scholarly journals U5 snRNA-specific proteins studies, RNA-protein interaction, assembly of the spliceosomal Sm complex, and function implications of splicing in Cyanidioschyson merolae

2018 ◽  
Author(s):  
Fatimat Almentina Ramos Shidi
Keyword(s):  
Protein Interaction ◽  
Specific Proteins ◽  
And Function ◽  
U5 Snrna

scholarly journals Protein-Protein and Protein-RNA Contacts both Contribute to the 15.5K-Mediated Assembly of the U4/U6 snRNP and the Box C/D snoRNPs

2006 ◽  
Vol 26 (13) ◽  
pp. 5146-5154 ◽  
Author(s):  
Annemarie Schultz ◽  
Stephanie Nottrott ◽  
Nicholas James Watkins ◽  
Reinhard Lührmann
Keyword(s):  
Binding Site ◽  
Protein Interaction ◽  
Protein Interactions ◽  
Protein Protein Interactions ◽  
Hierarchical Assembly ◽  
Protein Protein Interaction ◽  
Rnp Complex ◽  
Specific Proteins ◽  
And Function ◽  
Direct Recognition

ABSTRACT The k-turn-binding protein 15.5K is unique in that it is essential for the hierarchical assembly of three RNP complexes distinct in both composition and function, namely, the U4/U6 snRNP, the box C/D snoRNP, and the RNP complex assembled on the U3 box B/C motif. 15.5K interacts with the cognate RNAs via an induced fit mechanism, which results in the folding of the surrounding RNA to create a binding site(s) for the RNP-specific proteins. However, it is possible that 15.5K also mediates RNP formation via protein-protein interactions with the complex-specific proteins. To investigate this possibility, we created a series of 15.5K mutations in which the surface properties of the protein had been changed. We assessed their ability to support the formation of the three distinct RNP complexes and found that the formation of each RNP requires a distinct set of regions on the surface of 15.5K. This implies that protein-protein contacts are essential for RNP formation in each complex. Further supporting this idea, direct protein-protein interaction could be observed between hU3-55K and 15.5K. In conclusion, our data suggest that the formation of each RNP involves the direct recognition of specific elements in both 15.5K protein and the specific RNA.

scholarly journals Classification of Nonenzymatic Homologues of Protein Kinases

2009 ◽  
Vol 2009 ◽  
pp. 1-17 ◽  
Author(s):  
K. Anamika ◽  
K. R. Abhinandan ◽  
K. Deshmukh ◽  
N. Srinivasan
Keyword(s):  
Protein Kinase ◽  
Protein Kinases ◽  
Protein Interaction ◽  
Transmembrane Domain ◽  
Homo Sapiens ◽  
Interaction Domain ◽  
Protein Protein Interaction ◽  
Domain 3 ◽  
Eukaryotic Organisms ◽  
And Function

Protein Kinase-Like Non-kinases (PKLNKs), which are closely related to protein kinases, lack the crucial catalytic aspartate in the catalytic loop, and hence cannot function as protein kinase, have been analysed. Using various sensitive sequence analysis methods, we have recognized 82 PKLNKs from four higher eukaryotic organisms, namely,Homo sapiens,Mus musculus,Rattus norvegicus, andDrosophila melanogaster. On the basis of their domain combination and function, PKLNKs have been classified mainly into four categories: (1) Ligand binding PKLNKs, (2) PKLNKs with extracellular protein-protein interaction domain, (3) PKLNKs involved in dimerization, and (4) PKLNKs with cytoplasmic protein-protein interaction module. While members of the first two classes of PKLNKs have transmembrane domain tethered to the PKLNK domain, members of the other two classes of PKLNKs are cytoplasmic in nature. The current classification scheme hopes to provide a convenient framework to classify the PKLNKs from other eukaryotes which would be helpful in deciphering their roles in cellular processes.

scholarly journals Estrogen-related receptor alpha directly binds to p53 and cooperatively controls colon cancer growth through the regulation of mitochondrial biogenesis and function

2020 ◽  
Vol 8 (1) ◽  
Author(s):  
Humberto De Vitto ◽  
Joohyun Ryu ◽  
Ali Calderon-Aparicio ◽  
Josh Monts ◽  
Raja Dey ◽  
...  
Keyword(s):  
Colon Cancer ◽  
Protein Interaction ◽  
Mitochondrial Biogenesis ◽  
P53 Protein ◽  
Selection Criterion ◽  
In Vivo Studies ◽  
Clear Understanding ◽  
Protein Protein Interaction ◽  
Mutational Status ◽  
And Function

Abstract Background Of the genes that control mitochondrial biogenesis and function, ERRα emerges as a druggable metabolic target to be exploited for cancer therapy. Of the genes mutated in cancer, TP53 remains the most elusive to target. A clear understanding of how mitochondrial druggable targets can be accessed to exploit the underlying mechanism(s) explaining how p53-deficient tumors promote cell survival remains elusive. Methods We performed protein-protein interaction studies to demonstrate that ERRα binds to p53. Moreover, we used gene silencing and pharmacological approaches in tandem with quantitative proteomics analysis by SWATH-MS to investigate the role of the ERRα/p53 complex in mitochondrial biogenesis and function in colon cancer. Finally, we designed in vitro and in vivo studies to investigate the possibility of targeting colon cancers that exhibit defects in p53. Results Here, we are the first to identify a direct protein-protein interaction between the ligand-binding domain (LBD) of ERRα and the C-terminal domain (CTD) of p53. ERRα binds to p53 regardless of p53 mutational status. Furthermore, we show that the ERRα and p53 complex cooperatively control mitochondrial biogenesis and function. Targeting ERRα creates mitochondrial metabolic stresses, such as production of reactive oxygen species (ROS) and mitochondrial membrane permeabilization (MMP), leading to a greater cytotoxic effect that is dependent on the presence of p53. Pharmacological inhibition of ERRα impairs the growth of p53-deficient cells and of p53 mutant patient-derived colon xenografts (PDX). Conclusions Therefore, our data suggest that by using the status of the p53 protein as a selection criterion, the ERRα/p53 transcriptional axis can be exploited as a metabolic vulnerability.

scholarly journals An optimized optogenetic clustering tool for probing protein interaction and function

2014 ◽  
Vol 5 (1) ◽  
Author(s):  
Amir Taslimi ◽  
Justin D. Vrana ◽  
Daniel Chen ◽  
Sofya Borinskaya ◽  
Bruce J. Mayer ◽  
...  
Keyword(s):  
Protein Interaction ◽  
And Function

Costameres, focal adhesions, and cardiomyocyte mechanotransduction

2005 ◽  
Vol 289 (6) ◽  
pp. H2291-H2301 ◽  
Author(s):  
Allen M. Samarel
Keyword(s):  
Growth Factor ◽  
Focal Adhesions ◽  
Growth Factor Signaling ◽  
Cellular Mechanisms ◽  
Growth And Survival ◽  
Specific Proteins ◽  
And Function ◽  
Cytoskeletal Elements ◽  
Biochemical Signals ◽  
Cellular Components

Mechanotransduction refers to the cellular mechanisms by which load-bearing cells sense physical forces, transduce the forces into biochemical signals, and generate appropriate responses leading to alterations in cellular structure and function. This process affects the beat-to-beat regulation of cardiac performance but also affects the proliferation, differentiation, growth, and survival of the cellular components that comprise the human myocardium. This review focuses on the experimental evidence indicating that the costamere and its structurally related structure the focal adhesion complex are critical cytoskeletal elements involved in cardiomyocyte mechanotransduction. Biochemical signals originating from the extracellular matrix-integrin-costameric protein complex share many common features with those signals generated by growth factor receptors. The roles of key regulatory kinases and other muscle-specific proteins involved in mechanotransduction and growth factor signaling are discussed, and issues requiring further study in this field are outlined.

scholarly journals A toolbox of nanobodies developed and validated for diverse neuroscience research applications

2019 ◽  
Author(s):  
Jie-Xian Dong ◽  
Yongam Lee ◽  
Michael Kirmiz ◽  
Stephanie Palacio ◽  
Camelia Dumitras ◽  
...  
Keyword(s):  
Biomedical Research ◽  
Mammalian Cells ◽  
Structure And Function ◽  
Mammalian Brain ◽  
Tissue Penetration ◽  
Brain Neurons ◽  
Neuroscience Research ◽  
Form Part ◽  
Specific Proteins ◽  
And Function

SUMMARYNanobodies (nAbs) are small, minimal antibodies that have distinct attributes that make them uniquely suited for certain biomedical research, diagnostic and therapeutic applications. Prominent uses include as intracellular antibodies or intrabodies to bind and deliver cargo to specific proteins and/or subcellular sites within cells, and as nanoscale immunolabels for enhanced tissue penetration and improved spatial imaging resolution. Here, we report the generation and validation of nAbs against a set of proteins prominently expressed at specific subcellular sites in brain neurons. We describe a novel hierarchical validation pipeline to systematically evaluate nAbs isolated by phage display for effective and specific use as intrabodies and immunolabels in mammalian cells including brain neurons. These nAbs form part of a robust toolbox for targeting proteins with distinct and highly spatially-restricted subcellular localization in mammalian brain neurons, allowing for visualization and/or modulation of structure and function at those sites.

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