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04088nam a2200601Ia 4500 |
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10.1186-s12859-021-04380-5 |
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220427s2021 CNT 000 0 und d |
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|a 14712105 (ISSN)
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|a Enumeration and comprehensive in-silico modeling of three-helix bundle structures composed of typical αα-hairpins
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|b BioMed Central Ltd
|c 2021
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|z View Fulltext in Publisher
|u https://doi.org/10.1186/s12859-021-04380-5
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|a Background: The design of protein structures from scratch requires special attention to the combination of the types and lengths of the secondary structures and the loops required to build highly designable backbone structure models. However, it is difficult to predict the combinations that result in globular and protein-like conformations without simulations. In this study, we used single-chain three-helix bundles as simple models of protein tertiary structures and sought to thoroughly investigate the conditions required to construct them, starting from the identification of the typical αα-hairpin motifs. Results: First, by statistical analysis of naturally occurring protein structures, we identified three αα-hairpins motifs that were specifically related to the left- and right-handedness of helix-helix packing. Second, specifying these αα-hairpins motifs as junctions, we performed sequence-independent backbone-building simulations to comparatively build single-chain three-helix bundle structures and identified the promising combinations of the length of the α-helix and αα-hairpins types that results in tight packing between the first and third α-helices. Third, using those single-chain three-helix bundle backbone structures as template structures, we designed amino acid sequences that were predicted to fold into the target topologies, which supports that the compact single-chain three-helix bundles structures that we sampled show sufficient quality to allow amino-acid sequence design. Conclusion: The enumeration of the dominant subsets of possible backbone structures for small single-chain three-helical bundle topologies revealed that the compact foldable structures are discontinuously and sparsely distributed in the conformational space. Additionally, although the designs have not been experimentally validated in the present research, the comprehensive set of computational structural models generated also offers protein designers the opportunity to skip building similar structures by themselves and enables them to quickly focus on building specialized designs using the prebuilt structure models. The backbone and best design models in this study are publicly accessible from the following URL: https://doi.org/10.5281/zenodo.4321632. © 2021, The Author(s).
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|a alpha helix
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|a amino acid sequence
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|a Amino Acid Sequence
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|a Amino acids
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|a Architectural design
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|a article
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|a Backbone structures
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|a Bundle structures
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|a computer model
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|a controlled study
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|a DNA hairpin
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|a Fragment assembly
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|a Fragment assembly
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|a Helical bundle
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|a Helical bundle
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|a Helical proteins
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|a Helix bundle
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|a protein
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|a protein conformation
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|a Protein Conformation
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|a Protein Conformation, alpha-Helical
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|a Protein design
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|a Protein design
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|a protein secondary structure
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|a Protein Structure, Secondary
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|a protein tertiary structure
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|a Proteins
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|a Proteins
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|a right handedness
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|a simulation
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|a Single chains
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|a Structural design
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|a structural model
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|a Topology
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|a α-Helical protein
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|a Α-helical protein
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|a Αα-hairpin
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|a αα-Hairpins
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|a Minami, S.
|e author
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|a Sakuma, K.
|e author
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|t BMC Bioinformatics
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