@article{MTMT:34761990,
	title = {Complex formation of ML324, the histone demethylase inhibitor, with essential metal ions: Relationship between solution chemistry and anticancer activity},
	url = {https://m2.mtmt.hu/api/publication/34761990},
	author = {Kovács, Hilda and Jakusch, Tamás and May, Nóra Veronika and Tóth, Szilárd and Szakács, Gergely and Enyedy, Éva Anna},
	doi = {10.1016/j.jinorgbio.2024.112540},
	journal-iso = {J INORG BIOCHEM},
	journal = {JOURNAL OF INORGANIC BIOCHEMISTRY},
	volume = {255},
	unique-id = {34761990},
	issn = {0162-0134},
	year = {2024},
	eissn = {1873-3344},
	orcid-numbers = {Jakusch, Tamás/0000-0003-0532-5202; May, Nóra Veronika/0000-0003-4770-4681; Enyedy, Éva Anna/0000-0002-8058-8128}
}

@article{MTMT:34401705,
	title = {How AlphaFold2 shaped the structural coverage of the human transmembrane proteome},
	url = {https://m2.mtmt.hu/api/publication/34401705},
	author = {Jambrich, M.A. and Tusnády, Gábor and Dobson, László},
	doi = {10.1038/s41598-023-47204-7},
	journal-iso = {SCI REP},
	journal = {SCIENTIFIC REPORTS},
	volume = {13},
	unique-id = {34401705},
	issn = {2045-2322},
	abstract = {AlphaFold2 (AF2) provides a 3D structure for every known or predicted protein, opening up new prospects for virtually every field in structural biology. However, working with transmembrane protein molecules pose a notorious challenge for scientists, resulting in a limited number of experimentally determined structures. Consequently, algorithms trained on this finite training set also face difficulties. To address this issue, we recently launched the TmAlphaFold database, where predicted AlphaFold2 structures are embedded into the membrane plane and a quality assessment (plausibility of the membrane-embedded structure) is provided for each prediction using geometrical evaluation. In this paper, we analyze how AF2 has improved the structural coverage of membrane proteins compared to earlier years when only experimental structures were available, and high-throughput structure prediction was greatly limited. We also evaluate how AF2 can be used to search for (distant) homologs in highly diverse protein families. By combining quality assessment and homology search, we can pinpoint protein families where AF2 accuracy is still limited, and experimental structure determination would be desirable. © 2023, The Author(s).},
	year = {2023},
	eissn = {2045-2322}
}

@article{MTMT:34279727,
	title = {LeishMANIAdb: a comparative resource for Leishmania proteins},
	url = {https://m2.mtmt.hu/api/publication/34279727},
	author = {Tusnády, Gábor and Zeke, András and Kálmán, Zsófia Etelka and Fatoux, Marie and Ricard-Blum, Sylvie and Gibson, Toby J and Dobson, László},
	doi = {10.1093/database/baad074},
	journal-iso = {DATABASE-OXFORD},
	journal = {DATABASE-JOURNAL OF BIOLOGICAL DATABASES AND CURATION},
	volume = {2023},
	unique-id = {34279727},
	issn = {1758-0463},
	abstract = {Leishmaniasis is a detrimental disease causing serious changes in quality of life and some forms can lead to death. The disease is spread by the parasite Leishmania transmitted by sandfly vectors and their primary hosts are vertebrates including humans. The pathogen penetrates host cells and secretes proteins (the secretome) to repurpose cells for pathogen growth and to alter cell signaling via host–pathogen protein–protein interactions). Here, we present LeishMANIAdb, a database specifically designed to investigate how Leishmania virulence factors may interfere with host proteins. Since the secretomes of different Leishmania species are only partially characterized, we collated various experimental evidence and used computational predictions to identify Leishmania secreted proteins to generate a user-friendly unified web resource allowing users to access all information available on experimental and predicted secretomes. In addition, we manually annotated host–pathogen interactions of 211 proteins and the localization/function of 3764 transmembrane (TM) proteins of different Leishmania species. We also enriched all proteins with automatic structural and functional predictions that can provide new insights in the molecular mechanisms of infection. Our database may provide novel insights into Leishmania host–pathogen interactions and help to identify new therapeutic targets for this neglected disease.},
	year = {2023},
	eissn = {1758-0463},
	orcid-numbers = {Ricard-Blum, Sylvie/0000-0001-9263-1851}
}

@article{MTMT:33688209,
	title = {Organic anion transporting polypeptide 3A1 (OATP3A1)-gated bioorthogonal labeling of intracellular proteins},
	url = {https://m2.mtmt.hu/api/publication/33688209},
	author = {Németh, Krisztina and László, Zsófia and Biró, Adrienn and Szatmári, Ágnes and Cserép, Balázs Gergely and Várady, György and Bakos, Éva and Laczka, Csilla and Kele, Péter},
	doi = {10.3390/molecules28062521},
	journal-iso = {MOLECULES},
	journal = {MOLECULES},
	volume = {28},
	unique-id = {33688209},
	issn = {1420-3049},
	abstract = {Organic anion transporting polypeptides (OATPs) were found to readily deliver membrane impermeable, tetrazine bearing fluorescent probes into cells. This feature was explored in OATP3A1 conditioned bio-orthogonal labeling schemes of various intracellular proteins in live cells. Confocal microscopy and super-resolution microscopy (STED) studies have shown that highly specific and efficient staining of the selected intracellular proteins can be achieved with the otherwise non-permeable probes when OATP3A1 is present in the cell membrane of cells. Such a transport protein linked bio-orthogonal labeling scheme is believed to be useful in OATP3A1 activity-controlled protein expression studies in the future. © 2023 by the authors.},
	keywords = {PROTEINS; PROTEIN; Organic Anion Transporters; Flow Cytometry; Fluorescent Dyes; fluorescent dye; confocal microscopy; organic anion transporter; super-resolution microscopy; Cell permeability; Intracellular labeling; large Stokes shift fluorescent probes; live cell bio-orthogonal modification; organic anion transporter polypeptide 3A1; self-labeling enzyme tags},
	year = {2023},
	eissn = {1420-3049},
	orcid-numbers = {Szatmári, Ágnes/0000-0001-8768-8212; Cserép, Balázs Gergely/0000-0002-0779-0338; Várady, György/0000-0003-2012-9680}
}

@article{MTMT:33586305,
	title = {Comprehensive Discovery of the Accessible Primary Amino Group-Containing Segments from Cell Surface Proteins by Fine-Tuning a High-Throughput Biotinylation Method},
	url = {https://m2.mtmt.hu/api/publication/33586305},
	author = {Langó, Tamás and Kuffa, Katalin Rita and Tóth, Gábor and Turiák, Lilla and Drahos, László and Tusnády, Gábor},
	doi = {10.3390/ijms24010273},
	journal-iso = {INT J MOL SCI},
	journal = {INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES},
	volume = {24},
	unique-id = {33586305},
	issn = {1661-6596},
	abstract = {Cell surface proteins, including transmembrane and other surface-anchored proteins, play a key role in several critical cellular processes and have a strong diagnostic value. The development of quick and robust experimental methods remains vital for the accurate and comprehensive characterization of the cell surface subproteome of individual cells. Here we present a high-throughput technique which relies on the biotinylation of the accessible primary amino groups in the extracellular segments of the proteins, using HL60 as a model cell line. Several steps of the method have been thoroughly optimized to capture labeled surface proteins selectively and in larger quantities. These include the following: improving the efficiency of the cell surface biotinylation; reducing the endogen protease activity; applying an optimal amount of affinity column and elution steps for labeled peptide enrichment; and examining the effect of various solid-phase extraction methods, different HPLC gradients, and various tandem mass spectrometry settings. Using the optimized workflow, we identified at least 1700 surface-associated individual labeled peptides (~6000–7000 redundant peptides) from the model cell surface in a single nanoHPLC-MS/MS run. The presented method can provide a comprehensive and specific list of the cell surface available protein segments that could be potential targets in various bioinformatics and molecular biology research. © 2022 by the authors.},
	keywords = {PEPTIDES; HPLC; metabolism; PEPTIDE; Chemistry; Membrane Proteins; membrane protein; Cell Membrane; Cell Membrane; Mass spectrometry; SOLID-PHASE EXTRACTION; Biotinylation; Biotinylation; tandem mass spectrometry; tandem mass spectrometry; procedures; Cell surface proteins; surfaceome; Affinity enrichment; biotinylated peptides},
	year = {2023},
	eissn = {1422-0067},
	orcid-numbers = {Tóth, Gábor/0000-0003-1428-7906; Drahos, László/0000-0001-9589-6652}
}

@article{MTMT:33532438,
	title = {Metal Complexes of a 5-Nitro-8-Hydroxyquinoline-Proline Hybrid with Enhanced Water Solubility Targeting Multidrug Resistant Cancer Cells},
	url = {https://m2.mtmt.hu/api/publication/33532438},
	author = {Pivarcsik, Tamás and Pósa, Vivien and Kovács, Hilda and May, Nóra Veronika and Spengler, Gabriella and Pósa, Szonja P. and Tóth, Szilárd and Nezafat Yazdi, Zeinab and Laczka, Csilla and Ugrai, Imre and Szatmári, István and Szakács, Gergely and Enyedy, Éva Anna},
	doi = {10.3390/ijms24010593},
	journal-iso = {INT J MOL SCI},
	journal = {INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES},
	volume = {24},
	unique-id = {33532438},
	issn = {1661-6596},
	abstract = {Multidrug resistance (MDR) in cancer is one of the major obstacles of chemotherapy. We have recently identified a series of 8-hydroxyquinoline Mannich base derivatives with MDR-selective toxicity, however with limited solubility. In this work, a novel 5-nitro-8-hydroxyquinoline-proline hybrid and its Rh(η5-C5Me5) and Ru(η6-p-cymene) complexes with excellent aqueous solubility were developed, characterized, and tested against sensitive and MDR cells. Complex formation of the ligand with essential metal ions was also investigated using UV-visible, circular dichroism, 1H NMR (Zn(II)), and electron paramagnetic resonance (Cu(II)) spectroscopic methods. Formation of mono and bis complexes was found in all cases with versatile coordination modes, while tris complexes were also formed with Fe(II) and Fe(III) ions, revealing the metal binding affinity of the ligand at pH 7.4: Cu(II) > Zn(II) > Fe(II) > Fe(III). The ligand and its Rh(III) complex displayed enhanced cytotoxicity against the resistant MES-SA/Dx5 and Colo320 human cancer cell lines compared to their chemosensitive counterparts. Both organometallic complexes possess high stability in solution, however the Ru(II) complex has lower chloride ion affinity and slower ligand exchange processes, along with the readiness to lose the arene ring that is likely connected to its inactivity.},
	year = {2023},
	eissn = {1422-0067},
	orcid-numbers = {May, Nóra Veronika/0000-0003-4770-4681; Spengler, Gabriella/0000-0001-8085-0950; Pósa, Szonja P./0000-0002-7535-9689; Szatmári, István/0000-0002-8571-5229; Enyedy, Éva Anna/0000-0002-8058-8128}
}

@article{MTMT:33294693,
	title = {Interaction of luteolin, naringenin, and their sulfate and glucuronide conjugates with human serum albumin, cytochrome P450 (CYP2C9, CYP2C19, and CYP3A4) enzymes and organic anion transporting polypeptide (OATP1B1 and OATP2B1) transporters},
	url = {https://m2.mtmt.hu/api/publication/33294693},
	author = {Kaci, Hana and Bodnárová, Slávka and Fliszár-Nyúl, Eszter and Lemli, Beáta and Pelantová, Helena and Valentová, Kateřina and Bakos, Éva and Laczka, Csilla and Poór, Miklós},
	doi = {10.1016/j.biopha.2022.114078},
	journal-iso = {BIOMED PHARMACOTHER},
	journal = {BIOMEDICINE & PHARMACOTHERAPY},
	volume = {157},
	unique-id = {33294693},
	issn = {0753-3322},
	abstract = {Luteolin and naringenin are flavonoids found in various foods/beverages and present in certain dietary supplements. After a high intake of these flavonoids, their sulfate and glucuronide conjugates reach micromolar concentrations in the bloodstream. Some pharmacokinetic interactions of luteolin and naringenin have been investigated in previous studies; however, only limited data are available in regard to their metabolites. In this study, we aimed to investigate the interactions of the sulfate and glucuronic acid conjugates of luteolin and naringenin with human serum albumin, cytochrome P450 (CYP2C9, 2C19, and 3A4) enzymes, and organic anion transporting polypeptide (OATP1B1 and OATP2B1) transporters. Our main findings are as follows: (1) Sulfate conjugates formed more stable complexes with albumin than the parent flavonoids. (2) Luteolin and naringenin conjugates showed no or only weak inhibitory action on the CYP enzymes examined. (3) Certain conjugates of luteolin and naringenin are potent inhibitors of OATP1B1 and/or OATP2B1 enzymes. (4) Conjugated metabolites of luteolin and naringenin may play an important role in the pharmacokinetic interactions of these flavonoids.},
	year = {2023},
	eissn = {1950-6007},
	orcid-numbers = {Fliszár-Nyúl, Eszter/0000-0003-0923-0059; Lemli, Beáta/0000-0001-8903-1337}
}

@article{MTMT:33213881,
	title = {TmAlphaFold database: membrane localization and evaluation of AlphaFold2 predicted alpha-helical transmembrane protein structures},
	url = {https://m2.mtmt.hu/api/publication/33213881},
	author = {Dobson, László and Szekeres, Levente István and Gerdán, Csongor and Langó, Tamás and Zeke, András and Tusnády, Gábor},
	doi = {10.1093/nar/gkac928},
	journal-iso = {NUCLEIC ACIDS RES},
	journal = {NUCLEIC ACIDS RESEARCH},
	volume = {51},
	unique-id = {33213881},
	issn = {0305-1048},
	abstract = {AI-driven protein structure prediction, most notably AlphaFold2 (AF2) opens new frontiers for almost all fields of structural biology. As traditional structure prediction methods for transmembrane proteins were both complicated and error prone, AF2 is a great help to the community. Complementing the relatively meager number of experimental structures, AF2 provides 3D predictions for thousands of new alpha-helical membrane proteins. However, the lack of reliable structural templates and the fact that AF2 was not trained to handle phase boundaries also necessitates a delicate assessment of structural correctness. In our new database, Transmembrane AlphaFold database (TmAlphaFold database), we apply TMDET, a simple geometry-based method to visualize the likeliest position of the membrane plane. In addition, we calculate several parameters to evaluate the location of the protein into the membrane. This also allows TmAlphaFold database to show whether the predicted 3D structure is realistic or not. The TmAlphaFold database is available at https://tmalphafold.ttk.hu/.},
	year = {2023},
	eissn = {1362-4962},
	pages = {D517-D522}
}

@article{MTMT:33121755,
	title = {Structural insights into the pSer/pThr dependent regulation of the SHP2 tyrosine phosphatase in insulin and CD28 signaling},
	url = {https://m2.mtmt.hu/api/publication/33121755},
	author = {Zeke, András and Takács, Tamás and Sok, Péter Dániel and Németh, Krisztina and Kirsch, Klára and Egri, Péter and Póti, Ádám Levente and Bento, Isabel and Tusnády, Gábor and Reményi, Attila},
	doi = {10.1038/s41467-022-32918-5},
	journal-iso = {NAT COMMUN},
	journal = {NATURE COMMUNICATIONS},
	volume = {13},
	unique-id = {33121755},
	issn = {2041-1723},
	abstract = {Serine/threonine phosphorylation of insulin receptor substrate (IRS) proteins is well known to modulate insulin signaling. However, the molecular details of this process have mostly been elusive. While exploring the role of phosphoserines, we have detected a direct link between Tyr-flanking Ser/Thr phosphorylation sites and regulation of specific phosphotyrosine phosphatases. Here we present a concise structural study on how the activity of SHP2 phosphatase is controlled by an asymmetric, dual phosphorylation of its substrates. The structure of SHP2 has been determined with three different substrate peptides, unveiling the versatile and highly dynamic nature of substrate recruitment. What is more, the relatively stable pre-catalytic state of SHP2 could potentially be useful for inhibitor design. Our findings not only show an unusual dependence of SHP2 catalytic activity on Ser/Thr phosphorylation sites in IRS1 and CD28, but also suggest a negative regulatory mechanism that may also apply to other tyrosine kinase pathways as well.},
	year = {2022},
	eissn = {2041-1723},
	orcid-numbers = {Sok, Péter Dániel/0000-0001-8963-8163; Németh, Krisztina/0000-0003-1360-7648; Kirsch, Klára/0000-0003-0484-4473; Reményi, Attila/0000-0002-8345-1311}
}

@article{MTMT:32009571,
	title = {Design, synthesis and biological evaluation of novel estrone phosphonates as high affinity organic anion-transporting polypeptide 2B1 (OATP2B1) inhibitors},
	url = {https://m2.mtmt.hu/api/publication/32009571},
	author = {Jójárt, Rebeka and Laczkó-Rigó, Réka and Klement, Máté and Kőhl, Gabriella and Kecskeméti, Gábor and Laczka, Csilla and Mernyák, Erzsébet},
	doi = {10.1016/j.bioorg.2021.104914},
	journal-iso = {BIOORG CHEM},
	journal = {BIOORGANIC CHEMISTRY},
	volume = {112},
	unique-id = {32009571},
	issn = {0045-2068},
	year = {2021},
	eissn = {1090-2120},
	orcid-numbers = {Kecskeméti, Gábor/0000-0002-5584-6869; Mernyák, Erzsébet/0000-0003-4494-1817}
}