@article{MTMT:31177534,
	title = {Using MemBlob to Analyze Transmembrane Regions Based on Cryo-EM Maps},
	url = {https://m2.mtmt.hu/api/publication/31177534},
	author = {Gáspárné Csizmadia, Georgina and Farkas, Bianka Vivien and Katona, E. and Tusnády, Gábor and Hegedűs, Tamás},
	doi = {10.1007/978-1-0716-0270-6_9},
	journal-iso = {METHODS MOL BIOL},
	journal = {METHODS IN MOLECULAR BIOLOGY},
	volume = {2112},
	unique-id = {31177534},
	issn = {1064-3745},
	abstract = {Transmembrane proteins include membrane channels, pores, and receptors and, as such, comprise an important part of the proteome, yet our knowledge about them is much less complete than about soluble, globular proteins. An important aspect of transmembrane protein structure is their exact position within the lipid bilayer, a feature hard to investigate experimentally at the atomic level. Here we describe MemBlob, a novel approach utilizing difference electron density maps obtained by cryo-EM studies of transmembrane proteins. The idea behind is that the nonprotein part of such maps carries information on the exact localization of the membrane mimetics used in the experiment and can be used to extract the positional information of the protein within the membrane. MemBlob uses a structural model of the protein and an experimental electron density map to provide an estimation of the surface residues interacting with the membrane.},
	keywords = {transmembrane region; Cryo-EM map; Lipid interface},
	year = {2020},
	eissn = {1940-6029},
	pages = {123-130},
	orcid-numbers = {Gáspárné Csizmadia, Georgina/0000-0003-4321-9670; Farkas, Bianka Vivien/0000-0002-0258-6864; Hegedűs, Tamás/0000-0002-0331-9629}
}

@article{MTMT:30745372,
	title = {MemBlob database and server for identifying transmembrane regions using cryo-EM maps},
	url = {https://m2.mtmt.hu/api/publication/30745372},
	author = {Farkas, Bianka Vivien and Gáspárné Csizmadia, Georgina and Katona, Eszter and Tusnády, Gábor and Hegedűs, Tamás},
	doi = {10.1093/bioinformatics/btz539},
	journal-iso = {BIOINFORMATICS},
	journal = {BIOINFORMATICS},
	volume = {36},
	unique-id = {30745372},
	issn = {1367-4803},
	abstract = {The identification of transmembrane helices in transmembrane proteins is crucial, not only to understand their mechanism of action, but also to develop new therapies. While experimental data on the boundaries of membrane-embedded regions is sparse, this information is present in cryo-electron microscopy (cryo-EM) density maps and it has not been utilized yet for determining membrane regions. We developed a computational pipeline, where the inputs of a cryo-EM map, the corresponding atomistic structure, and the potential bilayer orientation determined by TMDET algorithm of a given protein result in an output defining the residues assigned to the bulk water phase, lipid interface, and the lipid hydrophobic core. Based on this method, we built a database involving published cryo-EM protein structures and a server to be able to compute this data for newly obtained structures.http://memblob.hegelab.org.Supplementary data are available at Bioinformatics online.},
	year = {2020},
	eissn = {1460-2059},
	pages = {2595-2598},
	orcid-numbers = {Farkas, Bianka Vivien/0000-0002-0258-6864; Gáspárné Csizmadia, Georgina/0000-0003-4321-9670; Hegedűs, Tamás/0000-0002-0331-9629}
}

@article{MTMT:30745347,
	title = {Discovering the chloride pathway in the CFTR channel},
	url = {https://m2.mtmt.hu/api/publication/30745347},
	author = {Farkas, Bianka Vivien and Tordai, Hedvig and Padányi, Rita and Tordai, Attila and Gera, János and Paragi, Gábor and Hegedűs, Tamás},
	doi = {10.1007/s00018-019-03211-4},
	journal-iso = {CELL MOL LIFE SCI},
	journal = {CELLULAR AND MOLECULAR LIFE SCIENCES},
	volume = {77},
	unique-id = {30745347},
	issn = {1420-682X},
	year = {2020},
	eissn = {1420-9071},
	pages = {765-778},
	orcid-numbers = {Farkas, Bianka Vivien/0000-0002-0258-6864; Tordai, Hedvig/0000-0002-0875-5569; Padányi, Rita/0000-0001-7798-0463; Tordai, Attila/0000-0001-6966-1622; Paragi, Gábor/0000-0001-5408-1748; Hegedűs, Tamás/0000-0002-0331-9629}
}

@article{MTMT:30924895,
	title = {Cellular Processing of the ABCG2 Transporter-Potential Effects on Gout and Drug Metabolism.},
	url = {https://m2.mtmt.hu/api/publication/30924895},
	author = {Mózner, Orsolya and Bartos, Zsuzsa and Zámbó, Boglárka and Homolya, László and Hegedűs, Tamás and Sarkadi, Balázs},
	doi = {10.3390/cells8101215},
	journal-iso = {CELLS-BASEL},
	journal = {CELLS},
	volume = {8},
	unique-id = {30924895},
	abstract = {The human ABCG2 is an important plasma membrane multidrug transporter, involved in uric acid secretion, modulation of absorption of drugs, and in drug resistance of cancer cells. Variants of the ABCG2 transporter, affecting cellular processing and trafficking, have been shown to cause gout and increased drug toxicity. In this paper, we overview the key cellular pathways involved in the processing and trafficking of large membrane proteins, focusing on ABC transporters. We discuss the information available for disease-causing polymorphic variants and selected mutations of ABCG2, causing increased degradation and impaired travelling of the transporter to the plasma membrane. In addition, we provide a detailed in silico analysis of an as yet unrecognized loop region of the ABCG2 protein, in which a recently discovered mutation may actually promote ABCG2 membrane expression. We suggest that post-translational modifications in this unstructured loop at the cytoplasmic surface of the protein may have special influence on ABCG2 processing and trafficking.},
	keywords = {drug metabolism; gout; ABC TRANSPORTERS; ABCG2 multidrug transporter; ABCG2 trafficking},
	year = {2019},
	eissn = {2073-4409},
	orcid-numbers = {Mózner, Orsolya/0000-0001-5784-7702; Bartos, Zsuzsa/0000-0001-9695-1422; Homolya, László/0000-0003-1639-8140; Hegedűs, Tamás/0000-0002-0331-9629; Sarkadi, Balázs/0000-0003-0592-4539}
}

@CONFERENCE{MTMT:30733928,
	title = {Defining Membrane Boundaries of Proteins Using Electron Density Maps: The MemBlob Database and Server},
	url = {https://m2.mtmt.hu/api/publication/30733928},
	author = {Gáspárné Csizmadia, Georgina and Farkas, Bianka and Katona, Eszter and Tusnády, Gábor E. and Hegedűs, Tamás},
	booktitle = {Mechanisms of Membrane Transport Gordon Research Conference},
	unique-id = {30733928},
	year = {2019},
	pages = {5},
	orcid-numbers = {Gáspárné Csizmadia, Georgina/0000-0003-4321-9670}
}

@CONFERENCE{MTMT:30681403,
	title = {USING CRYO-EM MAPS TO DETERMINE PROTEIN TRANSMEMBRANE REGIONS},
	url = {https://m2.mtmt.hu/api/publication/30681403},
	author = {Gáspárné Csizmadia, Georgina and Farkas, Bianka and Katona, Eszter and Tusnády, Gábor E. and Hegedűs, Tamás},
	booktitle = {PhD Tudományos Napok 2019. Előadáskivonatok},
	unique-id = {30681403},
	year = {2019},
	pages = {1},
	orcid-numbers = {Gáspárné Csizmadia, Georgina/0000-0003-4321-9670}
}

@misc{MTMT:30452624,
	title = {Ceramic core@shell nanospheres as vaccine carriers},
	url = {https://m2.mtmt.hu/api/publication/30452624},
	author = {Nagyné Naszályi, Lívia and Rein, Verbeke and Heleen, Dewitte and Fehér, Krisztina and Stefaan, De Smedt and José, Martins},
	unique-id = {30452624},
	abstract = {The need for new vaccines is evident, but avoiding side effects is crucial for patient compliance. To achieve this, new generation vaccines are being developed. They combine an antigen as a target with the inclusion of an immunostimulant to ensure the induction of immunity, rather than tolerance. 
		Nanoparticles (NPs) are also used as vaccine-delivery systems. With appropriate size and well-chosen injection they are prone to accumulate in immune cells. However, their successful integration into nanovaccines requires thorough analysis of the inorganic/organic interface. 
		I aimed at the elaboration of new vaccine carrier nanosystems, characterized them first by routinely used analytical methods and then by the recently developed solution state NMR spectroscopy toolbox developed at Ghent University [1].
		The synthesis of silica@zirconia core@shell nanoparticles was based on Stöber et al. and Kim and coworkers’ method [2, 3]. I decorated the surface of these ceramic NPs with model biomolecules and immune stimulators. The physico-chemical characterization of the particles was carried out using transmission electron microscopy, dynamic light scattering, zeta potential measurements, UV-visible and Fourier-transform infrared spectroscopies. The surface ligand structure was studied by NMR toolbox. Preliminary experiments on biological fate of the as-prepared NPs were carried out (blood stability tests, cell viability assays etc).},
	year = {2018},
	orcid-numbers = {Nagyné Naszályi, Lívia/0000-0003-2799-1150}
}

@article{MTMT:30421872,
	title = {Irány a kolloid motor. A kolloidika tudományának egy lehetséges mérnöki alkalmazása},
	url = {https://m2.mtmt.hu/api/publication/30421872},
	author = {Zrínyi, Miklós and Nakano, Masami},
	doi = {10.24100/MKF.2018.04.183},
	journal-iso = {MAGY KÉM FOLY KÉM KÖZL},
	journal = {MAGYAR KÉMIAI FOLYÓIRAT - KÉMIAI KÖZLEMÉNYEK (1997-)},
	volume = {124},
	unique-id = {30421872},
	issn = {1418-9933},
	year = {2018},
	eissn = {1418-8600},
	pages = {183-188},
	orcid-numbers = {Zrínyi, Miklós/0000-0002-9362-3199}
}

@article{MTMT:30336891,
	title = {Quantitative comparison of ABC membrane protein type I exporter structures in a standardized way},
	url = {https://m2.mtmt.hu/api/publication/30336891},
	author = {Gáspárné Csizmadia, Georgina and Farkas, Bianka Vivien and Spagina, Zoltán and Tordai, Hedvig and Hegedűs, Tamás},
	doi = {10.1016/j.csbj.2018.10.008},
	journal-iso = {CSBJ},
	journal = {COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL},
	volume = {16},
	unique-id = {30336891},
	issn = {2001-0370},
	abstract = {An increasing number of ABC membrane protein structures are determined by cryo-electron microscopy and X-ray crystallography, consequently identifying differences between their conformations has become an arising issue. Therefore, we propose to define standardized measures for ABC Type I exporter structure characterization. We set conformational vectors, conftors, which describe the relative orientation of domains and can highlight structural differences. In addition, continuum electrostatics calculations were performed to characterize the energetics of membrane insertion illuminating functionally crucial regions. In summary, the proposed metrics contribute to deeper understanding of ABC membrane proteins' structural features, structure validation, and analysis of movements observed in a molecular dynamics trajectory. Moreover, the concept of standardized metrics can be applied not only to ABC membrane protein structures (http://conftors.hegelab.org).},
	keywords = {Membrane Proteins; STRUCTURE VALIDATION; structure comparison; ABC proteins; ABC, ATP binding cassette; CFTR, cystic fibrosis transmembrane conductance regulator; CG, coarse grained; CH, coupling helix; COG, center of geometry; ICD, intracellular domain; NBD, nucleotide binding domain; Quantitative structural properties; TH, transmembrane helix; TM, transmembrane; TMD, transmembrane domain},
	year = {2018},
	eissn = {2001-0370},
	pages = {396-403},
	orcid-numbers = {Gáspárné Csizmadia, Georgina/0000-0003-4321-9670; Farkas, Bianka Vivien/0000-0002-0258-6864; Tordai, Hedvig/0000-0002-0875-5569; Hegedűs, Tamás/0000-0002-0331-9629}
}

@{MTMT:30610087,
	title = {ABC fehérjék 3D atlasza},
	url = {https://m2.mtmt.hu/api/publication/30610087},
	author = {Gáspárné Csizmadia, Georgina and Tordai, Hedvig and Spagina, Zoltán and Hegedűs, Tamás},
	booktitle = {A Magyar Biofizikai Társaság XXVI. Kongresszusa},
	unique-id = {30610087},
	year = {2017},
	pages = {65},
	orcid-numbers = {Gáspárné Csizmadia, Georgina/0000-0003-4321-9670; Tordai, Hedvig/0000-0002-0875-5569; Hegedűs, Tamás/0000-0002-0331-9629}
}