Molecular Dynamics Simulation as a Tool to Identify Mutual Synergistic Folding Proteins
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...
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| Format: | Article |
| Language: | English |
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MDPI AG
2023-01-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/24/2/1790 |
| _version_ | 1797440997366431744 |
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| author | Csaba Magyar Bálint Zoltán Németh Miklós Cserző István Simon |
| author_facet | Csaba Magyar Bálint Zoltán Németh Miklós Cserző István Simon |
| author_sort | Csaba Magyar |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-09T12:16:32Z |
| format | Article |
| id | doaj.art-2277943ed4154c4fa84fff21d969f89d |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-09T12:16:32Z |
| publishDate | 2023-01-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-2277943ed4154c4fa84fff21d969f89d2023-11-30T22:45:39ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672023-01-01242179010.3390/ijms24021790Molecular Dynamics Simulation as a Tool to Identify Mutual Synergistic Folding ProteinsCsaba Magyar0Bálint Zoltán Németh1Miklós Cserző2István Simon3Institute of Enzymology, Research Centre for Natural Sciences, Eötvös Loránd Research Network, 1117 Budapest, HungaryInstitute of Enzymology, Research Centre for Natural Sciences, Eötvös Loránd Research Network, 1117 Budapest, HungaryInstitute of Enzymology, Research Centre for Natural Sciences, Eötvös Loránd Research Network, 1117 Budapest, HungaryInstitute of Enzymology, Research Centre for Natural Sciences, Eötvös Loránd Research Network, 1117 Budapest, HungaryMutual 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.https://www.mdpi.com/1422-0067/24/2/1790mutual synergistic foldingdisordered proteinsoligomeric proteinsmolecular dynamics simulationscooperative two-state unfolding |
| spellingShingle | Csaba Magyar Bálint Zoltán Németh Miklós Cserző István Simon Molecular Dynamics Simulation as a Tool to Identify Mutual Synergistic Folding Proteins International Journal of Molecular Sciences mutual synergistic folding disordered proteins oligomeric proteins molecular dynamics simulations cooperative two-state unfolding |
| title | Molecular Dynamics Simulation as a Tool to Identify Mutual Synergistic Folding Proteins |
| title_full | Molecular Dynamics Simulation as a Tool to Identify Mutual Synergistic Folding Proteins |
| title_fullStr | Molecular Dynamics Simulation as a Tool to Identify Mutual Synergistic Folding Proteins |
| title_full_unstemmed | Molecular Dynamics Simulation as a Tool to Identify Mutual Synergistic Folding Proteins |
| title_short | Molecular Dynamics Simulation as a Tool to Identify Mutual Synergistic Folding Proteins |
| title_sort | molecular dynamics simulation as a tool to identify mutual synergistic folding proteins |
| topic | mutual synergistic folding disordered proteins oligomeric proteins molecular dynamics simulations cooperative two-state unfolding |
| url | https://www.mdpi.com/1422-0067/24/2/1790 |
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