Effect of the Water Model in Simulations of Protein–Protein Recognition and Association
We study self-association of ubiquitin and the disordered protein ACTR using the most commonly used water models. We find that dissociation events are found only with TIP4P-EW and TIP4P/2005, while the widely used TIP3P water model produces straightforward aggregation of the molecules due to the abs...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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MDPI AG
2021-01-01
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| Series: | Polymers |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2073-4360/13/2/176 |
| _version_ | 1797542175425167360 |
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| author | Agustí Emperador Ramon Crehuet Elvira Guàrdia |
| author_facet | Agustí Emperador Ramon Crehuet Elvira Guàrdia |
| author_sort | Agustí Emperador |
| collection | DOAJ |
| description | We study self-association of ubiquitin and the disordered protein ACTR using the most commonly used water models. We find that dissociation events are found only with TIP4P-EW and TIP4P/2005, while the widely used TIP3P water model produces straightforward aggregation of the molecules due to the absence of dissociation events. We also find that TIP4P/2005 is the only water model that reproduces the fast association/dissociation dynamics of ubiquitin and best identifies its binding surface. Our results show the critical role of the water model in the description of protein–protein interactions and binding. |
| first_indexed | 2024-03-10T13:26:55Z |
| format | Article |
| id | doaj.art-410280b8c01e4d6daa5191ba5b6219c8 |
| institution | Directory Open Access Journal |
| issn | 2073-4360 |
| language | English |
| last_indexed | 2024-03-10T13:26:55Z |
| publishDate | 2021-01-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Polymers |
| spelling | doaj.art-410280b8c01e4d6daa5191ba5b6219c82023-11-21T08:57:06ZengMDPI AGPolymers2073-43602021-01-0113217610.3390/polym13020176Effect of the Water Model in Simulations of Protein–Protein Recognition and AssociationAgustí Emperador0Ramon Crehuet1Elvira Guàrdia2Department of Physics, Universitat Politècnica de Catalunya, B4-B5 Campus Nord, Jordi Girona 1-3, 08034 Barcelona, SpainCSIC-Institute for Advanced Chemistry of Catalonia (IQAC), Jordi Girona 18-26, 08034 Barcelona, SpainDepartment of Physics, Universitat Politècnica de Catalunya, B4-B5 Campus Nord, Jordi Girona 1-3, 08034 Barcelona, SpainWe study self-association of ubiquitin and the disordered protein ACTR using the most commonly used water models. We find that dissociation events are found only with TIP4P-EW and TIP4P/2005, while the widely used TIP3P water model produces straightforward aggregation of the molecules due to the absence of dissociation events. We also find that TIP4P/2005 is the only water model that reproduces the fast association/dissociation dynamics of ubiquitin and best identifies its binding surface. Our results show the critical role of the water model in the description of protein–protein interactions and binding.https://www.mdpi.com/2073-4360/13/2/176water modelprotein associationprotein–protein interactionubiquitinACTRmolecular dynamics |
| spellingShingle | Agustí Emperador Ramon Crehuet Elvira Guàrdia Effect of the Water Model in Simulations of Protein–Protein Recognition and Association Polymers water model protein association protein–protein interaction ubiquitin ACTR molecular dynamics |
| title | Effect of the Water Model in Simulations of Protein–Protein Recognition and Association |
| title_full | Effect of the Water Model in Simulations of Protein–Protein Recognition and Association |
| title_fullStr | Effect of the Water Model in Simulations of Protein–Protein Recognition and Association |
| title_full_unstemmed | Effect of the Water Model in Simulations of Protein–Protein Recognition and Association |
| title_short | Effect of the Water Model in Simulations of Protein–Protein Recognition and Association |
| title_sort | effect of the water model in simulations of protein protein recognition and association |
| topic | water model protein association protein–protein interaction ubiquitin ACTR molecular dynamics |
| url | https://www.mdpi.com/2073-4360/13/2/176 |
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