@article{MTMT:34724664,
	title = {PtdIns4p is required for the autophagosomal recruitment of STX17 (syntaxin 17) to promote lysosomal fusion},
	url = {https://m2.mtmt.hu/api/publication/34724664},
	author = {Laczkó-Dobos, Hajnalka and Bhattacharjee, Arindam and Maddali, Asha Kiran and Kincses, András and Abuammar, Hussein and Sebőkné Nagy, Krisztina and Páli, Tibor and Dér, András and Hegedűs, Tamás and Csordás, Gábor and Juhász, Gábor},
	doi = {10.1080/15548627.2024.2322493},
	journal-iso = {AUTOPHAGY},
	journal = {AUTOPHAGY},
	volume = {AiP},
	unique-id = {34724664},
	issn = {1554-8627},
	year = {2024},
	eissn = {1554-8635},
	orcid-numbers = {Páli, Tibor/0000-0003-1649-1097; Hegedűs, Tamás/0000-0002-0331-9629; Csordás, Gábor/0000-0001-6871-6839; Juhász, Gábor/0000-0001-8548-8874}
}

@article{MTMT:33731782,
	title = {Plasma membrane Ca2+ pump isoform 4 function in cell migration and cancer metastasis},
	url = {https://m2.mtmt.hu/api/publication/33731782},
	author = {Naffa, R. and Hegedűs, L. and Hegedűs, Tamás and Tóth, Sarolta and Papp, B. and Tordai, Attila and Enyedi, Ágnes},
	doi = {10.1113/JP284179},
	journal-iso = {J PHYSIOL-LONDON},
	journal = {JOURNAL OF PHYSIOLOGY-LONDON},
	unique-id = {33731782},
	issn = {0022-3751},
	year = {2024},
	eissn = {1469-7793},
	orcid-numbers = {Hegedűs, Tamás/0000-0002-0331-9629; Tóth, Sarolta/0000-0002-0341-7675; Tordai, Attila/0000-0001-6966-1622; Enyedi, Ágnes/0000-0002-7366-9376}
}

@article{MTMT:34163279,
	title = {CoMemMoRFPred: Sequence-based Prediction of MemMoRFs by Combining Predictors of Intrinsic Disorder, MoRFs and Disordered Lipid-binding Regions},
	url = {https://m2.mtmt.hu/api/publication/34163279},
	author = {Basu, S. and Hegedűs, Tamás and Kurgan, L.},
	doi = {10.1016/j.jmb.2023.168272},
	journal-iso = {J MOL BIOL},
	journal = {JOURNAL OF MOLECULAR BIOLOGY},
	volume = {435},
	unique-id = {34163279},
	issn = {0022-2836},
	year = {2023},
	eissn = {1089-8638},
	orcid-numbers = {Hegedűs, Tamás/0000-0002-0331-9629}
}

@article{MTMT:34175360,
	title = {Expression, Function and Trafficking of the Human ABCG2 Multidrug Transporter Containing Mutations in an Unstructured Cytoplasmic Loop},
	url = {https://m2.mtmt.hu/api/publication/34175360},
	author = {Mózner, Orsolya and Zámbó, Boglárka and Bartos, Zsuzsa and Gergely, Anna and Szabó, Kata Sára and Jezsó, Bálint and Telbisz, Ágnes Mária and Várady, György and Homolya, László and Hegedűs, Tamás and Sarkadi, Balázs},
	doi = {10.3390/membranes13100822},
	journal-iso = {MEMBRANES-BASEL},
	journal = {MEMBRANES (BASEL)},
	volume = {13},
	unique-id = {34175360},
	abstract = {The human ABCG2 multidrug transporter plays a crucial role in the absorption and excretion of xeno- and endobiotics, contributes to cancer drug resistance and the development of gout. In this work, we have analyzed the effects of selected variants, residing in a structurally unresolved cytoplasmic region (a.a. 354–367) of ABCG2 on the function and trafficking of this protein. A cluster of four lysines (K357–360) and the phosphorylation of a threonine (T362) residue in this region have been previously suggested to significantly affect the cellular fate of ABCG2. Here, we report that the naturally occurring K360del variant in human cells increased ABCG2 plasma membrane expression and accelerated cellular trafficking. The variable alanine replacements of the neighboring lysines had no significant effect on transport function, and the apical localization of ABCG2 in polarized cells has not been altered by any of these mutations. Moreover, in contrast to previous reports, we found that the phosphorylation-incompetent T362A, or the phosphorylation-mimicking T362E variants in this loop had no measurable effects on the function or expression of ABCG2. Molecular dynamics simulations indicated an increased mobility of the mutant variants with no major effects on the core structure of the protein. These results may help to decipher the potential role of this unstructured region within this transporter.},
	year = {2023},
	eissn = {2077-0375},
	orcid-numbers = {Mózner, Orsolya/0000-0001-5784-7702; Bartos, Zsuzsa/0000-0001-9695-1422; Jezsó, Bálint/0000-0002-1306-4797; Telbisz, Ágnes Mária/0000-0003-0972-4606; Várady, György/0000-0003-2012-9680; Homolya, László/0000-0003-1639-8140; Hegedűs, Tamás/0000-0002-0331-9629; Sarkadi, Balázs/0000-0003-0592-4539}
}

@article{MTMT:34077112,
	title = {Synergistic Inhibitory Effect of Quercetin and Cyanidin-3O-Sophoroside on ABCB1},
	url = {https://m2.mtmt.hu/api/publication/34077112},
	author = {Singh, Kuljeet and Patil, Rajesh B. and Patel, Vikas and Gálné Remenyik, Judit and Hegedűs, Tamás and Kormosné, Goda Katalin},
	doi = {10.3390/ijms241411341},
	journal-iso = {INT J MOL SCI},
	journal = {INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES},
	volume = {24},
	unique-id = {34077112},
	issn = {1661-6596},
	abstract = {The human ABCB1 (P-glycoprotein, Pgp) protein is an active exporter expressed in the plasma membrane of cells forming biological barriers. In accordance with its broad substrate spectrum and tissue expression pattern, it affects the pharmacokinetics of numerous chemotherapeutic drugs and it is involved in unwanted drug–drug interactions leading to side effects or toxicities. When expressed in tumor tissues, it contributes to the development of chemotherapy resistance in malignancies. Therefore, the understanding of the molecular details of the ligand–ABCB1 interactions is of crucial importance. In a previous study, we found that quercetin (QUR) hampers both the transport and ATPase activity of ABCB1, while cyandin-3O-sophroside (C3S) stimulates the ATPase activity and causes only a weak inhibition of substrate transport. In the current study, when QUR and C3S were applied together, both a stronger ATPase inhibition and a robust decrease in substrate transport were observed, supporting their synergistic ABCB1 inhibitory effect. Similar to cyclosporine A, a potent ABCB1 inhibitor, co-treatment with QUR and C3S shifted the conformational equilibrium to the “inward-facing” conformer of ABCB1, as it was detected by the conformation-selective UIC2 mAb. To gain deeper insight into the molecular details of ligand–ABCB1 interactions, molecular docking experiments and MD simulations were also carried out. Our in silico studies support that QUR and C3S can bind simultaneously to ABCB1. The most favourable ligand–ABCB1 interaction is obtained when C3S binds to the central substrate binding site and QUR occupies the “access tunnel”. Our results also highlight that the strong ABCB1 inhibitory effect of the combined treatment with QUR and C3S may be exploited in chemotherapy protocols for the treatment of multidrug-resistant tumors or for improving drug delivery through pharmacological barriers.},
	year = {2023},
	eissn = {1422-0067},
	orcid-numbers = {Singh, Kuljeet/0000-0002-1811-6963; Patil, Rajesh B./0000-0003-2986-9546; Hegedűs, Tamás/0000-0002-0331-9629; Kormosné, Goda Katalin/0000-0003-2001-7400}
}

@article{MTMT:34257929,
	title = {Folding correctors can restore CFTR posttranslational folding landscape by allosteric domain–domain coupling},
	url = {https://m2.mtmt.hu/api/publication/34257929},
	author = {Soya, N. and Xu, H. and Roldan, A. and Yang, Z. and Ye, H. and Jiang, F. and Premchandar, A. and Veit, G. and Cole, S.P.C. and Kappes, J. and Hegedűs, Tamás and Lukacs, G.L.},
	doi = {10.1038/s41467-023-42586-8},
	journal-iso = {NAT COMMUN},
	journal = {NATURE COMMUNICATIONS},
	volume = {14},
	unique-id = {34257929},
	issn = {2041-1723},
	year = {2023},
	eissn = {2041-1723},
	orcid-numbers = {Hegedűs, Tamás/0000-0002-0331-9629}
}

@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},
	abstract = {Cystic fibrosis (CF) is a frequent genetic disease in Caucasians that is caused by the deletion of F508 (DF508) in the nucleotide binding domain 1 (NBD1) of the CF transmembrane conductance regulator (CFTR). The DF508 compromises the folding energetics of the NBD1, as well as the folding of three other CFTR domains. Combination of FDA approved corrector molecules can efficiently but incompletely rescue the DF508-CFTR folding and stability defect. Thus, new pharmacophores that would reinstate the wildtype-like conformational stability of the DF508-NBD1 would be highly beneficial. The most prominent molecule, 5-bromoindole-3-acetic acid (BIA) that can thermally stabilize the NBD1 has low potency and efficacy. To gain insights into the NBD1 (un)folding dynamics and BIA binding site localization, we combined molecular dynamics (MD) simulations, atomic force spectroscopy (AFM) and hydrogendeuterium exchange (HDX) experiments. We found that the NBD1 a-subdomain with three adjacent strands from the b-subdomain plays an important role in early folding steps, when crucial non-native interactions are formed via residue F508. Our AFM and HDX experiments showed that BIA associates with this a-core region and increases the resistance of the DF508-NBD1 against mechanical unfolding, a phenomenon that could be exploited in future developments of folding correctors. (c) 2022 The Authors. Published by Elsevier B.V. on behalf of Research Network of Computational and Structural Biotechnology. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).},
	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}
}