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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...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9369452/ https://www.ncbi.nlm.nih.gov/pubmed/35955828 http://dx.doi.org/10.3390/ijms23158692 |
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author | Then, Andre Zhang, Haotian Ibrahim, Bashar Schuster, Stefan |
author_facet | Then, Andre Zhang, Haotian Ibrahim, Bashar Schuster, Stefan |
author_sort | Then, Andre |
collection | PubMed |
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. |
format | Online Article Text |
id | pubmed-9369452 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-93694522022-08-12 Bioinformatics Analysis of the Periodicity in Proteins with Coiled-Coil Structure—Enumerating All Decompositions of Sequence Periods Then, Andre Zhang, Haotian Ibrahim, Bashar Schuster, Stefan Int J Mol Sci Article 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. MDPI 2022-08-04 /pmc/articles/PMC9369452/ /pubmed/35955828 http://dx.doi.org/10.3390/ijms23158692 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Then, Andre Zhang, Haotian Ibrahim, Bashar Schuster, Stefan Bioinformatics Analysis of the Periodicity in Proteins with Coiled-Coil Structure—Enumerating All Decompositions of Sequence Periods |
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 | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9369452/ https://www.ncbi.nlm.nih.gov/pubmed/35955828 http://dx.doi.org/10.3390/ijms23158692 |
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