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 - BOOK ED - Simon, István ED - Magyar, Csaba TI - Frontiers in Protein Structure Research PB - 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 - 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 - 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 N1 - Export Date: 13 April 2022 Correspondence Address: Simon, I.; Institute of Enzymology, Hungary; email: simon.istvan@ttk.hu Correspondence Address: Magyar, C.; Institute of Enzymology, Hungary; email: magyar.csaba@ttk.hu Funding details: Hungarian Scientific Research Fund, OTKA, K115698 Funding details: Nemzeti Kutatási, Fejlesztési és Innovaciós Alap, NKFIA Funding details: Innovációs és Technológiai Minisztérium Funding text 1: Funding: This work was financially supported by the Ministry of Innovation and Technology of Hungary from the National Research, Development and Innovation Fund (OTKA grant No. K115698). 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 LA - English DB - MTMT ER - TY - BOOK ED - Simon, István TI - Functionally Relevant Macromolecular Interactions of Disordered Proteins PB - Multidisciplinary Digital Publishing Institute CY - Basel PY - 2020 SP - 520 SN - 9783039365227 DO - 10.3390/books978-3-03936-522-7 UR - https://m2.mtmt.hu/api/publication/31599381 ID - 31599381 LA - English DB - MTMT ER - TY - JOUR AU - Simon, István TI - Macromolecular Interactions of Disordered Proteins JF - INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES J2 - INT J MOL SCI VL - 21 PY - 2020 IS - 2 PG - 7 SN - 1661-6596 DO - 10.3390/ijms21020504 UR - https://m2.mtmt.hu/api/publication/31127720 ID - 31127720 N1 - Export Date: 14 February 2020 LA - English DB - MTMT ER - TY - JOUR AU - Mészáros, Bálint AU - Dobson, László AU - Fichó, Erzsébet AU - Simon, István TI - Sequence and Structure Properties Uncover the Natural Classification of Protein Complexes Formed by Intrinsically Disordered Proteins via Mutual Synergistic Folding JF - INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES J2 - INT J MOL SCI VL - 20 PY - 2019 IS - 21 PG - 21 SN - 1661-6596 DO - 10.3390/ijms20215460 UR - https://m2.mtmt.hu/api/publication/30875480 ID - 30875480 N1 - MTA-ELTE Momentum Bioinformatics Research Group, Department of Biochemistry, Eötvös Loránd University, Pázmány Péter stny 1/c, Budapest, H-1117, Hungary European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstraße 1, Heidelberg, 69117, Germany Protein Structure Research Group, Institute of Enzymology, RCNS, HAS, Magyar Tudósok krt 2, Budapest, H-1117, Hungary Membrane Protein Bioinformatics Research Group, Institute of Enzymology, RCNS, HAS, Magyar Tudósok krt 2, Budapest, H-1117, Hungary Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Práter u. 50A, Budapest, H-1083, Hungary Cited By :2 Export Date: 31 March 2022 Correspondence Address: Mészáros, B.; MTA-ELTE Momentum Bioinformatics Research Group, Pázmány Péter stny 1/c, Hungary; email: bmeszaros@caesar.elte.hu LA - English DB - MTMT ER - TY - JOUR AU - Mentes, Anikó AU - Magyar, Csaba AU - Fichó, Erzsébet AU - Simon, István TI - Analysis of Heterodimeric “Mutual Synergistic Folding”-Complexes JF - INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES J2 - INT J MOL SCI VL - 20 PY - 2019 IS - 20 PG - 13 SN - 1661-6596 DO - 10.3390/ijms20205136 UR - https://m2.mtmt.hu/api/publication/30852006 ID - 30852006 N1 - Cited By :5 Export Date: 3 October 2022 Correspondence Address: Simon, I.; Institute of Enzymology, Magyar Tudósok krt. 2, Hungary; email: simon.istvan@ttk.mta.hu LA - English DB - MTMT ER - TY - JOUR AU - Dobson, László AU - Fichó, Erzsébet AU - Tusnády, Gábor AU - Simon, István AU - Dosztányi, Zsuzsanna AU - Mészáros, Bálint TI - How folding and binding intertwine during protein complex formation provides an additional layer of functional regulation JF - FEBS OPEN BIO J2 - FEBS OPEN BIO VL - 9 PY - 2019 SP - 265 EP - 265 PG - 1 SN - 2211-5463 UR - https://m2.mtmt.hu/api/publication/30846550 ID - 30846550 LA - English DB - MTMT ER -