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Dissecting protein loops with a statistical scalpel suggests a functional implication of some structural motifs

Leslie Regad, Juliette Martin, Anne-Claude Camproux
2011 BMC Bioinformatics  
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

Bianca C. Bernardo, Daniele Belluoccio, Lynn Rowley, Christopher B. Little, Uwe Hansen, John F. Bateman
2011 Journal of Biological Chemistry  
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

Sanghee Lim, Nicole Hermance, Tenny Mudianto, Hatim M. Mustaly, Ian Paolo Morelos Mauricio, Marc A. Vittoria, Ryan J. Quinton, Brian W. Howell, Hauke Cornils, Amity L. Manning, Neil J. Ganem
2019 Nature Communications  
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

Bauyrzhan Smailov, Sanzhar Alybayev, Izat Smekenov, Aibek Mursalimov, Murat Saparbaev, Dos Sarbassov, Amangeldy Bissenbaev
2020 Frontiers in Cell and Developmental Biology  
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

Chia-Feng Liu, Véronique Lefebvre
2015 Nucleic Acids Research  
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

Koichi Fujisawa, Shuji Terai, Toshihiko Matsumoto, Taro Takami, Naoki Yamamoto, Hiroshi Nishina, Makoto Furutani-Seiki, Isao Sakaida, Antonio Paolo Beltrami
2015 PLoS ONE  
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

Stacey E. Wahl, Brent H. Wyatt, Stephen D. Turner, Amanda J. G. Dickinson
2018 BMC Genomics  
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

Andrew M. Guarnaccia, Sara Rose Krivoshik, John S. Sparks, David F. Gruber, Jean P. Gaffney
2021 Frontiers in Marine Science  
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

L. Mohazab, L. Koivisto, G. Jiang, L. Kytomaki, M. Haapasalo, G. R. Owen, C. Wiebe, Y. Xie, K. Heikinheimo, T. Yoshida, C. E. Smith, J. Heino (+3 others)
2012 Journal of Cell Science  
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

Giuseppe Dionisio, Mohammad Uddin, Eva Vincze
2018 Proteomes  
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

Nathaniel Weygant, Dongfeng Qu, William L Berry, Randal May, Parthasarathy Chandrakesan, Daniel B Owen, Sripathi M Sureban, Naushad Ali, Ralf Janknecht, Courtney W Houchen
2014 Molecular Cancer  
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

Andrea Loreto, Carlo Angeletti, Weixi Gu, Andrew Osborne, Bart Nieuwenhuis, Jonathan Gilley, Peter Arthur-Farraj, Elisa Merlini, Adolfo Amici, Zhenyao Luo, Lauren Hartley-Tassell, Thomas Ve (+5 others)
2021 eLife  
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.)

Katarzyna Marciniak, Krzysztof Przedniczek
2021 BMC Plant Biology  
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

Guidenn Sulbarán, Lorenzo Alamo, Antonio Pinto, Gustavo Márquez, Franklin Méndez, Raúl Padrón, Roger Craig
2015 Proceedings of the National Academy of Sciences of the United States of America  
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

Shuo Chen, Junjun Jing, Yuan Yuan, Jifan Feng, Xia Han, Quan Wen, Thach-Vu Ho, Chelsea Lee, Yang Chai
2020 Cell Reports  
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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