@article{MTMT:32612583,
	title = {Ins and outs of AlphaFold2 transmembrane protein structure predictions},
	url = {https://m2.mtmt.hu/api/publication/32612583},
	author = {Hegedűs, Tamás and Geisler, Markus and Lukács, Gergely László and Farkas, Bianka Vivien},
	doi = {10.1007/s00018-021-04112-1},
	journal-iso = {CELL MOL LIFE SCI},
	journal = {CELLULAR AND MOLECULAR LIFE SCIENCES},
	volume = {79},
	unique-id = {32612583},
	issn = {1420-682X},
	year = {2022},
	eissn = {1420-9071},
	orcid-numbers = {Hegedűs, Tamás/0000-0002-0331-9629; Geisler, Markus/0000-0002-6641-5810; Lukács, Gergely László/0000-0003-0900-0675; Farkas, Bianka Vivien/0000-0002-0258-6864}
}

@article{MTMT:33293571,
	title = {The Reentry Helix Is Potentially Involved in Cholesterol Sensing of the ABCG1 Transporter Protein},
	url = {https://m2.mtmt.hu/api/publication/33293571},
	author = {Hegyi, Zoltán and Hegedűs, Tamás and Homolya, László},
	doi = {10.3390/ijms232213744},
	journal-iso = {INT J MOL SCI},
	journal = {INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES},
	volume = {23},
	unique-id = {33293571},
	issn = {1661-6596},
	year = {2022},
	eissn = {1422-0067},
	orcid-numbers = {Hegedűs, Tamás/0000-0002-0331-9629; Homolya, László/0000-0003-1639-8140}
}

@article{MTMT:32853643,
	title = {Nanomechanics combined with HDX reveals allosteric drug binding sites of CFTR NBD1},
	url = {https://m2.mtmt.hu/api/publication/32853643},
	author = {Padányi, Rita and Farkas, Bianka Vivien and Tordai, Hedvig and Kiss, Bálint and Grubmüller, Helmut and Soya, Naoto and Lukács, Gergely L. and Kellermayer, Miklós and Hegedűs, Tamás},
	doi = {10.1016/j.csbj.2022.05.036},
	journal-iso = {CSBJ},
	journal = {COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL},
	volume = {20},
	unique-id = {32853643},
	issn = {2001-0370},
	year = {2022},
	eissn = {2001-0370},
	pages = {2587-2599},
	orcid-numbers = {Padányi, Rita/0000-0001-7798-0463; Farkas, Bianka Vivien/0000-0002-0258-6864; Tordai, Hedvig/0000-0002-0875-5569; Kiss, Bálint/0000-0002-1595-0426; Kellermayer, Miklós/0000-0002-5553-6553; Hegedűs, Tamás/0000-0002-0331-9629}
}

@article{MTMT:33084278,
	title = {Comprehensive Collection and Prediction of ABC Transmembrane Protein Structures in the AI Era of Structural Biology},
	url = {https://m2.mtmt.hu/api/publication/33084278},
	author = {Tordai, Hedvig and Suhajda, Erzébet and Sillitoe, Ian and Nair, Sreenath and Varadi, Mihaly and Hegedűs, Tamás},
	doi = {10.3390/ijms23168877},
	journal-iso = {INT J MOL SCI},
	journal = {INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES},
	volume = {23},
	unique-id = {33084278},
	issn = {1661-6596},
	abstract = {The number of unique transmembrane (TM) protein structures doubled in the last four years, which can be attributed to the revolution of cryo-electron microscopy. In addition, AlphaFold2 (AF2) also provided a large number of predicted structures with high quality. However, if a specific protein family is the subject of a study, collecting the structures of the family members is highly challenging in spite of existing general and protein domain-specific databases. Here, we demonstrate this and assess the applicability and usability of automatic collection and presentation of protein structures via the ABC protein superfamily. Our pipeline identifies and classifies transmembrane ABC protein structures using the PFAM search and also aims to determine their conformational states based on special geometric measures, conftors. Since the AlphaFold database contains structure predictions only for single polypeptide chains, we performed AF2-Multimer predictions for human ABC half transporters functioning as dimers. Our AF2 predictions warn of possibly ambiguous interpretation of some biochemical data regarding interaction partners and call for further experiments and experimental structure determination. We made our predicted ABC protein structures available through a web application, and we joined the 3D-Beacons Network to reach the broader scientific community through platforms such as PDBe-KB.},
	keywords = {MECHANISM; CLASSIFICATION; MUTATIONS; CHANNEL; P-GLYCOPROTEIN; TRANSPORTERS; protein structure; inventory; ABC TRANSPORTERS; PROTEIN COMPLEX; Biochemistry & Molecular Biology; Structure database; AlphaFold2; AF-multimer},
	year = {2022},
	eissn = {1422-0067},
	orcid-numbers = {Tordai, Hedvig/0000-0002-0875-5569; Varadi, Mihaly/0000-0002-3687-0839; Hegedűs, Tamás/0000-0002-0331-9629}
}

@article{MTMT:33315002,
	title = {3D-Beacons: decreasing the gap between protein sequences and structures through a federated network of protein structure data resources},
	url = {https://m2.mtmt.hu/api/publication/33315002},
	author = {Varadi, M. and Nair, S. and Sillitoe, I. and Tauriello, G. and Anyango, S. and Bienert, S. and Borges, C. and Deshpande, M. and Green, T. and Hassabis, D. and Hatos, András and Hegedűs, Tamás and Hekkelman, M.L. and Joosten, R. and Jumper, J. and Laydon, A. and Molodenskiy, D. and Piovesan, D. and Salladini, E. and Salzberg, S.L. and Sommer, M.J. and Steinegger, M. and Suhajda, E. and Svergun, D. and Tenorio-Ku, L. and Tosatto, S. and Tunyasuvunakool, K. and Waterhouse, A.M. and Žídek, A. and Schwede, T. and Orengo, C. and Velankar, S.},
	doi = {10.1093/gigascience/giac118},
	journal-iso = {GIGASCIENCE},
	journal = {GIGASCIENCE},
	volume = {11},
	unique-id = {33315002},
	issn = {2047-217X},
	year = {2022},
	eissn = {2047-217X},
	orcid-numbers = {Hatos, András/0000-0001-9224-9820; Hegedűs, Tamás/0000-0002-0331-9629}
}

@article{MTMT:31821613,
	title = {The mechanism of non-blocking inhibition of sodium channels revealed by conformation-selective photolabeling},
	url = {https://m2.mtmt.hu/api/publication/31821613},
	author = {Földi, Mátyás Csaba and Pesti, Krisztina and Zboray, Katalin and Tóth, Ádám Viktor and Hegedűs, Tamás and Málnási Csizmadia, András and Lukács, Péter and Mike, Árpád},
	doi = {10.1111/bph.15365},
	journal-iso = {BR J PHARMACOL},
	journal = {BRITISH JOURNAL OF PHARMACOLOGY},
	volume = {178},
	unique-id = {31821613},
	issn = {0007-1188},
	abstract = {Sodium channel inhibitors can be used to treat hyperexcitability-related diseases, including epilepsies, pain syndromes, neuromuscular disorders, and cardiac arrhythmias. The applicability of these drugs is limited by their nonspecific effect on physiological function. They act mainly by sodium channel block and in addition by modulation of channel kinetics. While channel block inhibits healthy and pathological tissue equally, modulation can preferentially inhibit pathological activity. An ideal drug designed to target the sodium channels of pathological tissue would act predominantly by modulation. Thus far, no such drug has been described.Patch-clamp experiments with ultra-fast solution exchange and photolabeling-coupled electrophysiology were applied to describe the unique mechanism of riluzole on Nav1.4 sodium channels. In silico docking experiments were used to study the molecular details of binding.We present evidence that riluzole acts predominantly by non-blocking modulation. We propose that, being a relatively small molecule, riluzole is able to stay bound to the binding site, but nonetheless stay off the conduction pathway, by residing in one of the fenestrations. We demonstrate how this mechanism can be recognized.Our results identify riluzole as the prototype of this new class of sodium channel inhibitors. Drugs of this class are expected to selectively prevent hyperexcitability, while having minimal effect on cells firing at a normal rate from a normal resting potential.},
	keywords = {EPILEPSY; PAIN; BINDING SITES; Sodium Channels; ARRHYTHMIAS; riluzole; local anesthetics},
	year = {2021},
	eissn = {1476-5381},
	pages = {1200-1217},
	orcid-numbers = {Hegedűs, Tamás/0000-0002-0331-9629; Málnási Csizmadia, András/0000-0002-2430-8398; Mike, Árpád/0000-0002-9095-8161}
}

@article{MTMT:31623716,
	title = {The transport pathway in the ABCG2 protein and its regulation revealed by molecular dynamics simulations},
	url = {https://m2.mtmt.hu/api/publication/31623716},
	author = {Nagy, Tamás and Tóth, Á. and Telbisz, Ágnes Mária and Sarkadi, Balázs and Tordai, Hedvig and Tordai, Attila and Hegedűs, Tamás},
	doi = {10.1007/s00018-020-03651-3},
	journal-iso = {CELL MOL LIFE SCI},
	journal = {CELLULAR AND MOLECULAR LIFE SCIENCES},
	volume = {78},
	unique-id = {31623716},
	issn = {1420-682X},
	abstract = {Atomic-level structural insight on the human ABCG2 membrane protein, a pharmacologically important transporter, has been recently revealed by several key papers. In spite of the wealth of structural data, the pathway of transmembrane movement for the large variety of structurally different ABCG2 substrates and the physiological lipid regulation of the transporter has not been elucidated. The complex molecular dynamics simulations presented here may provide a breakthrough in understanding the steps of the substrate transport process and its regulation by cholesterol. Our analysis revealed drug binding cavities other than the central binding site and delineated a putative dynamic transport pathway for substrates with variable structures. We found that membrane cholesterol accelerated drug transport by promoting the closure of cytoplasmic protein regions. Since ABCG2 is present in all major biological barriers and drug-metabolizing organs, influences the pharmacokinetics of numerous clinically applied drugs, and plays a key role in uric acid extrusion, this information may significantly promote a reliable prediction of clinically important substrate characteristics and drug-drug interactions. © 2020, The Author(s).},
	keywords = {ABCG2; molecular dynamics; cholesterol regulation; Multidrug transport},
	year = {2021},
	eissn = {1420-9071},
	pages = {2329-2339},
	orcid-numbers = {Nagy, Tamás/0000-0002-0137-4341; Telbisz, Ágnes Mária/0000-0003-0972-4606; Sarkadi, Balázs/0000-0003-0592-4539; Tordai, Hedvig/0000-0002-0875-5569; Tordai, Attila/0000-0001-6966-1622; Hegedűs, Tamás/0000-0002-0331-9629}
}

@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:31641470,
	title = {The MemMoRF database for recognizing disordered protein regions interacting with cellular membranes},
	url = {https://m2.mtmt.hu/api/publication/31641470},
	author = {Gáspárné Csizmadia, Georgina and Erdős, Gábor and Tordai, Hedvig and Padányi, Rita and Tosatto, Silvio and Dosztányi, Zsuzsanna and Hegedűs, Tamás},
	doi = {10.1093/nar/gkaa954},
	journal-iso = {NUCLEIC ACIDS RES},
	journal = {NUCLEIC ACIDS RESEARCH},
	volume = {49},
	unique-id = {31641470},
	issn = {0305-1048},
	year = {2020},
	eissn = {1362-4962},
	pages = {D355-D360},
	orcid-numbers = {Gáspárné Csizmadia, Georgina/0000-0003-4321-9670; Tordai, Hedvig/0000-0002-0875-5569; Padányi, Rita/0000-0001-7798-0463; Dosztányi, Zsuzsanna/0000-0002-3624-5937; 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}
}