Waggawagga-CLI: A command-line tool for predicting stable single α-helices (SAH-domains), and the SAH-domain distribution across eukaryotes
@article{Simm2018WaggawaggaCLIAC, title={Waggawagga-CLI: A command-line tool for predicting stable single $\alpha$-helices (SAH-domains), and the SAH-domain distribution across eukaryotes}, author={Dominic Simm and Martin Kollmar}, journal={PLoS ONE}, year={2018}, volume={13} }
Stable single-alpha helices (SAH-domains) function as rigid connectors and constant force springs between structural domains, and can provide contact surfaces for protein-protein and protein-RNA interactions. SAH-domains mainly consist of charged amino acids and are monomeric and stable in polar solutions, characteristics which distinguish them from coiled-coil domains and intrinsically disordered regions. Although the number of reported SAH-domains is steadily increasing, genome-wide analyses…
8 Citations
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References
SHOWING 1-10 OF 33 REFERENCES
Distribution and evolution of stable single α-helices (SAH domains) in myosin motor proteins
- BiologyPloS one
- 2017
The largest available myosin sequence dataset is analysed consisting of 7919 manually annotated myOSin sequences from 938 species representing all major eukaryotic branches using the SAH-prediction algorithm of Waggawagga, a recently developed tool for the identification ofSAH-domains.
When a predicted coiled coil is really a single α-helix, in myosins and other proteins
- Biology
- 2009
This review summarises recent findings on SAH domains, their properties, their potential functions and some clues on how to recognise them.
Charged single α‐helix: A versatile protein structural motif
- BiologyProteins
- 2009
It is shown that these sequences represent a novel structural motif called “charged single α‐helix” (CSAH), which is based on sequence features characteristic for salt bridge stabilizedSingle α‐helices, and possible functional roles of the corresponding segments are revealed.
Harnessing the Unique Structural Properties of Isolated α-Helices*
- BiologyThe Journal of Biological Chemistry
- 2014
The structure and function of SAH domains are reviewed, as well as the tools to identify them in natural proteins, with a discussion of recent studies that have successfully used the modular ER/K linker for engineering chimeric myosin proteins with altered mechanical properties.
Waggawagga: comparative visualization of coiled-coil predictions and detection of stable single α-helices (SAH domains)
- Computer ScienceBioinform.
- 2015
UNLABELLED Waggawagga is a web-based tool for the comparative visualization of coiled-coil predictions and the detection of stable single α-helices (SAH domains) and a window-based score has been developed to predict SAH domains.
Dynamic charge interactions create surprising rigidity in the ER/K α-helical protein motif
- BiologyProceedings of the National Academy of Sciences
- 2008
The significant rigidity of the ER/K α-helix can help regulate protein function, as a force transducer between protein subdomains, making it a promising tool in designing synthetic proteins.
Characterization of long and stable de novo single alpha-helix domains provides novel insight into their stability
- BiologyScientific reports
- 2017
Combining a PDB analysis with molecular modelling provides a rational explanation, demonstrating that Glu and Arg form salt bridges more commonly, utilize a wider range of rotamer conformations, and are more dynamic than Glu–Lys.
An exceptionally stable helix from the ribosomal protein L9: implications for protein folding and stability.
- Biology, ChemistryJournal of molecular biology
- 1997
Results show that a peptide corresponding to the central helix of L9 is monomeric in aqueous solution and >85% helical at 1 degrees C and 68(+/-7)% helicals at 25 degrees C, considerably more helical than any other protein fragment studied to date.
The Predicted Coiled-coil Domain of Myosin 10 Forms a Novel Elongated Domain That Lengthens the Head*
- Chemistry, BiologyJournal of Biological Chemistry
- 2005
Myosin 10 contains a region of predicted coiled coil 120 residues long. However, the highly charged nature and pattern of charges in the proximal 36 residues appear incompatible with coiled-coil…