Snake cube puzzle and protein folding
The snake cube puzzle made of a linear array of 27 cubes and its modified and extended versions are used as theoretical models to study the mechanism of folding of proteins into their sequence-specific native three-dimensional structures. Each of the three versions is characterized by the respective...
| Main Author: | |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
The Biophysical Society of Japan
2019-11-01
|
| Series: | Biophysics and Physicobiology |
| Subjects: | |
| Online Access: | https://doi.org/10.2142/biophysico.16.0_256 |
| _version_ | 1811261934086914048 |
|---|---|
| author | Nobuhiro Go |
| author_facet | Nobuhiro Go |
| author_sort | Nobuhiro Go |
| collection | DOAJ |
| description | The snake cube puzzle made of a linear array of 27 cubes and its modified and extended versions are used as theoretical models to study the mechanism of folding of proteins into their sequence-specific native three-dimensional structures. Each of the three versions is characterized by the respective set of characteristics attributed to each of its constituent cubes and an array is characterized by its specific sequence of the cube characteristics. The aim of the puzzles is to fold the cube array into a compact 3×3×3 cubic structure. In all three versions, out of all possible sequences, only a limited fraction of sequences are found foldable into the compact cube. Even among foldable sequences, the structures folded into the compact 3×3×3 cube are found often not uniquely determined from the sequence. By comparing the results obtained for the three versions of models, we conclude that the power of the hydrophobic interactions to make the folded structure unique to the sequence is much weaker than the geometrical varieties of constituent cubes as modelled in the original snake cube puzzle. However, when this weak cube attribute is compounded to that of the original snake cube puzzle, the power is enhanced very effectively. This is a strong manifestation of the consistency principle: The sequence-specific native structure of protein is realized as a result of consistency of various types of interactions working in protein. |
| first_indexed | 2024-04-12T19:14:51Z |
| format | Article |
| id | doaj.art-92a0680c59f546eca15195eb215aba18 |
| institution | Directory Open Access Journal |
| issn | 2189-4779 |
| language | English |
| last_indexed | 2024-04-12T19:14:51Z |
| publishDate | 2019-11-01 |
| publisher | The Biophysical Society of Japan |
| record_format | Article |
| series | Biophysics and Physicobiology |
| spelling | doaj.art-92a0680c59f546eca15195eb215aba182022-12-22T03:19:46ZengThe Biophysical Society of JapanBiophysics and Physicobiology2189-47792019-11-011610.2142/biophysico.16.0_256Snake cube puzzle and protein foldingNobuhiro Go0Kyoto University, Professor Emeritus, Kyoto 606-8187, JapanThe snake cube puzzle made of a linear array of 27 cubes and its modified and extended versions are used as theoretical models to study the mechanism of folding of proteins into their sequence-specific native three-dimensional structures. Each of the three versions is characterized by the respective set of characteristics attributed to each of its constituent cubes and an array is characterized by its specific sequence of the cube characteristics. The aim of the puzzles is to fold the cube array into a compact 3×3×3 cubic structure. In all three versions, out of all possible sequences, only a limited fraction of sequences are found foldable into the compact cube. Even among foldable sequences, the structures folded into the compact 3×3×3 cube are found often not uniquely determined from the sequence. By comparing the results obtained for the three versions of models, we conclude that the power of the hydrophobic interactions to make the folded structure unique to the sequence is much weaker than the geometrical varieties of constituent cubes as modelled in the original snake cube puzzle. However, when this weak cube attribute is compounded to that of the original snake cube puzzle, the power is enhanced very effectively. This is a strong manifestation of the consistency principle: The sequence-specific native structure of protein is realized as a result of consistency of various types of interactions working in protein.https://doi.org/10.2142/biophysico.16.0_256sequence determination of the native structurehydrophobic interactionsgeometrical varieties of amino acid residueslattice model of proteinthe consistency principle |
| spellingShingle | Nobuhiro Go Snake cube puzzle and protein folding Biophysics and Physicobiology sequence determination of the native structure hydrophobic interactions geometrical varieties of amino acid residues lattice model of protein the consistency principle |
| title | Snake cube puzzle and protein folding |
| title_full | Snake cube puzzle and protein folding |
| title_fullStr | Snake cube puzzle and protein folding |
| title_full_unstemmed | Snake cube puzzle and protein folding |
| title_short | Snake cube puzzle and protein folding |
| title_sort | snake cube puzzle and protein folding |
| topic | sequence determination of the native structure hydrophobic interactions geometrical varieties of amino acid residues lattice model of protein the consistency principle |
| url | https://doi.org/10.2142/biophysico.16.0_256 |
| work_keys_str_mv | AT nobuhirogo snakecubepuzzleandproteinfolding |