A computationally directed screen identifying interacting coiled coils from
            <i>Saccharomyces cerevisiae</i>

Newman, J. Robert; Wolf, Ethan; Kim, Peter

doi:10.1073/pnas.97.24.13203

Cited by 152 publications

(138 citation statements)

References 57 publications

(74 reference statements)

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“…This is a much higher occurrence of coiled-coils than would be expected to occur randomly. Computer analyses of fully sequenced genomes indicates that 5-9% of the open reading frames are predicted to encode proteins that contain coiledcoils (16), and that only 2-3% of residues in all proteins are in regions that are predicted to form coiled-coils (17). In contrast, 34.7% of all the residues encoded by the interacting target cDNAs obtained in the two-hybrid screen described here are predicted to be in coiled-coils.…”

Section: Targets For Calcium Signaling Through Copinesmentioning

confidence: 82%

Identification of Targets for Calcium Signaling through the Copine Family of Proteins

Tomsig

Snyder

Creutz

2003

Journal of Biological Chemistry

120

119

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We provide evidence that copines, members of a ubiquitous family of calcium-dependent, membrane-binding proteins, may represent a universal transduction pathway for calcium signaling because we find copines are capable of interacting with a wide variety of "target" proteins including MEK1, protein phosphatase 5, and the CDC42-regulated kinase, that are themselves components of intracellular signaling pathways. The copine target proteins were identified by yeast two-hybrid screening and the interactions were verified in vitro using purified proteins. In the majority of cases the copine binds to a domain of the target protein that is predicted to form a characteristic coiled-coil. A consensus sequence for the coiled-coil copine-binding site was derived and found to have predictive value for identifying new copine targets. We also show that interaction with copines may result in recruitment of target proteins to membrane surfaces and regulation of the enzymatic activities of target proteins.

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Section: Targets For Calcium Signaling Through Copinesmentioning

confidence: 82%

Identification of Targets for Calcium Signaling through the Copine Family of Proteins

Tomsig

Snyder

Creutz

2003

Journal of Biological Chemistry

120

119

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“…Coiled-coils are a common and versatile folding motif found in proteins with cytoskeleton-like structural function, motor proteins, membrane fusion proteins, and transcription factors (Ref. 44 and references therein and Ref. 42).…”

Section: Discussionmentioning

confidence: 99%

Gemin5, a Novel WD Repeat Protein Component of the SMN Complex That Binds Sm Proteins

Gubitz¹,

Mourelatos²,

Abel³

et al. 2002

Journal of Biological Chemistry

137

123

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The survival of motor neurons (SMN) protein is the product of the disease gene of spinal muscular atrophy and is found both in the cytoplasm and the nucleus, where it is concentrated in gems. SMN is part of a multiprotein complex that includes Gemin2, Gemin3, and Gemin4. The SMN complex plays an important role in the cytoplasmic assembly of small nuclear ribonucleoproteins (snRNPs) and likely other RNPs in pre-mRNA splicing and in the assembly of transcriptosomes. Here, we report the identification of an additional component of the SMN complex, a novel WD repeat protein termed Gemin5. Gemin5 binds SMN directly and is a component of the SMN complex. Furthermore, Gemin5 interacts with several of the snRNP core proteins including SmB, SmD1, SmD2, SmD3, and SmE, suggesting that it participates in the activities of the SMN complex in snRNP assembly. Immunolocalization studies demonstrate that Gemin5 is found in the cytoplasm and in the nucleus, where it colocalizes with SMN in gems. The presence of 13 WD repeat domains in the amino-terminal half of Gemin5 and a coiled-coil motif near its carboxyl terminus indicate that it may form a large heteromeric complex and engage in multiple interactions.

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“…A good example of the involvement of helices in interactions is coiled-coil domains, which consist of two or more alpha-helices that wrap around each other with a slight left-handed superhelical twist (42,43). In the yeast genome, 121 proteins containing coiled-coil regions were identi®ed using the MULTICOIL algorithm (44). In the whole interaction dataset, there are 250 interacting pairs among 119 of these 121 proteins.…”

Section: Amino Acid Composition As Shown Inmentioning

confidence: 99%

TopNet: a tool for comparing biological sub-networks, correlating protein properties with topological statistics

Zhu

Greenbaum

et al. 2004

Nucleic Acids Research

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Biological networks are a topic of great current interest, particularly with the publication of a number of large genome-wide interaction datasets. They are globally characterized by a variety of graph-theoretic statistics, such as the degree distribution, clustering coef®cient, characteristic path length and diameter. Moreover, real protein networks are quite complex and can often be divided into many sub-networks through systematic selection of different nodes and edges. For instance, proteins can be sub-divided by expression level, length, amino-acid composition, solubility, secondary structure and function. A challenging research question is to compare the topologies of subnetworks, looking for global differences associated with different types of proteins. TopNet is an automated web tool designed to address this question, calculating and comparing topological characteristics for different sub-networks derived from any given protein network. It provides reasonable solutions to the calculation of network statistics for sub-networks embedded within a larger network and gives simpli®ed views of a sub-network of interest, allowing one to navigate through it. After constructing TopNet, we applied it to the interaction networks and protein classes currently available for yeast. We were able to ®nd a number of potential biological correlations. In particular, we found that soluble proteins had more interactions than membrane proteins. Moreover, amongst soluble proteins, those that were highly expressed, had many polar amino acids, and had many alpha helices, tended to have the most interaction partners. Interestingly, TopNet also turned up some systematic biases in the current yeast interaction network: on average, proteins with a known functional classi®cation had many more interaction partners than those without. This phenomenon may re¯ect the incompleteness of the experimentally determined yeast interaction network.

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A computationally directed screen identifying interacting coiled coils from Saccharomyces cerevisiae

Cited by 152 publications

References 57 publications

Identification of Targets for Calcium Signaling through the Copine Family of Proteins

Identification of Targets for Calcium Signaling through the Copine Family of Proteins

Gemin5, a Novel WD Repeat Protein Component of the SMN Complex That Binds Sm Proteins

TopNet: a tool for comparing biological sub-networks, correlating protein properties with topological statistics

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