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Dissecting protein loops with a statistical scalpel suggests a functional implication of some structural motifs
2011
BMC Bioinformatics
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Results: Here, we present a systematic extraction of structural motifs of seven residues from protein loops and we explore their correspondence with functional sites. ...
One of the strategies for protein function annotation is to search particular structural motifs that are known to be shared by proteins with a given function. ...
Christelle Reynès for critical reading of the manuscript and Dr. Gaelle Debret for her assistance. We thank Grégory Nuel for statistical discussions. ...
doi:10.1186/1471-2105-12-247
pmid:21689388
pmcid:PMC3158783
fatcat:v2de52nu3jcbxdzjt5jyhpnghe
Cartilage Intermediate Layer Protein 2 (CILP-2) Is Expressed in Articular and Meniscal Cartilage and Down-regulated in Experimental Osteoarthritis
2011
Journal of Biological Chemistry
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Ultrastructural analysis also suggested that CILP-2 may be associated with collagen VI microfibrils and thus may mediate interactions between matrix components in the territorial and inter-territorial ...
We demonstrated that Cilp2 has a restricted mRNA distribution at the surface of the mouse articular cartilage during development, becoming localized to the intermediate zone of articular cartilage and ...
Pilar Lorenzo (Lund) for their suggestions and for critically reading the manuscript. ...
doi:10.1074/jbc.m111.248039
pmid:21880736
pmcid:PMC3199518
fatcat:lmfmv2rgqvb7rownn43oqddgxm
Identification of the kinase STK25 as an upstream activator of LATS signaling
2019
Nature Communications
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Notably, STK25 activates LATS by promoting LATS activation loop phosphorylation independent of a preceding phosphorylation event at the hydrophobic motif, which represents a form of Hippo activation distinct ...
STK25 is significantly focally deleted across a wide spectrum of human cancers, suggesting STK25 loss may represent a common mechanism by which tumor cells functionally impair the Hippo tumor suppressor ...
We would also like to thank members of the Ganem lab for detailed comments on the manuscript. ...
doi:10.1038/s41467-019-09597-w
pmid:30948712
pmcid:PMC6449379
fatcat:afnfert5bngaldpu52hfsn2oay
Wheat Germination Is Dependent on Plant Target of Rapamycin Signaling
2020
Frontiers in Cell and Developmental Biology
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Rapamycin or torin1 interfered with GA function in germination because of a potent inhibitory effect on α-amylase and GAMYB gene expression. ...
The phosphorylation of serine 467 (S467) in a hydrophobic motif on TaS6K1 was induced in a process of germination triggered by GA. ...
Analysis of the kinase domain structure of TaS6K1 revealed an activation loop (T-loop) motif, turn motif (TM), and hydrophobic motif (HM) with their phosphorylation sites conserved in all S6 kinases belonging ...
doi:10.3389/fcell.2020.606685
pmid:33330509
pmcid:PMC7719826
fatcat:e5iebuvn7bctvmu3vrweainyqe
The transcription factors SOX9 and SOX5/SOX6 cooperate genome-wide through super-enhancers to drive chondrogenesis
2015
Nucleic Acids Research
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SOX9 recognizes pairs of inverted SOX motifs, whereas SOX6 favors pairs of tandem SOX motifs. The SOX proteins primarily target enhancers. ...
SOX9 is a transcriptional activator required for chondrogenesis, and SOX5 and SOX6 are closely related DNA-binding proteins that critically enhance its function. ...
ACKNOWLEDGEMENT We thank Pallavi Bhattaram, Daniel Factor, Kenji Kato, Steven Lietman, Paul Tesar and Baojin Yao for scientific insights and suggestions throughout the study; Abhilash Gadi for technical ...
doi:10.1093/nar/gkv688
pmid:26150426
pmcid:PMC4787819
fatcat:vu76okapnncjje4teimhczv22y
Evidence for a Role of the Transcriptional Regulator Maid in Tumorigenesis and Aging
2015
PLoS ONE
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Maid is a helix-loop-helix protein that is involved in cell proliferation. In order to further elucidate its physiological functions, we studied Maid activity in two small fish model systems. ...
Taken together, our results suggest that Maid levels can influence the progression of liver cancer. In conclusion, we found that Maid is important regulator of hepatocarconogenesis and aging. ...
HLH, helix-loop-helix motif; LZ, leucine zipper motif. (PDF) S2 Fig. Phylogenetic tree of Maid. Phylogenetic tree based on ClustalW alignment generated with the TreeView program. ...
doi:10.1371/journal.pone.0129950
pmid:26107180
pmcid:PMC4479567
fatcat:zxktol2wnfe7fagvoijptzbujq
Transcriptome analysis of Xenopus orofacial tissues deficient in retinoic acid receptor function
2018
BMC Genomics
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Development of the face and mouth is orchestrated by a large number of transcription factors, signaling pathways and epigenetic regulators. ...
are specified and later (60 hpf) when the mouth has formed and facial structures begin to differentiate. ...
Finally, we would like to especially thank Rob Tombes and Sarah Rothschild for sharing their vast knowledge of CaMKII function. ...
doi:10.1186/s12864-018-5186-8
pmid:30390632
pmcid:PMC6215681
fatcat:nwtbqlpm7negbhktog4vlfe6ge
Discovery and Characterization of a Bilirubin Inducible Green Fluorescent Protein From the Moray Eel Gymnothorax zonipectis
2021
Frontiers in Marine Science
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This protein, GymFP, is 15.6 kDa with a fluorescence excitation at 496 nm and an emission maximum at 532 nm upon addition of bilirubin. ...
The mechanisms of biofluorescence in marine organisms are also variable. To fluoresce, some organisms use fluorescent proteins, while others use small molecules. ...
All fluorescent fatty acid binding proteins discovered to date have a Glycine-Proline-Proline (GPP) motif that resides on a loop that may act to protect bilirubin from solvent. ...
doi:10.3389/fmars.2021.678571
fatcat:oimxey3xdbcppinnea35uicjq4
Critical role for v 6 integrin in enamel biomineralization
2012
Journal of Cell Science
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During the secretory stage of enamel formation, ameloblasts deposit an extracellular matrix that is in direct contact with the ameloblast plasma membrane. ...
This accumulation was related to increased synthesis of amelogenin, rather than to reduced removal of the matrix proteins. ...
proteins, some of which are avb6 integrin ligands. ...
doi:10.1242/jcs.112599
pmid:23264742
fatcat:shcegimmxbf7vb64624qfimdkm
Enrichment and Identification of the Most Abundant Zinc Binding Proteins in Developing Barley Grains by Zinc-IMAC Capture and Nano LC-MS/MS
2018
Proteomes
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An important role of the storage proteins in zinc binding has been recently suggested by the finding of a positive linear relationship between the increase of barley major prolamin fraction, B-hordein, ...
However, nowadays, a modified version of Osborne fractionation has been used by the replacement of ethanol with other alcohols (e.g., 50% (v/v) propanol), and the addition of a reducing agent to extract ...
Conflicts of Interest: The authors declare no conflict of interest. Proteomes 2018, 6, 3 ...
doi:10.3390/proteomes6010003
pmid:29342075
pmcid:PMC5874762
fatcat:ojmegyxpozb6xhwkmqtak5aarm
Small molecule kinase inhibitor LRRK2-IN-1 demonstrates potent activity against colorectal and pancreatic cancer through inhibition of doublecortin-like kinase 1
2014
Molecular Cancer
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The results of this study suggest that small molecule inhibitors of DCLK1 kinase should be further investigated as they may hold promise as anti-tumor stem cell drugs. ...
Previous in vitro and in vivo studies have demonstrated the therapeutic effects of inhibiting DCLK1 with small interfering RNA (siRNA) as well as genetically targeting the DCLK1 + cell for deletion. ...
Acknowledgements We would like to acknowledge Jim Henthorn and Scott Mitchell of the University of Oklahoma Health Sciences Center Flow Cytometry and Imaging Core for their assistance in FACS data collection ...
doi:10.1186/1476-4598-13-103
pmid:24885928
pmcid:PMC4030036
fatcat:bxaqaf2k5rbgppyumbcbnqy77m
Neurotoxin-mediated potent activation of the axon degeneration regulator SARM1
2021
eLife
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Here, we report a novel activator of SARM1, a metabolite of the pesticide and neurotoxin vacor. ...
We present the crystal structure the Drosophila SARM1 regulatory domain complexed with this activator, the vacor metabolite VMN, which as the most potent activator yet know is likely to support drug development ...
Acknowledgments We thank members of the Coleman lab, Kobe lab, Prof James Fawcett and Prof Nadia Raffaelli for useful discussions. ...
doi:10.7554/elife.72823
pmid:34870595
pmcid:PMC8758145
fatcat:q72jexjt4bgrphp2wwb3la5smy
Anther dehiscence is regulated by gibberellic acid in yellow lupine (Lupinus luteus L.)
2021
BMC Plant Biology
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The results also suggest that GA3 controls LlGAMYB expression via an LlMIR159-dependent pathway. ...
The expression profile of genes varied over time, with the most intense mRNA accumulation in the phases prior to or at the time of anther opening. ...
with the preparation of ultratinsections for microscopy experiments. ...
doi:10.1186/s12870-021-03085-4
fatcat:ajkzpjzy2zahdgfu3q3td6ropq
An invertebrate smooth muscle with striated muscle myosin filaments
2015
Proceedings of the National Academy of Sciences of the United States of America
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Here we have studied the structure of myosin filaments from the smooth muscles of the human parasite Schistosoma mansoni. ...
The structure of the filaments in smooth muscles is also different from that in striated muscles. ...
This work was supported by National Institutes of Health Grants R01 AR034711 (to R.C.) and P01 HL059408 (to D. Warshaw), and a grant from the Howard Hughes Medical Institute (to R.P.). ...
doi:10.1073/pnas.1513439112
pmid:26443857
pmcid:PMC4620896
fatcat:hxgdxn4mkjcerl5u4ks2tjai3q
Runx2+ Niche Cells Maintain Incisor Mesenchymal Tissue Homeostasis through IGF Signaling
2020
Cell Reports
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Stem cell niches provide a microenvironment to support the self-renewal and multi-lineage differentiation of stem cells. ...
This Runx2-mediated IGF signaling is crucial for regulating the MSC niche and maintaining tissue homeostasis to support continuous growth of the adult mouse incisor, providing a model for analysis of the ...
Bridget Samuels for critical reading of the manuscript. We thank USC Libraries Bioinformatics Service for assisting with data analysis. ...
doi:10.1016/j.celrep.2020.108007
pmid:32783935
pmcid:PMC7461627
fatcat:526vwdj4mrej5iduznnvpinsya
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