, Reichmann D, Skehel M, Snijder J, Strutzenberg TS, Underbakke ES, Wagner C, Wales TE, Walters BT, Weis DD, Wilson DJ, Wintrode PL, Zhang Z, Zheng J, Schriemer DC, Rand KD.
  Recommendations for performing, interpreting and reporting hydrogen deuterium exchange mass spectrometry (HDX-MS) experiments.
  Nat. Methods 2019 Jul;16(7):595-602. DOI: 10.1038/s41592-019-0459-y (PDF)
• Němcová-Fürstová V, Balušíková K, Halada P, Pavlíková N, Šrámek J, Kovář J.
  Stearate-Induced Apoptosis in Human Pancreatic β-Cells is Associated with Changes in Membrane Protein Expression and These Changes are Inhibited by Oleate.
  Proteomics Clin Appl. 2019 Jul; 13(4):e1800104. DOI: 10.1002/prca.201800104
• Moeller IR, Slivacka M, Hausner J, Nielsen AK, Pospisilova E, Merkle PS, Liskova R, Polak M, Loaland CJ, Kadek A, Man P, Rand KD
  Improving the sequence coverage of integral membrane proteins during hydrogen/deuterium exchange mass spectrometry experiments.
  Anal. Chem. 2019 Jun 20; 91(17): 10970-10978 DOI: 10.1021/acs.analchem.9b00973
• Daniel P, Halada P, Jelínek M, Balušíková K, Kovář J.
  Differentially Expressed Mitochondrial Proteins in Human MCF7 Breast Cancer Cells Resistant to Paclitaxel.
  Int J Mol Sci. 2019 Jun 19; 20(12):E2986. DOI: 10.3390/ijms20122986
• Iacobucci C, Piotrowski C, Aebersold R, Amaral BC, Andrews P, Bernfur K, Borchers C, Brodie NI, Bruce JE, Cao Y, Chaignepain S, Chavez JD, Claverol S, Cox J, Davis T, Degliesposti G, Dong MQ, Edinger N, Emanuelsson C, Gay M, Götze M, Gomes-Neto F, Gozzo FC, Gutierrez C, Haupt C, Heck AJR, Herzog F, Huang L, Hoopmann MR, Kalisman N, Klykov O, Kukačka Z, Liu F, MacCoss MJ, Mechtler K, Mesika R, Moritz RL, Nagaraj N, Nesati V, Neves-Ferreira AGC, Ninnis R, Novák P, O'Reilly FJ, Pelzing M, Petrotchenko E, Piersimoni L, Plasencia M, Pukala T, Rand KD, Rappsilber J, Reichmann D, Sailer C, Sarnowski CP, Scheltema RA, Schmidt C, Schriemer DC, Shi Y, Skehel JM, Slavin M, Sobott F, Solis-Mezarino V, Stephanowitz H, Stengel F, Stieger CE, Trabjerg E, Trnka M, Vilaseca M, Viner R, Xiang Y, Yilmaz S, Zelter A, Ziemianowicz D, Leitner A, Sinz A.
  First Community-Wide, Comparative Cross-Linking Mass Spectrometry Study.
  Anal. Chem. 2019 Jun 4; 91(11): 6953-6961. DOI: 10.1021/acs.analchem.9b00658 (PDF)
• Cazan CD, Păstrav IR, Ionică AM, Oguz G, Erisoz Kasap O, Dvorak V, Halada P, Dumitrache MO, Volf P, Alten B, Mihalca AD.
  Updates on the distribution and diversity of sand flies (Diptera: Psychodidae) in Romania.
  Parasit Vectors. 2019 May 20; 12(1):247. DOI: 10.1186/s13071-019-3507-7.
• Adámková L, Kvíčalová Z, Rozbeský D, Kukačka Z, Adámek D, Cebecauer M, Novák P.
  Oligomeric Architecture of Mouse Activating Nkrp1 Receptors on Living Cells.
  Int J Mol Sci. 2019 Apr 16;20(8). pii: E1884. DOI: 10.3390/ijms20081884
• Chumová J, Kourová H, Trögelová L, Halada P, Binarová P.
  Microtubular and Nuclear Functions of γ-Tubulin: Are They LINCed?
  Cells. 2019 Mar 19;8(3):E259. DOI: 10.3390/cells8030259.
• Nováková J, Talacko P, Novák P, Vališ K
  The MEK-ERK-MST1 Axis Potentiates the Activation of the Extrinsic Apoptotic Pathway during GDC-0941 Treatment in Jurkat T Cells.
  Cells 2019 Feb 21, 8(2). pii: E191. DOI: 10.3390/cells8020191
• Trcka F, Durech M, Vankova P, Chmelik J, Martinkova V, Hausner J, Kadek A, Marcoux J, Klumpler T, Vojtesek B, Muller P, Man P
  Human stress-inducible Hsp70 has a high propensity to form ATP-dependent antiparallel dimers that are differentially regulated by co-chaperone binding.
  Mol Cell Proteomics. 2019 Feb, 18(2): 320-337. DOI: 10.1074/mcp.RA118.001044
• Man P, Fábry M, Sieglová I, Kavan D, Novák P, Hnízda A.
  Thiopurine intolerance-causing mutations in NUDT15 induce temperature-dependent destabilization of the catalytic site.
  Biochim Biophys Acta Proteins Proteom. 2019, 1867(4): 376-381.
  DOI: 10.1016/j.bbapap.2019.01.006
• Hernychová L, Rosůlek M, Kádek A, Mareška V, Chmelík J, Adámková L, Grobárová V, Šebesta O, Kukačka Z, Skála K, Spiwok V, Černý J, Novák P.
  The C-type lectin-like receptor Nkrp1b: Structural proteomics reveals features affecting protein conformation and interactions.
  J Proteomics. 2019 Mar 30, 196:162-172. DOI: 10.1016/j.jprot.2018.11.007

2018

• Darebna P, Spicka J, Kucera R, Topolcan O, Navratilova E, Ruzicka V, Volny M, Novak P, Pompach P
  Detection and Quantification of Carbohydrate-Deficient Transferrin by MALDI-Compatible Protein Chips Prepared by Ambient Ion Soft Landing.
  Clin Chem, 2018 Sep;64(9):1319-1326. DOI: 10.1373/clinchem.2017.285452
• Sharma S, Cermakova K, De Rijck J, Demeulemeester J, Fabry M, El Ashkar S, Van Belle S, Lepsik M, Tesina P, Duchoslav V, Novak P, Hubalek M, Srb P, Christ F, Rezacova P, Hodges C, Debyser Z, Veverka V
  Affinity switching of the LEDGF/p75 IBD interactome is governed by kinase-dependent phosphorylation.
  Proc Natl Acad Sci USA. 2018 Jul 24; 115(30): E7053-E7062.
  DOI: 10.1073/pnas.1803909115
• Jurnecka D, Man P, Sebo P, Bumba L
  Bordetella pertussis and Bordetella bronchiseptica filamentous hemagglutinins are processed at different sites.
  FEBS Open Bio. 2018 Jun 20; 8(8): 1256-1266. DOI: 10.1002/2211-5463.12474
• Hnízda A, Fábry M, Moriyama T, Pachl P, Kugler M, Brinsa V, Ascher DB, Carroll WL, Novák P, Žaliová M, Trka J, Řezáčová P, Yang JJ, Veverka V
  Relapsed acute lymphoblastic leukemia-specific mutations in NT5C2 cluster into hotspots driving intersubunit stimulation.
  Leukemia 2018 Feb; 32(6): 1393-1403. DOI: 10.1038/s41375-018-0073-5
• Škerlová J, Bláha J, Pachl P, Hofbauerová K, Kukačka Z, Man P, Pompach P, Novák P, Otwinowski Z, Brynda J, Vaněk O, Řezáčová P
  Crystal structure of native β-N-acetylhexosaminidase isolated from Aspergillus oryzae sheds light onto its substrate specificity, high stability, and regulation by propeptide.
  FEBS J. 2018 Feb; 285(3): 580-598. DOI: 10.1111/febs.14360
• Rozbesky D, Rosulek M, Kukacka Z, Chmelik J, Man P, Novak P
  Impact of Chemical Cross-Linking on Protein Structure and Function.
  Anal Chem 2018 Jan 16; 90(2): 1104-1113. DOI: 10.1021/acs.analchem.7b02863

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, Dec 22;292(51):20921-20935
  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