Dynamics of hydrogen bonds in the secondary structures of allosteric protein Avena Sativa phototropin 1
The Light-Oxygen-Voltage 2 (LOV2) domain of Avena Sativa phototropin 1 (AsLOV2) protein is one of the most studied domains in the field of designing photoswitches. This is due to the several unique features in the AsLOV2, such as the monomeric structure of the protein in both light and dark states a...
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| Format: | Article |
| Language: | English |
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Elsevier
2022-01-01
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| Series: | Computational and Structural Biotechnology Journal |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2001037021005031 |
| _version_ | 1828088060856762368 |
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| author | Mayar Tarek Ibrahim Francesco Trozzi Peng Tao |
| author_facet | Mayar Tarek Ibrahim Francesco Trozzi Peng Tao |
| author_sort | Mayar Tarek Ibrahim |
| collection | DOAJ |
| description | The Light-Oxygen-Voltage 2 (LOV2) domain of Avena Sativa phototropin 1 (AsLOV2) protein is one of the most studied domains in the field of designing photoswitches. This is due to the several unique features in the AsLOV2, such as the monomeric structure of the protein in both light and dark states and the relatively short transition time between the two states. Despite that, not many studies focus on the effect of the secondary structures on the drastic conformational change between the light and dark states. In this study, we focus on the role of A’α helix as a key player in the transition between both states using various computational tools as: 1.5 μs molecular dynamics simulations for each configuration, Markov state model, different machine learning techniques, and community analysis. The impact of the A’α helix was studied on the atomistic level by introducing two groups of mutations, helicity enhancing mutations (T406A and T407A) and helicity disrupting mutations (L408D and R410P), as well as on the overall secondary structure by using the community analysis. Maintaining the N-terminal hydrogen bond network was found to be essential for the transition between the two states. Via in-depth hydrogen bonding and contact analysis we were able to identify key residues (Thr407 and Arg410) involved in the functional conformational switch and their impact on the overall protein dynamics. Moreover, the community analysis highlighted the significant role of the β sheets in the overall protein allosteric process. |
| first_indexed | 2024-04-11T05:20:31Z |
| format | Article |
| id | doaj.art-9c35c888895e480c875f8870a747113a |
| institution | Directory Open Access Journal |
| issn | 2001-0370 |
| language | English |
| last_indexed | 2024-04-11T05:20:31Z |
| publishDate | 2022-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Computational and Structural Biotechnology Journal |
| spelling | doaj.art-9c35c888895e480c875f8870a747113a2022-12-24T04:50:48ZengElsevierComputational and Structural Biotechnology Journal2001-03702022-01-01205064Dynamics of hydrogen bonds in the secondary structures of allosteric protein Avena Sativa phototropin 1Mayar Tarek Ibrahim0Francesco Trozzi1Peng Tao2Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas, United StatesDepartment of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas, United StatesCorresponding author.; Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas, United StatesThe Light-Oxygen-Voltage 2 (LOV2) domain of Avena Sativa phototropin 1 (AsLOV2) protein is one of the most studied domains in the field of designing photoswitches. This is due to the several unique features in the AsLOV2, such as the monomeric structure of the protein in both light and dark states and the relatively short transition time between the two states. Despite that, not many studies focus on the effect of the secondary structures on the drastic conformational change between the light and dark states. In this study, we focus on the role of A’α helix as a key player in the transition between both states using various computational tools as: 1.5 μs molecular dynamics simulations for each configuration, Markov state model, different machine learning techniques, and community analysis. The impact of the A’α helix was studied on the atomistic level by introducing two groups of mutations, helicity enhancing mutations (T406A and T407A) and helicity disrupting mutations (L408D and R410P), as well as on the overall secondary structure by using the community analysis. Maintaining the N-terminal hydrogen bond network was found to be essential for the transition between the two states. Via in-depth hydrogen bonding and contact analysis we were able to identify key residues (Thr407 and Arg410) involved in the functional conformational switch and their impact on the overall protein dynamics. Moreover, the community analysis highlighted the significant role of the β sheets in the overall protein allosteric process.http://www.sciencedirect.com/science/article/pii/S2001037021005031LOV domainAllosteryAsLOV2Hydrogen bond networkMachine learning |
| spellingShingle | Mayar Tarek Ibrahim Francesco Trozzi Peng Tao Dynamics of hydrogen bonds in the secondary structures of allosteric protein Avena Sativa phototropin 1 Computational and Structural Biotechnology Journal LOV domain Allostery AsLOV2 Hydrogen bond network Machine learning |
| title | Dynamics of hydrogen bonds in the secondary structures of allosteric protein Avena Sativa phototropin 1 |
| title_full | Dynamics of hydrogen bonds in the secondary structures of allosteric protein Avena Sativa phototropin 1 |
| title_fullStr | Dynamics of hydrogen bonds in the secondary structures of allosteric protein Avena Sativa phototropin 1 |
| title_full_unstemmed | Dynamics of hydrogen bonds in the secondary structures of allosteric protein Avena Sativa phototropin 1 |
| title_short | Dynamics of hydrogen bonds in the secondary structures of allosteric protein Avena Sativa phototropin 1 |
| title_sort | dynamics of hydrogen bonds in the secondary structures of allosteric protein avena sativa phototropin 1 |
| topic | LOV domain Allostery AsLOV2 Hydrogen bond network Machine learning |
| url | http://www.sciencedirect.com/science/article/pii/S2001037021005031 |
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