Výpis publikací

PLANAS IGLESIAS, Joan; Marika MAJEROVÁ; Daniel PLUSKAL; Michal VAŠINA; Jiří DAMBORSKÝ; Zbyněk PROKOP; Martin MAREK a David BEDNÁŘ. Automated Engineering Protein Dynamics via Loop Grafting: Improving Renilla Luciferase Catalysis. ACS Catalysis. WASHINGTON: AMER CHEMICAL SOC, 2025, roč. 15, č. 4, s. 3391-3404. ISSN 2155-5435. Dostupné z: https://doi.org/10.1021/acscatal.4c06207.

KOHOUT, Pavel; Michal VAŠINA; Marika MAJEROVÁ; Veronika NOVÁKOVÁ; Jiří DAMBORSKÝ; David BEDNÁŘ; Martin MAREK; Zbyněk PROKOP a Stanislav MAZURENKO. Engineering Dehalogenase Enzymes Using Variational Autoencoder-Generated Latent Spaces and Microfluidics. JACS Au. WASHINGTON: AMER CHEMICAL SOC, 2025, roč. 5, č. 2, s. 838-850. ISSN 2691-3704. Dostupné z: https://doi.org/10.1021/jacsau.4c01101.

SITTE, Martin; Daniel PLUSKAL; Marie ŠULOVÁ; Laurent DUCHATELET; Jiří DAMBORSKÝ; Jérôme DELROISSE a Martin MAREK. Functional characterisation of the luminous apparatus of the sea pen Pennatula phosphorea. In The XXVIII Biochemistry congress. 2025. ISBN 978-80-907779-5-8.

LAU, Emily S.; Marika MAJEROVÁ; Nicholai M. HENSLEY; Arnab MUKHERJEE; Michal VAŠINA; Daniel PLUSKAL; Jiří DAMBORSKÝ; Zbyněk PROKOP; Jerome DELROISSE; Wendy-Shirley BAYAERT; Elise PAREY; Paola OLIVERI; Ferdinand MARLETAZ; Martin MAREK a Todd H. OAKLEY. Functional Characterization of Luciferase in a Brittle Star Indicates Parallel Evolution Influenced by Genomic Availability of Haloalkane Dehalogenase. Molecular Biology and Evolution. OXFORD: Oxford University Press, 2025, roč. 42, č. 5, s. 1-10. ISSN 0737-4038. Dostupné z: https://doi.org/10.1093/molbev/msaf081.

MIKUŠOVÁ, Petra; Zuzana TOUŠOVÁ; Luděk SEHNAL; Jan KUTA; K. GRABICOVA; G. FEDOROVA; Martin MAREK; R. GRABIC a Klára HILSCHEROVÁ. Identification of new endocrine disruptive transthyretin ligands in polluted waters using pull-down assay coupled to non-target mass spectrometry. Journal of Hazardous Materials. Amsterdam: Elsevier Science BV., 2024, roč. 471, June 2024, s. 1-12. ISSN 0304-3894. Dostupné z: https://doi.org/10.1016/j.jhazmat.2024.134240.

MAJEROVÁ, Marika; Michal VAŠINA; Daniel PLUSKAL; Karolina SEDLÁČKOVÁ; Zbyněk PROKOP; Jiří DAMBORSKÝ a Martin MAREK. Nová duální dehalogenáza-luciferáza z hvězdice křehké Amphiura filiformis. 2024.

MAJEROVÁ, Marika; Michal VAŠINA; Daniel PLUSKAL; Karolina SEDLÁČKOVÁ; Zbyněk PROKOP; Jiří DAMBORSKÝ a Martin MAREK. Nová vysoce aktivní luciferáza z hvězdice křehké Amphiura filiformis. 2024.

DE LA BOURDONNAYE, Gabin; Martin MAREK; Tereza GHAZALOVÁ; Jiří DAMBORSKÝ; Petr PACHL; Jiri BRYNDA; Veronika ŠTĚPÁNKOVÁ a Radka CHALOUPKOVÁ. Structural analysis of the stable form of fibroblast growth factor 2 - FGF2-STAB. Journal of Structural Biology: X. AMSTERDAM: ELSEVIER, 2024, roč. 10, December 2024, s. 1-8. ISSN 2590-1524. Dostupné z: https://doi.org/10.1016/j.yjsbx.2024.100112.

BAYAERT, Wendy Shirley; Laurent DUCHATELET; Kirsikka SILLANPAEAE; Sam DUPONT; Martin MAREK; Patrick FLAMMANG a Jerome DELROISSE. Ultrastructural description of surface receptors in the bioluminescent brittle star Amphiura filiformis (Müller, 1776). CAHIERS DE BIOLOGIE MARINE. FRANCE: CAHIERS DE BIOLOGIE MARINE, 2024, roč. 65, č. 4, s. 343-355. ISSN 0007-9723. Dostupné z: https://doi.org/10.21411/CBM.A.8AC9D29C.

KUNKA, Antonín; Sérgio Manuel MARQUES; Martin HAVLÁSEK; Michal VAŠINA; Nikola VELÁTOVÁ; Lucia CENGELOVÁ; David KOVÁŘ; Jiří DAMBORSKÝ; Martin MAREK; David BEDNÁŘ a Zbyněk PROKOP. Advancing Enzyme's Stability and Catalytic Efficiency through Synergy of Force-Field Calculations, Evolutionary Analysis, and Machine Learning. ACS Catalysis. WASHINGTON: AMER CHEMICAL SOC, 2023, roč. 13, č. 19, s. 12506-12518. ISSN 2155-5435. Dostupné z: https://doi.org/10.1021/acscatal.3c02575.

ŠNAJDAROVÁ, Karolína; Sérgio Manuel MARQUES; Jiří DAMBORSKÝ; David BEDNÁŘ a Martin MAREK. Atypical homodimerization revealed by the structure of the (S)-enantioselective haloalkane dehalogenase DmmarA from Mycobacterium marinum. Acta Crystallographica Section D: Structural Biology. Chester: International Union of Crystallography, 2023, roč. 79, November, s. 956-970. ISSN 2059-7983. Dostupné z: https://doi.org/10.1107/S2059798323006642.

SMITH, Andrea; Martin TOUL; Daniel PLUSKAL; Racha BAATALLAH; Glwadys GAGNOT; José Gaspar RANGEL PAMPLONA PIZARRO PINTO; Vinicius T. T. SANTANA; Markéta STUCHLÁ; Petr NEUGEBAUER; Pimchai CHAIYEN; Jiří DAMBORSKÝ; David BEDNÁŘ; Yves L. L. JANIN; Zbyněk PROKOP a Martin MAREK. Catalytic mechanism for Renilla-type luciferases. Nature Catalysis. Nature Portfolio, 2023, roč. 6, č. 1, s. 23-38. ISSN 2520-1158. Dostupné z: https://doi.org/10.1038/s41929-022-00895-z.

GAO, Tadeja; Jiří DAMBORSKÝ; Yves L. JANIN a Martin MAREK. Deciphering Enzyme Mechanisms with Engineered Ancestors and Substrate Analogues. ChemCatChem. WEINHEIM: WILEY-V C H VERLAG GMBH, 2023, roč. 15, č. 19, s. 1-16. ISSN 1867-3880. Dostupné z: https://doi.org/10.1002/cctc.202300745.

NEMERGUT, Michal; Sérgio Manuel MARQUES; Lukáš UHRÍK; Tereza VÁŇOVÁ; Markéta NEZVEDOVÁ; Darshak Chandulal GADARA; Durga JHA; Jan TULIS; Veronika NOVÁKOVÁ; Joan PLANAS IGLESIAS; Antonín KUNKA; Anthony Thomas P LEGRAND; Hana HŘÍBKOVÁ; Veronika POSPÍŠILOVÁ; Jiří SEDMÍK; Jan RAŠKA; Zbyněk PROKOP; Jiří DAMBORSKÝ; Dáša BOHAČIAKOVÁ; Zdeněk SPÁČIL; Lenka HERNYCHOVÁ; David BEDNÁŘ a Martin MAREK. Domino-like effect of C112R mutation on ApoE4 aggregation and its reduction by Alzheimer’s Disease drug candidate. Molecular Neurodegeneration. England: BMC, 2023, roč. 18, č. 1, s. 1-25. ISSN 1750-1326. Dostupné z: https://doi.org/10.1186/s13024-023-00620-9.

NEMERGUT, Michal; Daniel PLUSKAL; Jana HORÁČKOVÁ; Tereza ŠUSTROVÁ; Jan TULIS; Tomáš BÁRTA; Racha BAATALLAH; Glwadys GAGNOT; Veronika NOVÁKOVÁ; Marika MAJEROVÁ; Karolina SEDLÁČKOVÁ; Sérgio Manuel MARQUES; Martin TOUL; Jiří DAMBORSKÝ; Zbyněk PROKOP; David BEDNÁŘ; Yves L. JANIN a Martin MAREK. Illuminating the mechanism and allosteric behavior of NanoLuc luciferase. Nature Communications. Berlin: Nature, 2023, roč. 14, č. 1, s. 1-20. ISSN 2041-1723. Dostupné z: https://doi.org/10.1038/s41467-023-43403-y.

GUERRA-SLOMPO, Eloise Pavao; Gisele Fernanda Assine PICCHI-CONSTANTE; Martin MAREK; Christophe ROMIER; Wolfgang SIPPL a Nilson Ivo Tonin ZANCHIN. In cellulo and in vivo assays for compound testing against Trypanosoma cruzi. STAR Protocols. United States: Cell Press, 2023, roč. 4, č. 1, s. 1-42. ISSN 2666-1667. Dostupné z: https://doi.org/10.1016/j.xpro.2023.102058.

CHMELOVÁ, Klaudia; Tadeja GAO; Martin POLÁK; Andrea SMITH; Tristan I. CROLL; Tanvir SHAIKH; Jana ŠKAŘUPOVÁ; Radka CHALOUPKOVÁ; Kay DIEDERICHS; Randy J. READ; Jiří DAMBORSKÝ; Jiří NOVÁČEK a Martin MAREK. Multimeric structure of a subfamily III haloalkane dehalogenase-like enzyme solved by combination of cryo-EM and x-ray crystallography. Protein Science. Hoboken: Wiley, 2023, roč. 32, č. 10, s. 1-22. ISSN 0961-8368. Dostupné z: https://doi.org/10.1002/pro.4751.

UHRIK, Lukas; Tomas HENEK; Joan PLANAS IGLESIAS; Josef KUCERA; Jiří DAMBORSKÝ; Martin MAREK a Lenka HERNYCHOVA. Study of Protein Conformational Dynamics Using Hydrogen/Deuterium Exchange Mass Spectrometry. In Ângela Sousa, Luis Passarinha. Advanced Methods in Structural Biology. New York: Springer Nature, 2023, s. 293-318. 1. ISBN 978-1-0716-3146-1. Dostupné z: https://doi.org/10.1007/978-1-0716-3147-8_18.

NIKITIN, Dmitri; Jan MIČAN; Martin TOUL; David BEDNÁŘ; Michaela PEŠKOVÁ; Patrícia KITTOVÁ; Sandra THALEROVÁ; Jan VÍTEČEK; Jiří DAMBORSKÝ; Robert MIKULÍK; Sarel J. FLEISHMAN; Zbyněk PROKOP a Martin MAREK. Computer-aided engineering of staphylokinase toward enhanced affinity and selectivity for plasmin. Computational and Structural Biotechnology Journal. Amsterdam: Elsevier, 2022, roč. 20, May 2022, s. 1366-1377. ISSN 2001-0370. Dostupné z: https://doi.org/10.1016/j.csbj.2022.03.004.

TOUL, Martin; Dmitri NIKITIN; Martin MAREK; Jiří DAMBORSKÝ a Zbyněk PROKOP. Extended Mechanism of the Plasminogen Activator Staphylokinase Revealed by Global Kinetic Analysis: 1000-fold Higher Catalytic Activity than That of Clinically Used Alteplase. ACS Catalysis. WASHINGTON: AMER CHEMICAL SOC, 2022, roč. 12, č. 7, s. 3807-3814. ISSN 2155-5435. Dostupné z: https://doi.org/10.1021/acscatal.1c05042.

TOUL, Martin; Jan MIČAN; Veronika SLONKOVÁ; Dmitri NIKITIN; Martin MAREK; David BEDNÁŘ; Jiří DAMBORSKÝ a Zbyněk PROKOP. Hidden Potential of Highly Efficient and Widely Accessible Thrombolytic Staphylokinase. Stroke. Dallas: Lippincott Williams & Wilkins, 2022, roč. 53, č. 10, s. 3235-3237. ISSN 0039-2499. Dostupné z: https://doi.org/10.1161/STROKEAHA.122.040219.

NEMERGUT, Michal; Tereza BÁŤKOVÁ; Dana VIGAŠOVÁ; Milan BARTOŠ; Martina HLOZANKOVA; Andrea SMITH; Barbora LIŠKOVÁ; Kateřina SHEARDOVÁ; Martin VYHNALEK; Jakub HORT; Jan LACZO; Ingrid KOVÁČOVÁ; Michal ŠITINA; Radoslav MATEJ; Radim JANČÁLEK; Martin MAREK a Jiří DAMBORSKÝ. Increased occurrence of Treponema spp. and double-species infections in patients with Alzheimer's disease. Science of the Total Environment. Amsterdam: Elsevier Science, 2022, roč. 844, October 2022, s. 1-7. ISSN 0048-9697. Dostupné z: https://doi.org/10.1016/j.scitotenv.2022.157114.

MARQUES, Sérgio Manuel; Michaela SLÁNSKÁ; Klaudia CHMELOVÁ; Radka CHALOUPKOVÁ; Martin MAREK; Spencer CLARK; Jiří DAMBORSKÝ; Eric T. KOOL; David BEDNÁŘ a Zbyněk PROKOP. Mechanism-Based Strategy for Optimizing HaloTag Protein Labeling. JACS AU. WASHINGTON: AMER CHEMICAL SOC, 2022, roč. 2, č. 6, s. 1324-1337. ISSN 2691-3704. Dostupné z: https://doi.org/10.1021/jacsau.2c00002.

DAMBORSKÝ, Jiří; David BEDNÁŘ; Zbyněk PROKOP; Martin MAREK; Stanislav MAZURENKO; Jan ŠTOURAČ; Sérgio Manuel MARQUES; Gabriela Filipa FONSECA PINTO; Joan PLANAS IGLESIAS; Miloš MUSIL; Jiří HON; Ondřej VÁVRA; Rayyan Tariq KHAN; Jiří FILIPOVIČ a Barbora KOZLÍKOVÁ. Computational enzyme design for metabolic engineering. In The 45th FEBS Congress. 2021. ISSN 2211-5463.

MARKOVÁ, Klára; Antonín KUNKA; Klaudia CHMELOVÁ; Martin HAVLÁSEK; Petra BABKOVÁ; Sérgio Manuel MARQUES; Michal VAŠINA; Joan PLANAS IGLESIAS; Radka CHALOUPKOVÁ; David BEDNÁŘ; Zbyněk PROKOP; Jiří DAMBORSKÝ a Martin MAREK. Computational Enzyme Stabilization Can Affect Folding Energy Landscapes and Lead to Catalytically Enhanced Domain-Swapped Dimers. ACS Catalysis. WASHINGTON: AMER CHEMICAL SOC, 2021, roč. 11, č. 21, s. 12864-12885. ISSN 2155-5435. Dostupné z: https://doi.org/10.1021/acscatal.1c03343.

MAREK, Martin; Jiří DAMBORSKÝ; David BEDNÁŘ; Daniel PLUSKAL; Marika MAJEROVÁ a Joan PLANAS IGLESIAS. Designované a syntetizované geny kódující nově zkonstruované proteinové katalyzátory (luciferázy) s ověřenými vlastnostmi. 2021.

TOUL, Martin; Andrea SMITH; José Gaspar RANGEL PAMPLONA PIZARRO PINTO; Martin MAREK; Lenka HERNYCHOVÁ; Veronika LIŠKOVÁ; Daniel PLUSKAL; Stephane EMOND; Mark DÖRR; Joan PLANAS IGLESIAS; Radka CHALOUPKOVÁ; David BEDNÁŘ; Zbyněk PROKOP; Uwe T. BORNSCHEUER; Florian HOLLFELDER a Jiří DAMBORSKÝ. Engineering protein dynamics for the understanding of divergent evolution of the Renilla luciferase. In The 45th FEBS Congress. 2021. ISSN 2211-5463.

SCHENKMAYEROVÁ, Andrea; José Gaspar RANGEL PAMPLONA PIZARRO PINTO; Martin TOUL; Martin MAREK; Lenka HERNYCHOVÁ; Joan PLANAS IGLESIAS; Veronika LIŠKOVÁ; Daniel PLUSKAL; Michal VAŠINA; Stephane EMOND; Mark DÖRR; Radka CHALOUPKOVÁ; David BEDNÁŘ; Zbyněk PROKOP; Florian HOLLFELDER; Uwe T. BORNSCHEUER a Jiří DAMBORSKÝ. Engineering the protein dynamics of an ancestral luciferase. Nature Communications. London: Nature Publishing Group, 2021, roč. 12, č. 1, s. 3616-3631. ISSN 2041-1723. Dostupné z: https://doi.org/10.1038/s41467-021-23450-z.

MAREK, Martin; E. RAMOS-MORALES; G.F.A. PICCHI-CONSTANTE; T. BAYER; C. NORSTROM; D. HERP; P.A. SALES; E.P. GUERRA-SLOMPO; K. HAUSMANN; A. CHAKRABARTI; T.B. SHAIK; A. MERZ; E. TROESCH; K. SCHMIDTKUNZ; S. GOLDENBERG; R.J. PIERCE; MM MOURAO; M.M. JUNG; J. SCHULTZ; W. SIPPL; N.I.T. ZANCHIN a C. ROMIER. Species-selective targeting of pathogens revealed by the atypical structure and active site of Trypanosoma cruzi histone deacetylase DAC2. Cell Reports. CAMBRIDGE: Cell Press, 2021, roč. 37, č. 12, s. 1-17, "e1-e9", 26 s. ISSN 2211-1247. Dostupné z: https://doi.org/10.1016/j.celrep.2021.110129.

RAMOS-MORALES, Elizabeth; Efil BAYAM; Jordi DEL-POZO-RODRIGUEZ; Thalia SALINAS-GIEGE; Martin MAREK; Ramos-Morales, E (Ramos- TILLY; Philippe WOLFF; Edouard TROESCH; Eric ENNIFAR; Laurence DROUARD; Juliette D. GODIN a Christophe ROMIER. The structure of the mouse ADAT2/ADAT3 complex reveals the molecular basis for mammalian tRNA wobble adenosine-to-inosine deamination. Nucleic acids research. Oxford: Oxford University Press, 2021, roč. 49, č. 11, s. 6529-6548. ISSN 0305-1048. Dostupné z: https://doi.org/10.1093/nar/gkab436.

MARKOVÁ, Klára; Klaudia CHMELOVÁ; Sérgio Manuel MARQUES; Philippe CARPENTIER; David BEDNÁŘ; Jiří DAMBORSKÝ a Martin MAREK. Decoding the intricate network of molecular interactions of a hyperstable engineered biocatalyst. Chemical Science. Cambridge: Royal Society of Chemistry, 2020, roč. 11, č. 41, s. 11162-11178. ISSN 2041-6520. Dostupné z: https://doi.org/10.1039/d0sc03367g.

MAREK, Martin; Radka CHALOUPKOVÁ; Tanyana PRUDNIKOVA; Yukari SATO; Pavlina REZACOVA; Yuji NAGATA; Ivana SMATANOVA KUTA a Jiří DAMBORSKÝ. Structural and catalytic effects of surface loop-helix transplantation within haloalkane dehalogenase family. Computational and Structural Biotechnology Journal. Amsterdam: Elsevier, 2020, roč. 18, December 2020, s. 1352-1362. ISSN 2001-0370. Dostupné z: https://doi.org/10.1016/j.csbj.2020.05.019.

BABKOVÁ, Petra; Zuzana DUNAJOVÁ; Radka CHALOUPKOVÁ; Jiří DAMBORSKÝ; David BEDNÁŘ a Martin MAREK. Structures of hyperstable ancestral haloalkane dehalogenases show restricted conformational dynamics. Computational and Structural Biotechnology Journal. Amsterdam: Elsevier, 2020, roč. 18, č. 2020, s. 1497-1508. ISSN 2001-0370. Dostupné z: https://doi.org/10.1016/j.csbj.2020.06.021.

SCHENKMAYEROVA, A.; G. PINTO; Martin MAREK; Martin TOUL; Lenka HERNYCHOVÁ; Veronika LIŠKOVÁ; S. EMOND; David BEDNÁŘ; Zbyněk PROKOP; Radka CHALOUPKOVÁ; F. HOLLFELDER a U.T. BORNSCHEUER. Functional switching based on altered enzyme flexibility via InDel mutagenesis of a reconstructed ancestor. In European Biotechnology Congress. 2019. ISSN 0168-1656. Dostupné z: https://doi.org/10.1016/j.jbiotec.2019.05.118.

CHALOUPKOVÁ, Radka; Veronika LIŠKOVÁ; Martin TOUL; Klára MARKOVÁ; Eva ŠEBESTOVÁ; Lenka HERNYCHOVÁ; Martin MAREK; José Gaspar RANGEL PAMPLONA PIZARRO PINTO; Daniel PLUSKAL; Jitka WATERMAN; Zbyněk PROKOP a Jiří DAMBORSKÝ. Light-Emitting Dehalogenases: Reconstruction of Multifunctional Biocatalysts. ACS Catalysis. Washington, D.C.: AMER CHEMICAL SOC, 2019, roč. 9, č. 6, s. 4810-4823. ISSN 2155-5435. Dostupné z: https://doi.org/10.1021/acscatal.9b01031.

ZESSIN, M.; Z. KUTIL; M. MELESHIN; Z. NOVAKOVA; E. GHAZY; D. KALBAS; Martin MAREK; C. ROMIER; W. SIPPL; C. BARINKA a M. SCHUTKOWSKI. One-Atom Substitution Enables Direct and Continuous Monitoring of Histone Deacylase Activity. Biochemistry. Washington: American Chemical Society, 2019, roč. 58, č. 48, s. 4777-4789. ISSN 0006-2960. Dostupné z: https://doi.org/10.1021/acs.biochem.9b00786.

SIMOBEN, Conrad V.; Dina ROBAA; Alokta CHAKRABARTI; Karin SCHMIDTKUNZ; Martin MAREK; Julien LANCELOT; Srinivasaraghavan KANNAN; Jelena MELESINA; Tajith B. SHAIK; Raymond J. PIERCE; Christophe ROMIER; Manfred JUNG a Wolfgang SIPPL. A Novel Class of Schistosoma mansoni Histone Deacetylase 8 (HDAC8) Inhibitors Identified by Structure-Based Virtual Screening and In Vitro Testing. Molecules. BASEL: Mayer und Muller, 2018, roč. 23, č. 3, s. 1-14. ISSN 1420-3049. Dostupné z: https://doi.org/10.3390/molecules23030566.

MAREK, Martin; Tajith B. SHAIK; Tino HEIMBURG; Alokta CHAKRABARTI; Julien LANCELOT; Elizabeth RAMOS-MORALES; Cyrielle DA VEIGA; Dmitrii KALININ; Jelena MELESINA; Dina ROBAA; Karin SCHMIDTKUNZ; Takayoshi SUZUKI; Ralph HOLL; Eric ENNIFAR; Raymond J. PIERCE; Manfred JUNG; Wolfgang SIPPL a Christophe ROMIER. Characterization of Histone Deacetylase 8 (HDAC8) Selective Inhibition Reveals Specific Active Site Structural and Functional Determinants. Journal of Medicinal Chemistry. Washington: American Chemical Society, 2018, roč. 61, č. 22, s. 10000-10016. ISSN 0022-2623. Dostupné z: https://doi.org/10.1021/acs.jmedchem.8b01087.

LECOINTRE, Bertrand; Remy NAROZNY; Maria Teresa BORRELLO; Johanna SENGER; Alokta CHAKRABARTI; Manfred JUNG; Martin MAREK; Christophe ROMIER; Jelena MELESINA; Wolfgang SIPPL; Laurent BISCHOFF a A. GANESAN. Isoform-selective HDAC1/16/8 inhibitors with an imidazo-ketopiperazine cap containing stereochemical diversity. PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES. LONDON: ROYAL SOC, 2018, roč. 373, č. 1748, s. 1-7. ISSN 0962-8436. Dostupné z: https://doi.org/10.1098/rstb.2017.0364.