Paircoil2: improved prediction of coiled coils from sequence

McDonnell, Andrew V.; Jiang, Taijiao; Keating, Amy E.; Berger, Bonnie

doi:10.1093/bioinformatics/bti797

Cited by 408 publications

(399 citation statements)

References 21 publications

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“…The intensity of the 90°light scattering is plotted in arbitrary units versus time. Proline is known to be detrimental to the secondary structure of ␣-helices, and is not found at the d position in the rod of any muscle myosin isoform from any species (4,33,34). Although some computational algorithms such as COILS and PAIRCOIL predict this mutation to have a negative effect on secondary structure, our CD results reveal no difference in the ␣-helical content of mutant protein when compared with WT.…”

Section: Discussionmentioning

confidence: 62%

Mutations in the β-myosin rod cause myosin storage myopathy via multiple mechanisms

Armel

Leinwand

2009

Proc. Natl. Acad. Sci. U.S.A.

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Myosin storage myopathy (MSM) is a congenital myopathy characterized by the presence of subsarcolemmal inclusions of myosin in the majority of type I muscle fibers, and has been linked to 4 mutations in the slow/cardiac muscle myosin, ␤-MyHC (MYH7). Although the majority of the >230 disease causing mutations in MYH7 are located in the globular head region of the molecule, those responsible for MSM are part of a subset of MYH7 mutations that are located in the ␣-helical coiled-coil tail. Mutations in the myosin head are thought to affect the ATPase and actin-binding properties of the molecule. To date, however, there are no reports of the molecular mechanism of pathogenesis for mutations in the rod region of muscle myosins. Here, we present analysis of 4 mutations responsible for MSM: L1793P, R1845W, E1886K, and H1901L. We show that each MSM mutation has a different molecular phenotype, suggesting that there are multiple mechanisms by which MSM can be caused. These mechanisms range from thermodynamic and functional irregularities of individual proteins (L1793P), to varying defects in the assembly and stability of filaments formed from the proteins (R1845W, E1886K, and H1901L). In addition to furthering our understanding of MSM, these observations provide the first insight into how mutations affect the rod region of muscle myosins, and provide a framework for future studies of disease-causing mutations in this region of the molecule.

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Section: Discussionmentioning

confidence: 62%

Mutations in the β-myosin rod cause myosin storage myopathy via multiple mechanisms

Armel

Leinwand

2009

Proc. Natl. Acad. Sci. U.S.A.

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“…The cytoplasmic region is identical for the most abundant GBR1 isoforms, GBR1a and GBR1b (17). To determine the boundary of the coiled-coil domain within each subunit, we carried out coiled-coil predictions using the programs COILS (18) and Paircoil2 (19). Based on these predictions, we generated several pairs of GBR1b and GBR2 constructs with different N-and C-terminal truncations of their intracellular regions.…”

Section: Resultsmentioning

confidence: 99%

Heterodimeric coiled-coil interactions of human GABA _B receptor

Burmakina¹,

Geng²,

Chen³

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

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Metabotropic GABA B receptor is a G protein-coupled receptor that mediates inhibitory neurotransmission in the CNS. It functions as an obligatory heterodimer of GABA B receptor 1 (GBR1) and GABA B receptor 2 (GBR2) subunits. The association between GBR1 and GBR2 masks an endoplasmic reticulum (ER) retention signal in the cytoplasmic region of GBR1 and facilitates cell surface expression of both subunits. Here, we present, to our knowledge, the first crystal structure of an intracellular coiled-coil heterodimer of human GABA B receptor. We found that polar interactions buried within the hydrophobic core determine the specificity of heterodimer pairing. Disruption of the hydrophobic coiled-coil interface with single mutations in either subunit impairs surface expression of GBR1, confirming that the coiled-coil interaction is required to inactivate the adjacent ER retention signal of GBR1. The coiled-coil assembly buries an internalization motif of GBR1 at the heterodimer interface. The ER retention signal of GBR1 is not part of the core coiled-coil structure, suggesting that it is sterically shielded by GBR2 upon heterodimer formation.

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“…Their supercoiled structures are encoded by a seven-residue repeat that can often be detected in sequence data [1,2]. The heptad repeat, denoted [abcdefg] n , typically has hydrophobic residues at a and d, and polar/charged residues at e and g ( Figure 1).…”

Section: Introductionmentioning

confidence: 99%

Structural specificity in coiled-coil interactions

Grigoryan

Keating

2008

Current Opinion in Structural Biology

267

283

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Coiled coils have a rich history in the field of protein design and engineering. Novel structures, such as the first 7-helix coiled coil, continue to provide surprises and insights. Large-scale data sets quantifying the influence of systematic mutations on coiled-coil stability are a valuable new asset to the area. Scoring methods based on sequence and/or structure can predict interaction preferences in coiled-coil-mediated bZIP transcription factor dimerization. Experimental and computational methods for dealing with the near-degeneracy of many coiled-coil structures appear promising for future design applications.

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Paircoil2: improved prediction of coiled coils from sequence

Cited by 408 publications

References 21 publications

Mutations in the β-myosin rod cause myosin storage myopathy via multiple mechanisms

Mutations in the β-myosin rod cause myosin storage myopathy via multiple mechanisms

Heterodimeric coiled-coil interactions of human GABA _B receptor

Structural specificity in coiled-coil interactions

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Paircoil2: improved prediction of coiled coils from sequence

Cited by 408 publications

References 21 publications

Mutations in the β-myosin rod cause myosin storage myopathy via multiple mechanisms

Mutations in the β-myosin rod cause myosin storage myopathy via multiple mechanisms

Heterodimeric coiled-coil interactions of human GABA B receptor

Structural specificity in coiled-coil interactions

Contact Info

Product

Resources

About

Heterodimeric coiled-coil interactions of human GABA _B receptor