Symmetry and Dissymmetry in Protein Structure—System-Coding Its Biological Specificity
The solenoid is a highly ordered structure observed in proteins, characterized by a set of symmetries. A group of enzymes—lyases containing solenoid fragments—was subjected to analysis with focus on their distribution of hydrophobicity/hydrophilicity, applying the fuzzy oil drop...
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| Format: | Article |
| Language: | English |
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MDPI AG
2019-09-01
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| Series: | Symmetry |
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| Online Access: | https://www.mdpi.com/2073-8994/11/10/1215 |
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| author | Mateusz Banach Leszek Konieczny Irena Roterman |
| author_facet | Mateusz Banach Leszek Konieczny Irena Roterman |
| author_sort | Mateusz Banach |
| collection | DOAJ |
| description | The solenoid is a highly ordered structure observed in proteins, characterized by a set of symmetries. A group of enzymes—lyases containing solenoid fragments—was subjected to analysis with focus on their distribution of hydrophobicity/hydrophilicity, applying the fuzzy oil drop model. The model differentiates between a monocentric distribution hydrophobic core (spherical symmetry—mathematically modeled by a 3D Gaussian) and linear propagation of hydrophobicity (symmetry based on translation of structural units, i.e., chains—evident in amyloids). The linearly ordered solenoid carries information that affects the structure of the aqueous solvent in its neighborhood. Progressive disruption of its symmetry (via incorporation of asymmetrical fragments of varying size) appears to facilitate selective interaction with the intended substrate during enzymatic catalysis. |
| first_indexed | 2024-04-14T01:43:52Z |
| format | Article |
| id | doaj.art-39b0930677714b638e6acbad5d246d96 |
| institution | Directory Open Access Journal |
| issn | 2073-8994 |
| language | English |
| last_indexed | 2024-04-14T01:43:52Z |
| publishDate | 2019-09-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Symmetry |
| spelling | doaj.art-39b0930677714b638e6acbad5d246d962022-12-22T02:19:36ZengMDPI AGSymmetry2073-89942019-09-011110121510.3390/sym11101215sym11101215Symmetry and Dissymmetry in Protein Structure—System-Coding Its Biological SpecificityMateusz Banach0Leszek Konieczny1Irena Roterman2Department of Bioinformatics and Telemedicine, Medical College, Jagiellonian University, Łazarza 16, 31-530 Krakow, PolandMedical Biochemistry, Medical College, Jagiellonian University, Kopernika 7, 31-034 Kraków, PolandDepartment of Bioinformatics and Telemedicine, Medical College, Jagiellonian University, Łazarza 16, 31-530 Krakow, PolandThe solenoid is a highly ordered structure observed in proteins, characterized by a set of symmetries. A group of enzymes—lyases containing solenoid fragments—was subjected to analysis with focus on their distribution of hydrophobicity/hydrophilicity, applying the fuzzy oil drop model. The model differentiates between a monocentric distribution hydrophobic core (spherical symmetry—mathematically modeled by a 3D Gaussian) and linear propagation of hydrophobicity (symmetry based on translation of structural units, i.e., chains—evident in amyloids). The linearly ordered solenoid carries information that affects the structure of the aqueous solvent in its neighborhood. Progressive disruption of its symmetry (via incorporation of asymmetrical fragments of varying size) appears to facilitate selective interaction with the intended substrate during enzymatic catalysis.https://www.mdpi.com/2073-8994/11/10/1215symmetrydissymmetryspecificityhydrophobicityhydrophilicityhydrophobic corefuzzy oil drop modellyasesactive sitestructuralization of waterforce field |
| spellingShingle | Mateusz Banach Leszek Konieczny Irena Roterman Symmetry and Dissymmetry in Protein Structure—System-Coding Its Biological Specificity Symmetry symmetry dissymmetry specificity hydrophobicity hydrophilicity hydrophobic core fuzzy oil drop model lyases active site structuralization of water force field |
| title | Symmetry and Dissymmetry in Protein Structure—System-Coding Its Biological Specificity |
| title_full | Symmetry and Dissymmetry in Protein Structure—System-Coding Its Biological Specificity |
| title_fullStr | Symmetry and Dissymmetry in Protein Structure—System-Coding Its Biological Specificity |
| title_full_unstemmed | Symmetry and Dissymmetry in Protein Structure—System-Coding Its Biological Specificity |
| title_short | Symmetry and Dissymmetry in Protein Structure—System-Coding Its Biological Specificity |
| title_sort | symmetry and dissymmetry in protein structure system coding its biological specificity |
| topic | symmetry dissymmetry specificity hydrophobicity hydrophilicity hydrophobic core fuzzy oil drop model lyases active site structuralization of water force field |
| url | https://www.mdpi.com/2073-8994/11/10/1215 |
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