Bioinformatics Analysis of the Periodicity in Proteins with Coiled-Coil Structure—Enumerating All Decompositions of Sequence Periods
A coiled coil is a structural motif in proteins that consists of at least two α-helices wound around each other. For structural stabilization, these α-helices form interhelical contacts via their amino acid side chains. However, there are restrictions as to the distances along the amino acid sequenc...
| Main Authors: | , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2022-08-01
|
| Series: | International Journal of Molecular Sciences |
| Subjects: | |
| Online Access: | https://www.mdpi.com/1422-0067/23/15/8692 |
| _version_ | 1797441751759192064 |
|---|---|
| author | Andre Then Haotian Zhang Bashar Ibrahim Stefan Schuster |
| author_facet | Andre Then Haotian Zhang Bashar Ibrahim Stefan Schuster |
| author_sort | Andre Then |
| collection | DOAJ |
| description | A coiled coil is a structural motif in proteins that consists of at least two α-helices wound around each other. For structural stabilization, these α-helices form interhelical contacts via their amino acid side chains. However, there are restrictions as to the distances along the amino acid sequence at which those contacts occur. As the spatial period of the α-helix is 3.6, the most frequent distances between hydrophobic contacts are 3, 4, and 7. Up to now, the multitude of possible decompositions of α-helices participating in coiled coils at these distances has not been explored systematically. Here, we present an algorithm that computes all non-redundant decompositions of sequence periods of hydrophobic amino acids into distances of 3, 4, and 7. Further, we examine which decompositions can be found in nature by analyzing the available data and taking a closer look at correlations between the properties of the coiled coil and its decomposition. We find that the availability of decompositions allowing for coiled-coil formation without putting too much strain on the α-helix geometry follows an oscillatory pattern in respect of period length. Our algorithm supplies the basis for exploring the possible decompositions of coiled coils of any period length. |
| first_indexed | 2024-03-09T12:29:37Z |
| format | Article |
| id | doaj.art-551d076022734e1aa4c7421c288cf26f |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-09T12:29:37Z |
| publishDate | 2022-08-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-551d076022734e1aa4c7421c288cf26f2023-11-30T22:30:18ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672022-08-012315869210.3390/ijms23158692Bioinformatics Analysis of the Periodicity in Proteins with Coiled-Coil Structure—Enumerating All Decompositions of Sequence PeriodsAndre Then0Haotian Zhang1Bashar Ibrahim2Stefan Schuster3Department of Bioinformatics, Matthias Schleiden Institute, University of Jena, Ernst-Abbe-Platz 2, 07743 Jena, GermanyDepartment of Bioinformatics, Matthias Schleiden Institute, University of Jena, Ernst-Abbe-Platz 2, 07743 Jena, GermanyDepartment of Bioinformatics, Matthias Schleiden Institute, University of Jena, Ernst-Abbe-Platz 2, 07743 Jena, GermanyDepartment of Bioinformatics, Matthias Schleiden Institute, University of Jena, Ernst-Abbe-Platz 2, 07743 Jena, GermanyA coiled coil is a structural motif in proteins that consists of at least two α-helices wound around each other. For structural stabilization, these α-helices form interhelical contacts via their amino acid side chains. However, there are restrictions as to the distances along the amino acid sequence at which those contacts occur. As the spatial period of the α-helix is 3.6, the most frequent distances between hydrophobic contacts are 3, 4, and 7. Up to now, the multitude of possible decompositions of α-helices participating in coiled coils at these distances has not been explored systematically. Here, we present an algorithm that computes all non-redundant decompositions of sequence periods of hydrophobic amino acids into distances of 3, 4, and 7. Further, we examine which decompositions can be found in nature by analyzing the available data and taking a closer look at correlations between the properties of the coiled coil and its decomposition. We find that the availability of decompositions allowing for coiled-coil formation without putting too much strain on the α-helix geometry follows an oscillatory pattern in respect of period length. Our algorithm supplies the basis for exploring the possible decompositions of coiled coils of any period length.https://www.mdpi.com/1422-0067/23/15/8692coiled coildecomposition algorithmhydrophobic interactionmoney-changing problemrecursive algorithmhexaprenyl diphosphate synthase |
| spellingShingle | Andre Then Haotian Zhang Bashar Ibrahim Stefan Schuster Bioinformatics Analysis of the Periodicity in Proteins with Coiled-Coil Structure—Enumerating All Decompositions of Sequence Periods International Journal of Molecular Sciences coiled coil decomposition algorithm hydrophobic interaction money-changing problem recursive algorithm hexaprenyl diphosphate synthase |
| title | Bioinformatics Analysis of the Periodicity in Proteins with Coiled-Coil Structure—Enumerating All Decompositions of Sequence Periods |
| title_full | Bioinformatics Analysis of the Periodicity in Proteins with Coiled-Coil Structure—Enumerating All Decompositions of Sequence Periods |
| title_fullStr | Bioinformatics Analysis of the Periodicity in Proteins with Coiled-Coil Structure—Enumerating All Decompositions of Sequence Periods |
| title_full_unstemmed | Bioinformatics Analysis of the Periodicity in Proteins with Coiled-Coil Structure—Enumerating All Decompositions of Sequence Periods |
| title_short | Bioinformatics Analysis of the Periodicity in Proteins with Coiled-Coil Structure—Enumerating All Decompositions of Sequence Periods |
| title_sort | bioinformatics analysis of the periodicity in proteins with coiled coil structure enumerating all decompositions of sequence periods |
| topic | coiled coil decomposition algorithm hydrophobic interaction money-changing problem recursive algorithm hexaprenyl diphosphate synthase |
| url | https://www.mdpi.com/1422-0067/23/15/8692 |
| work_keys_str_mv | AT andrethen bioinformaticsanalysisoftheperiodicityinproteinswithcoiledcoilstructureenumeratingalldecompositionsofsequenceperiods AT haotianzhang bioinformaticsanalysisoftheperiodicityinproteinswithcoiledcoilstructureenumeratingalldecompositionsofsequenceperiods AT basharibrahim bioinformaticsanalysisoftheperiodicityinproteinswithcoiledcoilstructureenumeratingalldecompositionsofsequenceperiods AT stefanschuster bioinformaticsanalysisoftheperiodicityinproteinswithcoiledcoilstructureenumeratingalldecompositionsofsequenceperiods |