TY - JOUR AU - Németh, Zoltán Bálint AU - Kiss, Bence AU - Sahin-Tóth, Miklós AU - Magyar, Csaba AU - Pál, Gábor TI - The High-Affinity Chymotrypsin Inhibitor Eglin C Poorly Inhibits Human Chymotrypsin-Like Protease: Gln192 and Lys218 Are Key Determinants JF - PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS J2 - PROTEINS VL - 93 PY - 2025 IS - 2 SP - 543 EP - 554 PG - 12 SN - 0887-3585 DO - 10.1002/prot.26750 UR - https://m2.mtmt.hu/api/publication/35438535 ID - 35438535 N1 - Department of Biochemistry, ELTE Eötvös Loránd University, Budapest, Hungary Institute of Molecular Life Sciences, Protein Bioinformatics Research Group, Hungarian Research Network, Budapest, Hungary Department of Surgery, University of California Los Angeles, Los Angeles, CA, United States Export Date: 07 October 2024; Cited By: 0; Correspondence Address: G. Pál; Department of Biochemistry, ELTE Eötvös Loránd University, Budapest, Hungary; email: gabor.pal@ttk.elte.hu; C. Magyar; Institute of Molecular Life Sciences, Protein Bioinformatics Research Group, Hungarian Research Network, Budapest, Hungary; email: magyar.csaba@ttk.hu AB - Eglin C, a small protein from the medicinal leech, has been long considered a general high-affinity inhibitor of chymotrypsins and elastases. Here, we demonstrate that eglin C inhibits human chymotrypsin-like protease (CTRL) weaker by several orders of magnitude than other chymotrypsins. In order to identify the underlying structural aspects of this unique deviation, we performed comparative molecular dynamics simulations on experimental and AlphaFold model structures of bovine CTRA and human CTRL. Our results indicate that in CTRL, the primary determinants of the observed weak inhibition are amino-acid positions 192 and 218 (using conventional chymotrypsin numbering), which participate in shaping the S1 substrate-binding pocket and thereby affect the stability of the protease-inhibitor complexes. © 2024 The Author(s). PROTEINS: Structure, Function, and Bioinformatics published by Wiley Periodicals LLC. LA - English DB - MTMT ER - TY - JOUR AU - Fichó, Erzsébet AU - Pancsa, Rita AU - Magyar, Csaba AU - Kálmán, Zsófia Etelka AU - Schád, Éva AU - Németh, Zoltán Bálint AU - Simon, István AU - Dobson, László AU - Tusnády, Gábor TI - MFIB 2.0: a major update of the database of protein complexes formed by mutual folding of the constituting protein chains JF - NUCLEIC ACIDS RESEARCH J2 - NUCLEIC ACIDS RES VL - 53 PY - 2025 IS - D1 SP - D487 EP - D494 PG - 8 SN - 0305-1048 DO - 10.1093/nar/gkae976 UR - https://m2.mtmt.hu/api/publication/35599157 ID - 35599157 AB - While the majority of proteins with available structures are able to fold independently and mediate interactions only after acquiring their folded state, a subset of the known protein complexes contains protein chains that are intrinsically disordered in isolation. The Mutual Folding Induced by Binding (MFIB) database collects and classifies protein complexes, wherein all constituent protein chains would be unstable / disordered in isolation but fold into a well-defined 3D complex structure upon binding. This phenomenon is often termed as cooperative folding and binding or mutual synergistic folding (MSF). Here we present a major update to the database: we collected and annotated hundreds of new protein complexes fulfilling the criteria of MSF, leading to an almost six-fold increase in the size of the database. Many novel features have also been introduced, such as clustering of the complexes based on structural similarity and domain types, assigning different evidence levels to each entry and adding the evidence coverage label that allowed us to include complexes of multi(sub)domain monomers with partial MSF. LA - English DB - MTMT ER - TY - JOUR AU - Köller, Zsombor AU - Németh, Zoltán Bálint AU - Kiss, Bence AU - Nagy, Zoltán Attila AU - Schlosser, Gitta AU - Magyar, Csaba AU - Demcsák, Alexandra AU - Sahin‐Tóth, Miklós AU - Pál, Gábor TI - To be, or not to be cleaved: Directed evolution of a canonical serine protease inhibitor against active and inactive protease pair identifies binding loop residue critical for prevention of proteolytic cleavage JF - PROTEIN SCIENCE J2 - PROTEIN SCI VL - 34 PY - 2025 IS - 5 PG - 22 SN - 0961-8368 DO - 10.1002/pro.70146 UR - https://m2.mtmt.hu/api/publication/36114086 ID - 36114086 N1 - Department of Biochemistry, ELTE Eötvös Loránd University, Budapest, Hungary Institute of Molecular Life Sciences, Systems Biology of Reproduction Research Group, Hungarian Research Network, Budapest, Hungary Department of Surgery, University of California Los Angeles, Los Angeles, CA, United States Department of Analytical Chemistry, MTA-ELTE Lendület Ion Mobility Mass Spectrometry Research Group, Institute of Chemistry, ELTE Eötvös Loránd University, Budapest, Hungary Institute of Molecular Life Sciences, Protein Bioinformatics Research Group, Hungarian Research Network, Budapest, Hungary Export Date: 13 May 2025; Cited By: 0; Correspondence Address: G. Pál; Department of Biochemistry, Eötvös Loránd University, Budapest, Pázmány Péter sétány 1/C, H-1117, Hungary; email: gabor.pal@ttk.elte.hu; CODEN: PRCIE AB - Canonical serine protease inhibitor proteins occupy the substrate‐binding groove of their target enzyme via a surface loop. Unlike true substrates, inhibitors are cleaved by the target protease extremely slowly. Here, we applied an unbiased directed evolution approach to investigate which loop residues hamper proteolytic cleavage while maintaining high‐affinity binding. As a protease inhibitor model system, we used human chymotrypsin C (CTRC) and Schistocerca gregaria protease inhibitor 2 (SGPI‐2). We created an SGPI‐2 library displayed on M13 phage by randomizing the binding loop amino acid positions, with the exception of the structurally indispensable Cys residues. We selected binding phage clones against active CTRC and the inactive mutant Ser195Ala. All CTRC‐selected binders inhibited CTRC activity and also bound to the inactive Ser195Ala mutant, but the Ser195Ala‐selected clones proved to be either inhibitors or substrates of active CTRC. Substrate‐like behavior of SGPI‐2 variants was associated with the absence of the P2 Thr, the residue next to the specificity determinant P1 amino acid. The selected SGPI‐2 variants containing a P2 Thr bound strongly to CTRC even if the other loop residues deviated from the optimal inhibitory consensus sequence. In the absence of a P2 Thr, however, SGPI‐2 variants became substrates unless all other loop residues were optimal for binding. Structural modeling confirmed that P2 Thr is important for organizing a stabilizing H‐bond network. The observations indicate that binding loops of canonical serine protease inhibitors evolved amino acids not only to support tight binding to the target enzyme but also to inhibit proteolytic cleavage. LA - English DB - MTMT ER - TY - JOUR AU - Füredi, András AU - Tóth, Szilárd AU - Hegedüs, Kristóf AU - Szabó, Pál Tamás AU - Gaál, Anikó AU - Barta, Gergő AU - Nagyné Naszályi, Lívia AU - Kiss, Krisztina AU - Bölcskei, Kata AU - Szeltner, Zoltán AU - Bajtai, Eszter AU - Gombos, Balázs AU - Kiss, Dániel AU - Cserepes, Tamás Mihály AU - Kiss, Attila AU - Pokreisz, Peter AU - Kenner, Lukas AU - Högler, Sandra AU - Magyar, Csaba AU - Cowles, Jamie D. AU - Csiszar, Agnes AU - Tóvári, József AU - Szüts, Dávid AU - Helyes, Zsuzsanna AU - Varga, Zoltán AU - Mező, Gábor AU - Szakács, Gergely TI - Safe delivery of a highly toxic anthracycline derivative through liposomal nanoformulation achieves complete cancer regression JF - MOLECULAR CANCER J2 - MOL CANCER VL - 24 PY - 2025 IS - 1 PG - 18 SN - 1476-4598 DO - 10.1186/s12943-025-02444-1 UR - https://m2.mtmt.hu/api/publication/36405317 ID - 36405317 AB - Background: Chemotherapy remains the cornerstone of cancer treatment despite its well-documented challenges, including toxic side effects and drug resistance. Here, we demonstrate that a novel, highly toxic, daunosamine-modified derivative of daunorubicin (2-pyrrolino-daunorubicin, PyDau) can be safely administered to mice when encapsulated in liposome. Methods: PyDau was synthesized from daunorubicin in a one-step reaction. Its increased in vitro cytotoxicity was confirmed across 42 human cell lines representing 12 cancer types, including multidrug resistant cells. The activity profile of this new derivative was analyzed in the context of 13 commonly used cancer drugs across a panel of lymphoblast cell lines missing individual components of DNA-repair enzymes. To enable in vivo application, PyDau was encapsulated in pegylated liposome, resulting in liposomal PyDau (LiPyDau). In vivo efficacy of LiPyDau was evaluated in three allograft models (melanoma, breast, lung), a xenograft model (uterine sarcoma), a patient-derived xenograft model (lung), and a genetically engineered mouse model of mammary cancer, including two models of drug resistance. Results: While PyDau exhibited up to 1000-fold greater cytotoxicity than daunomycin and doxorubicin against cancer cell lines, its in vivo application was hindered by an extremely narrow therapeutic window. Liposomal nanoformulation mitigated the limiting toxicity, allowing LiPyDau to be tested in preclinical allograft and xenograft mouse models. LiPyDau demonstrated robust efficacy across all models including multidrug-resistant cancer, completely eradicating tumors in a genetically engineered mouse model of triple-negative breast cancer. LiPyDau exerts its anticancer effect through a unique mechanism involving the crosslinking of complementary DNA strands, resulting in irreversible DNA damage. Conclusion: Liposomal formulations of extremely cytotoxic anthracycline analogs, such as LiPyDau, represent a promising and highly effective therapeutic approach for combating drug resistant cancer. LA - English DB - MTMT ER - TY - JOUR AU - Magyar, Csaba AU - Németh, Zoltán Bálint AU - Cserző, Miklós AU - Simon, István TI - Molecular Dynamics Simulation as a Tool to Identify Mutual Synergistic Folding Proteins JF - INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES J2 - INT J MOL SCI VL - 24 PY - 2023 IS - 2 PG - 8 SN - 1661-6596 DO - 10.3390/ijms24021790 UR - https://m2.mtmt.hu/api/publication/33585703 ID - 33585703 N1 - Institute of Enzymology, Research Centre for Natural Sciences, Eötvös Loránd Research Network, Budapest, 1117, Hungary Department of Physiology, Faculty of Medicine, Semmelweis University, Budapest, 1094, Hungary Export Date: 4 July 2023 Correspondence Address: Magyar, C.; Institute of Enzymology, Hungary; email: magyar.csaba@ttk.hu Chemicals/CAS: protein, 67254-75-5; Proteins AB - Mutual synergistic folding (MSF) proteins belong to a recently emerged subclass of disordered proteins, which are disordered in their monomeric forms but become ordered in their oligomeric forms. They can be identified by experimental methods following their unfolding, which happens in a single-step cooperative process, without the presence of stable monomeric intermediates. Only a limited number of experimentally validated MSF proteins are accessible. The amino acid composition of MSF proteins shows high similarity to globular ordered proteins, rather than to disordered ones. However, they have some special structural features, which makes it possible to distinguish them from globular proteins. Even in the possession of their oligomeric three-dimensional structure, classification can only be performed based on unfolding experiments, which are frequently absent. In this work, we demonstrate a simple protocol using molecular dynamics simulations, which is able to indicate that a protein structure belongs to the MSF subclass. The presumption of the known atomic resolution quaternary structure is an obvious limitation of the method, and because of its high computational time requirements, it is not suitable for screening large databases; still, it is a valuable in silico tool for identification of MSF proteins. LA - English DB - MTMT ER - TY - BOOK ED - Simon, István ED - Magyar, Csaba TI - Frontiers in Protein Structure Research PB - Multidisciplinary Digital Publishing Institute (MDPI) CY - Basel PY - 2023 SN - 9783036567815 DO - 10.3390/books978-3-0365-6780-8 UR - https://m2.mtmt.hu/api/publication/33770993 ID - 33770993 N1 - This book is a reprint of the Special Issue Frontiers in Protein Structure Research that was published in IJMS LA - English DB - MTMT ER - TY - JOUR AU - Cserző, Miklós AU - Eisenhaber, Birgit AU - Eisenhaber, Frank AU - Magyar, Csaba AU - Simon, István TI - The First Quarter Century of the Dense Alignment Surface Transmembrane Prediction Method JF - INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES J2 - INT J MOL SCI VL - 24 PY - 2023 IS - 18 PG - 9 SN - 1661-6596 DO - 10.3390/ijms241814016 UR - https://m2.mtmt.hu/api/publication/34173459 ID - 34173459 AB - The dense alignment surface (DAS) transmembrane (TM) prediction method was first published more than 25 years ago. DAS was the one of the earliest tools to discriminate TM proteins from globular ones and to predict the sequence positions of TM helices in proteins with high accuracy from their amino acid sequence alone. The algorithmic improvements that followed in 2002 (DAS-TMfilter) made it one of the best performing tools among those relying on local sequence information for TM prediction. Since then, many more experimental data about membrane proteins (including thousands of 3D structures of membrane proteins) have accumulated but there has been no significant improvement concerning performance in the area of TM helix prediction tools. Here, we report a new implementation of the DAS-TMfilter prediction web server. We reevaluated the performance of the method using a five-times-larger, updated test dataset. We found that the method performs at essentially the same accuracy as the original even without any change to the parametrization of the program despite the much larger dataset. Thus, the approach captures the physico-chemistry of TM helices well, essentially solving this scientific problem. LA - English DB - MTMT ER - TY - JOUR AU - Simon, István AU - Magyar, Csaba TI - Assortment of Frontiers in Protein Science JF - INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES J2 - INT J MOL SCI VL - 23 PY - 2022 IS - 7 SN - 1661-6596 DO - 10.3390/ijms23073685 UR - https://m2.mtmt.hu/api/publication/32782154 ID - 32782154 AB - Recent decades have brought significant changes to the protein structure research field [...] LA - English DB - MTMT ER - TY - PAT AU - Magyar, Csaba TI - Novel IAP antagonists and their therapeutic applications PY - 2021 UR - https://m2.mtmt.hu/api/publication/32471327 ID - 32471327 LA - English DB - MTMT ER - TY - JOUR AU - Magyar, Csaba AU - Mentes, Anikó AU - Cserző, Miklós AU - Simon, István TI - Origin of increased solvent accessibility of peptide bonds in mutual synergetic folding proteins JF - INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES J2 - INT J MOL SCI VL - 22 PY - 2021 IS - 24 PG - 10 SN - 1661-6596 DO - 10.3390/ijms222413404 UR - https://m2.mtmt.hu/api/publication/32552670 ID - 32552670 N1 - Institute of Enzymology, Research Centre for Natural Sciences, Eötvös Loránd Research Network, Budapest, 1117, Hungary Department of Physiology, Faculty of Medicine, Semmelweis University, Budapest, 1094, Hungary Export Date: 29 December 2021 Correspondence Address: Simon, I.; Institute of Enzymology, Hungary; email: simon.istvan@ttk.hu AB - Mutual Synergetic Folding (MSF) proteins belong to a recently discovered class of proteins. These proteins are disordered in their monomeric but ordered in their oligomeric forms. Their amino acid composition is more similar to globular proteins than to disordered ones. Our preceding work shed light on important structural aspects of the structural organization of these proteins, but the background of this behavior is still unknown. We suggest that solvent accessibility is an important factor, especially solvent accessibility of the peptide bonds can be accounted for this phenomenon. The side chains of the amino acids which form a peptide bond have a high local contribution to the shielding of the peptide bond from the solvent. During the oligomerization step, other non-local residues contribute to the shielding. We investigated these local and non-local effects of shielding based on Shannon information entropy calculations. We found that MSF and globular homodimeric proteins have different local contributions resulting from different amino acid pair frequencies. Their non-local distribution is also different because of distinctive inter-subunit contacts. LA - English DB - MTMT ER -