CCHMM_PROF: a HMM-based coiled-coil predictor with evolutionary information

Bartoli, Lisa; Fariselli, Piero; Krogh, Anders; Casadio, Rita

doi:10.1093/bioinformatics/btp539

Cited by 45 publications

(41 citation statements)

References 33 publications

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“…This study found the CCHMM_PROF algorithm to give the best indicator of coiled-coil; however, it does not yield a registry prediction for the coiled-coil. Thus, it was not used in this study (61). Multicoil2 also performed well, but its results were consistent with that of MARCOIL and COILS-28 (62).…”

Section: Coiled-coil Predictions Do Not Accurately Reflect the Startsupporting

confidence: 58%

Family-specific Kinesin Structures Reveal Neck-linker Length Based on Initiation of the Coiled-coil

Phillips

Peter

Gilbert

et al. 2016

Journal of Biological Chemistry

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and -7 generate processive hand-over-hand 8-nm steps to transport intracellular cargoes toward the microtubule plus end. This processive motility requires gating mechanisms to coordinate the mechanochemical cycles of the two motor heads to sustain the processive run. A key structural element believed to regulate the degree of processivity is the necklinker, a short peptide of 12-18 residues, which connects the motor domain to its coiled-coil stalk. Although a shorter necklinker has been correlated with longer run lengths, the structural data to support this hypothesis have been lacking. To test this hypothesis, seven kinesin structures were determined by x-ray crystallography. Each included the neck-linker motif, followed by helix ␣7 that constitutes the start of the coiled-coil stalk. In the majority of the structures, the neck-linker length differed from predictions because helix ␣7, which initiates the coiled-coil, started earlier in the sequence than predicted. A further examination of structures in the Protein Data Bank reveals that there is a great disparity between the predicted and observed starting residues. This suggests that an accurate prediction of the start of a coiled-coil is currently difficult to achieve. These results are significant because they now exclude simple comparisons between members of the kinesin superfamily and add a further layer of complexity when interpreting the results of mutagenesis or protein fusion. They also re-emphasize the need to consider factors beyond the kinesin neck-linker motif when attempting to understand how inter-head communication is tuned to achieve the degree of processivity required for cellular function.

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Section: Coiled-coil Predictions Do Not Accurately Reflect the Startsupporting

confidence: 58%

Family-specific Kinesin Structures Reveal Neck-linker Length Based on Initiation of the Coiled-coil

Phillips

Peter

Gilbert

et al. 2016

Journal of Biological Chemistry

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“…Secondary structure was predicted using PSIPRED 18 , whereas domains, repeats and other features were predicted with InterproScan 19 . COILS 20 , MARCOIL 21 and CCHMM-PROF 22 were used to assess previously predicted coiled-coil regions, and TPR modules were predicted with TPRpred 23 . A repeat consensus was manually curated with Jalview from the MAFFT alignment.…”

Section: Methodsmentioning

confidence: 99%

Dynamic scaffolds for neuronal signaling: in silico analysis of the TANC protein family

Gasparini

Tosatto

Murgia

et al. 2017

Sci Rep

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The emergence of genes implicated across multiple comorbid neurologic disorders allows to identify shared underlying molecular pathways. Recently, investigation of patients with diverse neurologic disorders found TANC1 and TANC2 as possible candidate disease genes. While the TANC proteins have been reported as postsynaptic scaffolds influencing synaptic spines and excitatory synapse strength, their molecular functions remain unknown. Here, we conducted a comprehensive in silico analysis of the TANC protein family to characterize their molecular role and understand possible neurobiological consequences of their disruption. The known Ankyrin and tetratricopeptide repeat (TPR) domains have been modeled. The newly predicted N-terminal ATPase domain may function as a regulated molecular switch for downstream signaling. Several putative conserved protein binding motifs allowed to extend the TANC interaction network. Interestingly, we highlighted connections with different signaling pathways converging to modulate neuronal activity. Beyond a known role for TANC family members in the glutamate receptor pathway, they seem linked to planar cell polarity signaling, Hippo pathway, and cilium assembly. This suggests an important role in neuron projection, extension and differentiation.

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“…The amino acid sequences of kRz and the unrelated functional equivalent from T7, gp18.5, were examined for their propensity to form coiled-coils through the use of the COILS 29 and CCHMM_PROF 30 programs.…”

Section: Coiled-coil Predictionmentioning

confidence: 99%

The lambda spanin components Rz and Rz1 undergo tertiary and quaternary rearrangements upon complex formation

et al. 2010

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Phage holins and endolysins have long been known to play key roles in lysis of the host cell, disrupting the cytoplasmic membrane and peptidoglycan (PG) layer, respectively. For phages of Gram-negative hosts, a third class of proteins, the spanins, are involved in disrupting the outer membrane (OM). Rz and Rz1, the components of the lambda spanin, are, respectively, a class II inner membrane protein and an OM lipoprotein, are thought to span the entire periplasm by virtue of C-terminal interactions of their soluble domains. Here, the periplasmic domains of Rz and Rz1 have been purified and shown to form dimeric and monomeric species, respectively, in solution. Circular dichroism analysis indicates that Rz has significant alpha-helical character, but much less than predicted, whereas Rz1, which is 25% proline, is unstructured. Mixture of the two proteins leads to complex formation and an increase in secondary structure, especially alpha-helical content. Moreover, transmission electron-microscopy reveals that Rz-Rz1 complexes form large rod-shaped structures which, although heterogeneous, exhibit periodicities that may reflect coiledcoil bundling as well as a long dimension that matches the width of the periplasm. A model is proposed suggesting that the formation of such bundles depends on the removal of the PG and underlies the Rz-Rz1 dependent disruption of the OM.

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CCHMM_PROF: a HMM-based coiled-coil predictor with evolutionary information

Abstract: piero@biocomp.unibo.it.

Cited by 45 publications

References 33 publications

Family-specific Kinesin Structures Reveal Neck-linker Length Based on Initiation of the Coiled-coil

Family-specific Kinesin Structures Reveal Neck-linker Length Based on Initiation of the Coiled-coil

Dynamic scaffolds for neuronal signaling: in silico analysis of the TANC protein family

The lambda spanin components Rz and Rz1 undergo tertiary and quaternary rearrangements upon complex formation

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