Alternative Hydrophobic Core in Proteins—The Effect of Specific Synergy
Proteins with a high degree of sequence similarity representing different structures provide a key to understand how protein sequence codes for 3D structure. An analysis using the fuzzy oil drop model was carried out on two pairs of proteins with different secondary structures and with high sequence...
| Main Authors: | , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2020-02-01
|
| Series: | Symmetry |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2073-8994/12/2/273 |
| _version_ | 1798041285650546688 |
|---|---|
| author | Piotr Fabian Katarzyna Stapor Mateusz Banach Magdalena Ptak-Kaczor Leszek Konieczny Irena Roterman |
| author_facet | Piotr Fabian Katarzyna Stapor Mateusz Banach Magdalena Ptak-Kaczor Leszek Konieczny Irena Roterman |
| author_sort | Piotr Fabian |
| collection | DOAJ |
| description | Proteins with a high degree of sequence similarity representing different structures provide a key to understand how protein sequence codes for 3D structure. An analysis using the fuzzy oil drop model was carried out on two pairs of proteins with different secondary structures and with high sequence identities. It has been shown that distributions of hydrophobicity for these proteins are approximated well using single 3D Gaussian function. In other words, the similar sequences fold into different 3D structures, however, alternative structures also have symmetric and monocentric hydrophobic cores. It should be noted that a significant change in the helical to beta-structured form in the N-terminal section takes places in the fragment much preceding the location of the mutated regions. It can be concluded that the final structure is the result of a complicated synergy effect in which the whole chain participates simultaneously. |
| first_indexed | 2024-04-11T22:19:23Z |
| format | Article |
| id | doaj.art-ab4afb6d297843a7aa89c99074db0e52 |
| institution | Directory Open Access Journal |
| issn | 2073-8994 |
| language | English |
| last_indexed | 2024-04-11T22:19:23Z |
| publishDate | 2020-02-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Symmetry |
| spelling | doaj.art-ab4afb6d297843a7aa89c99074db0e522022-12-22T04:00:14ZengMDPI AGSymmetry2073-89942020-02-0112227310.3390/sym12020273sym12020273Alternative Hydrophobic Core in Proteins—The Effect of Specific SynergyPiotr Fabian0Katarzyna Stapor1Mateusz Banach2Magdalena Ptak-Kaczor3Leszek Konieczny4Irena Roterman5Institute of Computer Science, Silesian University of Technology, Akademicka 16, 44-100 Gliwice, PolandInstitute of Computer Science, Silesian University of Technology, Akademicka 16, 44-100 Gliwice, PolandDepartment of Bioinformatics and Telemedicine, Medical College, Jagiellonian University, Lazarza 16, 31-530 Krakow, PolandDepartment of Bioinformatics and Telemedicine, Medical College, Jagiellonian University, Lazarza 16, 31-530 Krakow, PolandChair of Medical Biochemistry, Medical College, Jagiellonian University, Kopernika 7, 31-034 Krakow, PolandDepartment of Bioinformatics and Telemedicine, Medical College, Jagiellonian University, Lazarza 16, 31-530 Krakow, PolandProteins with a high degree of sequence similarity representing different structures provide a key to understand how protein sequence codes for 3D structure. An analysis using the fuzzy oil drop model was carried out on two pairs of proteins with different secondary structures and with high sequence identities. It has been shown that distributions of hydrophobicity for these proteins are approximated well using single 3D Gaussian function. In other words, the similar sequences fold into different 3D structures, however, alternative structures also have symmetric and monocentric hydrophobic cores. It should be noted that a significant change in the helical to beta-structured form in the N-terminal section takes places in the fragment much preceding the location of the mutated regions. It can be concluded that the final structure is the result of a complicated synergy effect in which the whole chain participates simultaneously.https://www.mdpi.com/2073-8994/12/2/273homologyprotein structurehydrophobic corehydrophobicitysynergyspherical symmetry |
| spellingShingle | Piotr Fabian Katarzyna Stapor Mateusz Banach Magdalena Ptak-Kaczor Leszek Konieczny Irena Roterman Alternative Hydrophobic Core in Proteins—The Effect of Specific Synergy Symmetry homology protein structure hydrophobic core hydrophobicity synergy spherical symmetry |
| title | Alternative Hydrophobic Core in Proteins—The Effect of Specific Synergy |
| title_full | Alternative Hydrophobic Core in Proteins—The Effect of Specific Synergy |
| title_fullStr | Alternative Hydrophobic Core in Proteins—The Effect of Specific Synergy |
| title_full_unstemmed | Alternative Hydrophobic Core in Proteins—The Effect of Specific Synergy |
| title_short | Alternative Hydrophobic Core in Proteins—The Effect of Specific Synergy |
| title_sort | alternative hydrophobic core in proteins the effect of specific synergy |
| topic | homology protein structure hydrophobic core hydrophobicity synergy spherical symmetry |
| url | https://www.mdpi.com/2073-8994/12/2/273 |
| work_keys_str_mv | AT piotrfabian alternativehydrophobiccoreinproteinstheeffectofspecificsynergy AT katarzynastapor alternativehydrophobiccoreinproteinstheeffectofspecificsynergy AT mateuszbanach alternativehydrophobiccoreinproteinstheeffectofspecificsynergy AT magdalenaptakkaczor alternativehydrophobiccoreinproteinstheeffectofspecificsynergy AT leszekkonieczny alternativehydrophobiccoreinproteinstheeffectofspecificsynergy AT irenaroterman alternativehydrophobiccoreinproteinstheeffectofspecificsynergy |