Downhill, Ultrafast and Fast Folding Proteins Revised
Research on the protein folding problem differentiates the protein folding process with respect to the duration of this process. The current structure encoded in sequence dogma seems to be clearly justified, especially in the case of proteins referred to as fast-folding, ultra-fast-folding or downhi...
| Main Authors: | , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2020-10-01
|
| Series: | International Journal of Molecular Sciences |
| Subjects: | |
| Online Access: | https://www.mdpi.com/1422-0067/21/20/7632 |
| _version_ | 1797550818452307968 |
|---|---|
| author | Mateusz Banach Katarzyna Stapor Leszek Konieczny Piotr Fabian Irena Roterman |
| author_facet | Mateusz Banach Katarzyna Stapor Leszek Konieczny Piotr Fabian Irena Roterman |
| author_sort | Mateusz Banach |
| collection | DOAJ |
| description | Research on the protein folding problem differentiates the protein folding process with respect to the duration of this process. The current structure encoded in sequence dogma seems to be clearly justified, especially in the case of proteins referred to as fast-folding, ultra-fast-folding or downhill. In the present work, an attempt to determine the characteristics of this group of proteins using fuzzy oil drop model is undertaken. According to the fuzzy oil drop model, a protein is a specific micelle composed of bi-polar molecules such as amino acids. Protein folding is regarded as a spherical micelle formation process. The presence of covalent peptide bonds between amino acids eliminates the possibility of free mutual arrangement of neighbors. An example would be the construction of co-micelles composed of more than one type of bipolar molecules. In the case of fast folding proteins, the amino acid sequence represents the optimal bipolarity system to generate a spherical micelle. In order to achieve the native form, it is enough to have an external force field provided by the water environment which directs the folding process towards the generation of a centric hydrophobic core. The influence of the external field can be expressed using the 3D Gaussian function which is a mathematical model of the folding process orientation towards the concentration of hydrophobic residues in the center with polar residues exposed on the surface. The set of proteins under study reveals a hydrophobicity distribution compatible with a 3D Gaussian distribution, taken as representing an idealized micelle-like distribution. The structure of the present hydrophobic core is also discussed in relation to the distribution of hydrophobic residues in a partially unfolded form. |
| first_indexed | 2024-03-10T15:35:50Z |
| format | Article |
| id | doaj.art-bbf620e2733749fe8b0a5116901fab2e |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-10T15:35:50Z |
| publishDate | 2020-10-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-bbf620e2733749fe8b0a5116901fab2e2023-11-20T17:17:12ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672020-10-012120763210.3390/ijms21207632Downhill, Ultrafast and Fast Folding Proteins RevisedMateusz Banach0Katarzyna Stapor1Leszek Konieczny2Piotr Fabian3Irena Roterman4Department of Bioinformatics and Telemedicine, Jagiellonian University—Medical College, Lazarza 16, 31-533 Krakow, PolandInstitute of Computer Science, Silesian University of Technology, Akademicka 16, 44-100 Gliwice, PolandChair of Medical Biochemistry, Medical College, Jagiellonian University, Kopernika 7, 31-034 Krakow, PolandInstitute of Computer Science, Silesian University of Technology, Akademicka 16, 44-100 Gliwice, PolandDepartment of Bioinformatics and Telemedicine, Jagiellonian University—Medical College, Lazarza 16, 31-533 Krakow, PolandResearch on the protein folding problem differentiates the protein folding process with respect to the duration of this process. The current structure encoded in sequence dogma seems to be clearly justified, especially in the case of proteins referred to as fast-folding, ultra-fast-folding or downhill. In the present work, an attempt to determine the characteristics of this group of proteins using fuzzy oil drop model is undertaken. According to the fuzzy oil drop model, a protein is a specific micelle composed of bi-polar molecules such as amino acids. Protein folding is regarded as a spherical micelle formation process. The presence of covalent peptide bonds between amino acids eliminates the possibility of free mutual arrangement of neighbors. An example would be the construction of co-micelles composed of more than one type of bipolar molecules. In the case of fast folding proteins, the amino acid sequence represents the optimal bipolarity system to generate a spherical micelle. In order to achieve the native form, it is enough to have an external force field provided by the water environment which directs the folding process towards the generation of a centric hydrophobic core. The influence of the external field can be expressed using the 3D Gaussian function which is a mathematical model of the folding process orientation towards the concentration of hydrophobic residues in the center with polar residues exposed on the surface. The set of proteins under study reveals a hydrophobicity distribution compatible with a 3D Gaussian distribution, taken as representing an idealized micelle-like distribution. The structure of the present hydrophobic core is also discussed in relation to the distribution of hydrophobic residues in a partially unfolded form.https://www.mdpi.com/1422-0067/21/20/7632ultrafast foldingdownhill foldinghydrophobic core |
| spellingShingle | Mateusz Banach Katarzyna Stapor Leszek Konieczny Piotr Fabian Irena Roterman Downhill, Ultrafast and Fast Folding Proteins Revised International Journal of Molecular Sciences ultrafast folding downhill folding hydrophobic core |
| title | Downhill, Ultrafast and Fast Folding Proteins Revised |
| title_full | Downhill, Ultrafast and Fast Folding Proteins Revised |
| title_fullStr | Downhill, Ultrafast and Fast Folding Proteins Revised |
| title_full_unstemmed | Downhill, Ultrafast and Fast Folding Proteins Revised |
| title_short | Downhill, Ultrafast and Fast Folding Proteins Revised |
| title_sort | downhill ultrafast and fast folding proteins revised |
| topic | ultrafast folding downhill folding hydrophobic core |
| url | https://www.mdpi.com/1422-0067/21/20/7632 |
| work_keys_str_mv | AT mateuszbanach downhillultrafastandfastfoldingproteinsrevised AT katarzynastapor downhillultrafastandfastfoldingproteinsrevised AT leszekkonieczny downhillultrafastandfastfoldingproteinsrevised AT piotrfabian downhillultrafastandfastfoldingproteinsrevised AT irenaroterman downhillultrafastandfastfoldingproteinsrevised |