Recognizing and Defining True Ras Binding Domains II: In Silico Prediction Based on Homology Modelling and Energy Calculations

Kiel, Christina; Wohlgemuth, Sabine; Rousseau, Frédéric; Schymkowitz, Joost; Ferkinghoff‐Borg, Jesper; Wittinghofer, Fred; Serrano, Luís

doi:10.1016/j.jmb.2005.02.046

Cited by 104 publications

(136 citation statements)

References 54 publications

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“…Construction of Plasmids for Protein Expression-The following RAPL plasmids used in this study were described previously: a plasmid encoding the Myc-tagged full-length human RAPL protein (pcDNARAPLmyc) (15) and a plasmid encoding mouse sequences corresponding to amino acid residues 52-265 or amino acid residues 52-212 in human RAPL fused to GST (pGexNore199 -413 and pGexNore199 -358) (7,21). These plasmids were used to generate other constructs (namely RAPL42 (aa 42-265myc), RAPL42⌬C (aa 42-222myc), RAPL⌬C (aa 52-212), and RAPL SARAH (aa 212-265)).…”

Section: Methodsmentioning

confidence: 99%

Characterization of Interactions of Adapter Protein RAPL/Nore1B with RAP GTPases and Their Role in T Cell Migration

Miertzschke

Stanley

Bunney

et al. 2007

Journal of Biological Chemistry

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Section: Methodsmentioning

confidence: 99%

Characterization of Interactions of Adapter Protein RAPL/Nore1B with RAP GTPases and Their Role in T Cell Migration

Miertzschke

Stanley

Bunney

et al. 2007

Journal of Biological Chemistry

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“…Assuming that similar amino acid sequences have a similar fold and that domains within a similar fold interact in a similar way (Aloy and Russell 2006), it is possible to predict novel proteinprotein interactions based on existing structural information (Kiel et al 2005(Kiel et al , 2007. By generating homology models of proteins with similar sequences, protein design algorithms (Kiel et al 2007) can then be used to calculate the relative interaction energies of related binary interactions.…”

Section: True Homology Modeling Of Human E2/e3-ring Interactionsmentioning

confidence: 99%

“…Prediction of free-energy values for different human E2/E3-RING complexes was performed in accordance with previously published methods (Kiel et al 2005(Kiel et al , 2007. As the pdb:1fbv structure was the only available template for modeling the E2/E3-RING with a range of isolated UBC (1i7k, 1x23, 2csv, 2cyx, and 1a3s) or E3-RING (1rmd, 1z6u, and 2ckl) structures.…”

Section: True Homology Modelingmentioning

confidence: 99%

Analysis of the human E2 ubiquitin conjugating enzyme protein interaction network

Markson¹,

Kiel²,

Hyde³

et al. 2009

Genome Res.

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In eukaryotic cells the stability and function of many proteins are regulated by the addition of ubiquitin or ubiquitin-like peptides. This process is dependent upon the sequential action of an E1-activating enzyme, an E2-conjugating enzyme, and an E3 ligase. Different combinations of these proteins confer substrate specificity and the form of protein modification. However, combinatorial preferences within ubiquitination networks remain unclear. In this study, yeast two-hybrid (Y2H) screens were combined with true homology modeling methods to generate a high-density map of human E2/E3-RING interactions. These data include 535 experimentally defined novel E2/E3-RING interactions and >1300 E2/E3-RING pairs with more favorable predicted free-energy values than the canonical UBE2L3-CBL complex. The significance of Y2H predictions was assessed by both mutagenesis and functional assays. Significantly, 74/80 (>92%) of Y2H predicted complexes were disrupted by point mutations that inhibit verified E2/E3-RING interactions, and a ;93% correlation was observed between Y2H data and the functional activity of E2/E3-RING complexes in vitro. Analysis of the high-density human E2/E3-RING network reveals complex combinatorial interactions and a strong potential for functional redundancy, especially within E2 families that have undergone evolutionary expansion. Finally, a one-step extended human E2/E3-RING network, containing 2644 proteins and 5087 edges, was assembled to provide a resource for future functional investigations.

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“…A novel model to investigate the role of BAT in healthful aging and lifespan is the mouse model of the disruption of the regulator for G protein signaling 14 (RGS14), which has increased BAT. RGS14 is a complex RGS family member that contains a canonical RGS domain, a tandem (R1 and R2) Ras/Rap binding domain (Kiel et al., 2005; Wohlgemuth et al., 2005), as well as a GoLoco/GPR motif. Most prior work on RGS14 focused on its effects on embryonic development and on the visual cortex and central nervous system (Evans, Lee, Smith & Hepler, 2014; Lee et al., 2010; Lopez‐Aranda et al., 2009; Shu, Ramineni & Hepler, 2010; Vellano, Brown, Blumer & Hepler, 2013).…”

Section: Introductionmentioning

confidence: 99%

Enhanced longevity and metabolism by brown adipose tissue with disruption of the regulator of G protein signaling 14

et al. 2018

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SummaryDisruption of the regulator for G protein signaling 14 (RGS14) knockout (KO) in mice extends their lifespan and has multiple beneficial effects related to healthful aging, that is, protection from obesity, as reflected by reduced white adipose tissue, protection against cold exposure, and improved metabolism. The observed beneficial effects were mediated by improved mitochondrial function. But most importantly, the main mechanism responsible for the salutary properties of the RGS14 KO involved an increase in brown adipose tissue (BAT), which was confirmed by surgical BAT removal and transplantation to wild‐type (WT) mice, a surgical simulation of a molecular knockout. This technique reversed the phenotype of the RGS14 KO and WT, resulting in loss of the improved metabolism and protection against cold exposure in RGS14 KO and conferring this protection to the WT BAT recipients. Another mechanism mediating the salutary features in the RGS14 KO was increased SIRT3. This mechanism was confirmed in the RGS14 X SIRT3 double KO, which no longer demonstrated improved metabolism and protection against cold exposure. Loss of function of the Caenorhabditis elegans RGS‐14 homolog confirmed the evolutionary conservation of this mechanism. Thus, disruption of RGS14 is a model of healthful aging, as it not only enhances lifespan, but also protects against obesity and cold exposure and improves metabolism with a key mechanism of increased BAT, which, when removed, eliminates the features of healthful aging.

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Recognizing and Defining True Ras Binding Domains II: In Silico Prediction Based on Homology Modelling and Energy Calculations

Cited by 104 publications

References 54 publications

Characterization of Interactions of Adapter Protein RAPL/Nore1B with RAP GTPases and Their Role in T Cell Migration

Characterization of Interactions of Adapter Protein RAPL/Nore1B with RAP GTPases and Their Role in T Cell Migration

Analysis of the human E2 ubiquitin conjugating enzyme protein interaction network

Enhanced longevity and metabolism by brown adipose tissue with disruption of the regulator of G protein signaling 14

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