MultiCoil: A program for predicting two‐and three‐stranded coiled coils

Wolf, Ethan; Kim, Peter; Berger, Bonnie

doi:10.1002/pro.5560060606

Cited by 703 publications

(618 citation statements)

References 67 publications

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“…Three coiled-coil stretches can be identified at fig. 2A), as suggested by the prediction programs COILS and MUL-TICOIL [35,40]. In contrast to metazoan reggies/flotillins, we found bacterial yuaG to contain only one predicted transmembrane stretch between residues 6 and 40 ( fig.…”

Section: Resultssupporting

confidence: 50%

Ancient origin of reggie (flotillin), reggie-like, and other lipid-raft proteins: convergent evolution of the SPFH domain

Rivera-Milla

Stuermer

Málaga-Trillo

2006

Cell. Mol. Life Sci.

145

150

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Abstract. Reggies (flotillins) are detergent-resistant microdomains involved in the scaffolding of large heteromeric complexes that signal across the plasma membrane. Based on the presence of an evolutionarily widespread motif, reggies/flotillins have been included within the SPFH (stomatin-prohibitin-flotillin-HflC/K) protein superfamily. To better understand the origin and evolution of reggie/flotillin structure and function, we searched databases for reggie/flotillin and SPFH-like proteins in organisms at the base and beyond the animal kingdom, and used the resulting dataset to compare their structural Cell. Mol. Life Sci. 63 (2006) 343-357 1420-682X/06/030343-15 DOI 10.1007/s00018-005-5434-3 © Birkhäuser Verlag, Basel, 2006 and functional domains. Our analysis shows that the SPFH grouping has little phylogenetic support, probably due to convergent evolution of its members. We also find that reggie/flotillin homologues are highly conserved among metazoans but are absent in plants, fungi and bacteria, where only proteins with 'reggie-like' domains can be found. However, despite their low sequence similarities, reggie/flotillin and 'reggie-like' domains appear to subserve related functions, suggesting that their basic biological role was acquired independently during evolution.

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Section: Resultssupporting

confidence: 50%

Ancient origin of reggie (flotillin), reggie-like, and other lipid-raft proteins: convergent evolution of the SPFH domain

Rivera-Milla

Stuermer

Málaga-Trillo

2006

Cell. Mol. Life Sci.

145

150

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“…Predictions for Cnm67 were ambiguous with respect to whether there may be one long coiled coil (Cnm67_2) or two shorter coiled coils (Cnm67_3 and Cnm67_4) in this protein; constructs accounting for both possibilities were tested ( Figure S1 in Supporting Information). Multicoil was used to predict whether each coiledcoil region was more likely to form a dimer or a trimer (26).…”

Section: Methodsmentioning

confidence: 99%

Analysis of Coiled-Coil Interactions between Core Proteins of the Spindle Pole Body

et al. 2008

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The spindle pole body (SPB) is a multiprotein complex that organizes microtubules in yeast. Due to its large size and association with the nuclear membrane, little is known about its detailed structure. In particular, although many SPB components and some of the interactions between them have been identified, the molecular details of how most of these interactions occur are not known. The prevalence of predicted coiled-coil regions in SPB proteins suggests that some interactions may occur via coiled coils. Here this hypothesis is supported by biochemical characterization of isolated coiled-coil peptides derived from SPB proteins. Formation of four strongly self-associating coiled-coil complexes from Spc29, Spc42, and Spc72 was demonstrated by circular dichroism (CD) spectroscopy and a fluorescence resonance energy transfer (FRET) assay. Many weaker self-and heteroassociations were also detected by CD, FRET, and/or cross-linking. The thermal stabilities of nine candidate homooligomers were assessed; six unfolded cooperatively with melting temperatures ranging from <11 to >50 °C. Solution studies established that coiled-coil peptides derived from Spc42 and Spc72 form parallel dimers, and this was confirmed for Spc42 by a high-resolution crystal structure. These data contribute to a growing body of knowledge that will ultimately provide a detailed model of the SPB structure.

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“…S1B, red bar) and that either the predicted sequence in The Arabidopsis Information Resource has incorrectly predicted splice sites or multiple splice variants exist. TNO1, a previously uncharacterized protein of predicted mass 209 kD, was predicted to have six coiled-coil domains in the Arabi-Coil database (Rose et al, 2004) based on the MultiCoil algorithm (Wolf et al, 1997) and immunoprecipitate. Detergent-solubilized Arabidopsis suspension cell extracts were applied to a column containing resin cross-linked to either immobilized SYP41 antibodies (I) or SYP41 preimmune serum (P).…”

Section: Identification Of Tno1mentioning

confidence: 99%

TNO1 Is Involved in Salt Tolerance and Vacuolar Trafficking in Arabidopsis

Kim

Bassham

2011

Plant Physiology

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The Arabidopsis (Arabidopsis thaliana) soluble N-ethylmaleimide-sensitive factor attachment protein receptor SYP41 is involved in vesicle fusion at the trans-Golgi network (TGN) and interacts with AtVPS45, SYP61, and VTI12. These proteins are involved in diverse cellular processes, including vacuole biogenesis and stress tolerance. A previously uncharacterized protein, named TNO1 (for TGN-localized SYP41-interacting protein), was identified by coimmunoprecipitation as a SYP41-interacting protein.TNO1 was found to localize to the TGN by immunofluorescence microscopy. A tno1 mutant showed increased sensitivity to high concentrations of NaCl, KCl, and LiCl and also to mannitol-induced osmotic stress. Localization of SYP61, which is involved in the salt stress response, was disrupted in the tno1 mutant. Vacuolar proteins were partially secreted to the apoplast in the tno1 mutant, suggesting that TNO1 is required for efficient protein trafficking to the vacuole. The tno1 mutant had delayed formation of the brefeldin A (BFA) compartment in cotyledons upon application of BFA, suggesting less efficient membrane fusion processes in the mutant. Unlike most TGN proteins, TNO1 does not relocate to the BFA compartment upon BFA treatment. These data demonstrate that TNO1 is involved in vacuolar trafficking and salt tolerance, potentially via roles in vesicle fusion and in maintaining TGN structure or identity.

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MultiCoil: A program for predicting two‐and three‐stranded coiled coils

Cited by 703 publications

References 67 publications

Ancient origin of reggie (flotillin), reggie-like, and other lipid-raft proteins: convergent evolution of the SPFH domain

Ancient origin of reggie (flotillin), reggie-like, and other lipid-raft proteins: convergent evolution of the SPFH domain

Analysis of Coiled-Coil Interactions between Core Proteins of the Spindle Pole Body

TNO1 Is Involved in Salt Tolerance and Vacuolar Trafficking in Arabidopsis

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