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Cserző M, Eisenhaber B, Eisenhaber F, Magyar C, Simon I. The First Quarter Century of the Dense Alignment Surface Transmembrane Prediction Method. Int J Mol Sci 2023; 24:14016. [PMID: 37762320 PMCID: PMC10531424 DOI: 10.3390/ijms241814016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 09/05/2023] [Accepted: 09/09/2023] [Indexed: 09/29/2023] Open
Abstract
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.
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Affiliation(s)
- Miklós Cserző
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary; (M.C.); (C.M.)
- Department of Physiology, Faculty of Medicine, Semmelweis University, 1094 Budapest, Hungary
| | - Birgit Eisenhaber
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore 138671, Singapore; (B.E.); (F.E.)
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore 138671, Singapore
- LASA—Lausitz Advanced Scientific Applications gGmbH, 02943 Weißwasser, Germany
| | - Frank Eisenhaber
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore 138671, Singapore; (B.E.); (F.E.)
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore 138671, Singapore
- LASA—Lausitz Advanced Scientific Applications gGmbH, 02943 Weißwasser, Germany
- School of Biological Sciences, Nanyang Technological University (NTU), Singapore 637551, Singapore
| | - Csaba Magyar
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary; (M.C.); (C.M.)
| | - István Simon
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary; (M.C.); (C.M.)
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Magyar C, Németh BZ, Cserző M, Simon I. Molecular Dynamics Simulation as a Tool to Identify Mutual Synergistic Folding Proteins. Int J Mol Sci 2023; 24:ijms24021790. [PMID: 36675304 PMCID: PMC9861041 DOI: 10.3390/ijms24021790] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/12/2023] [Accepted: 01/13/2023] [Indexed: 01/18/2023] Open
Abstract
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.
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Affiliation(s)
- Csaba Magyar
- Institute of Enzymology, Research Centre for Natural Sciences, Eötvös Loránd Research Network, 1117 Budapest, Hungary
- Correspondence:
| | - Bálint Zoltán Németh
- Institute of Enzymology, Research Centre for Natural Sciences, Eötvös Loránd Research Network, 1117 Budapest, Hungary
| | - Miklós Cserző
- Institute of Enzymology, Research Centre for Natural Sciences, Eötvös Loránd Research Network, 1117 Budapest, Hungary
- Department of Physiology, Faculty of Medicine, Semmelweis University, 1094 Budapest, Hungary
| | - István Simon
- Institute of Enzymology, Research Centre for Natural Sciences, Eötvös Loránd Research Network, 1117 Budapest, Hungary
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Turu G, Soltész-Katona E, Tóth AD, Juhász C, Cserző M, Misák Á, Balla A, Caron MG, Hunyady L. Biased Coupling to β-Arrestin of Two Common Variants of the CB 2 Cannabinoid Receptor. Front Endocrinol (Lausanne) 2021; 12:714561. [PMID: 34484125 PMCID: PMC8415483 DOI: 10.3389/fendo.2021.714561] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 07/08/2021] [Indexed: 01/14/2023] Open
Abstract
β-arrestins are partners of the G protein-coupled receptors (GPCRs), regulating their intracellular trafficking and signaling. Development of biased GPCR agonists, selectively targeting either G protein or β-arrestin pathways, are in the focus of interest due to their therapeutic potential in different pathological conditions. The CB2 cannabinoid receptor (CB2R) is a GPCR involved in various functions in the periphery and the central nervous system. Two common occurring variants of CB2R, harboring Q63R or L133I missense mutations, have been implicated in the development of a diverse set of disorders. To evaluate the effect of these mutations, we characterized the binding profile of these mutant CB2 receptors to G proteins and β-arrestin2. Although their ability to inhibit cAMP signaling was similar, the Q63R mutant had increased, whereas the L133I mutant receptor had decreased β-arrestin2 binding. In line with these observations, the variants also had altered intracellular trafficking. Our results show that two common variants of the CB2 receptor have biased signaling properties, which may contribute to the pathogenesis of the associated disorders and may offer CB2R as a target for further development of biased receptor activation strategies.
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Affiliation(s)
- Gábor Turu
- Department of Physiology, Faculty of Medicine, Semmelweis University, Budapest, Hungary
- MTA-SE Laboratory of Molecular Physiology, Hungarian Academy of Sciences and Semmelweis University, Budapest, Hungary
- Department of Cell Biology, Duke University Medical Center, Duke University School of Medicine, Durham, NC, United States
- *Correspondence: Gábor Turu, ; László Hunyady,
| | - Eszter Soltész-Katona
- Department of Physiology, Faculty of Medicine, Semmelweis University, Budapest, Hungary
- MTA-SE Laboratory of Molecular Physiology, Hungarian Academy of Sciences and Semmelweis University, Budapest, Hungary
| | - András Dávid Tóth
- Department of Physiology, Faculty of Medicine, Semmelweis University, Budapest, Hungary
- MTA-SE Laboratory of Molecular Physiology, Hungarian Academy of Sciences and Semmelweis University, Budapest, Hungary
| | - Cintia Juhász
- Department of Physiology, Faculty of Medicine, Semmelweis University, Budapest, Hungary
| | - Miklós Cserző
- Department of Physiology, Faculty of Medicine, Semmelweis University, Budapest, Hungary
- MTA-SE Laboratory of Molecular Physiology, Hungarian Academy of Sciences and Semmelweis University, Budapest, Hungary
| | - Ádám Misák
- Department of Physiology, Faculty of Medicine, Semmelweis University, Budapest, Hungary
| | - András Balla
- Department of Physiology, Faculty of Medicine, Semmelweis University, Budapest, Hungary
- MTA-SE Laboratory of Molecular Physiology, Hungarian Academy of Sciences and Semmelweis University, Budapest, Hungary
| | - Marc G. Caron
- Department of Cell Biology, Duke University Medical Center, Duke University School of Medicine, Durham, NC, United States
| | - László Hunyady
- Department of Physiology, Faculty of Medicine, Semmelweis University, Budapest, Hungary
- MTA-SE Laboratory of Molecular Physiology, Hungarian Academy of Sciences and Semmelweis University, Budapest, Hungary
- *Correspondence: Gábor Turu, ; László Hunyady,
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Magyar C, Mentes A, Fichó E, Cserző M, Simon I. Physical Background of the Disordered Nature of "Mutual Synergetic Folding" Proteins. Int J Mol Sci 2018; 19:ijms19113340. [PMID: 30373142 PMCID: PMC6274838 DOI: 10.3390/ijms19113340] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 10/17/2018] [Accepted: 10/21/2018] [Indexed: 01/16/2023] Open
Abstract
Intrinsically disordered proteins (IDPs) lack a well-defined 3D structure. Their disordered nature enables them to interact with several other proteins and to fulfil their vital biological roles, in most cases after coupled folding and binding. In this paper, we analyze IDPs involved in a new mechanism, mutual synergistic folding (MSF). These proteins define a new subset of IDPs. Recently we collected information on these complexes and created the Mutual Folding Induced by Binding (MFIB) database. These protein complexes exhibit considerable structural variation, and almost half of them are homodimers, but there is a significant amount of heterodimers and various kinds of oligomers. In order to understand the basic background of the disordered character of the monomers found in MSF complexes, the simplest part of the MFIB database, the homodimers are analyzed here. We conclude that MFIB homodimeric proteins have a larger solvent-accessible main-chain surface area on the contact surface of the subunits, when compared to globular homodimeric proteins. The main driving force of the dimerization is the mutual shielding of the water-accessible backbones and the formation of extra intermolecular interactions.
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Affiliation(s)
- Csaba Magyar
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar Tudósok krt. 2, H-1117 Budapest, Hungary.
| | - Anikó Mentes
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar Tudósok krt. 2, H-1117 Budapest, Hungary.
| | - Erzsébet Fichó
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar Tudósok krt. 2, H-1117 Budapest, Hungary.
| | - Miklós Cserző
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar Tudósok krt. 2, H-1117 Budapest, Hungary.
- Department of Physiology, Faculty of Medicine, Semmelweis University, Tűzoltó u. 37-47, H-1094 Budapest, Hungary.
| | - István Simon
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar Tudósok krt. 2, H-1117 Budapest, Hungary.
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