scholarly journals LPI-SKF: Predicting lncRNA-Protein Interactions Using Similarity Kernel Fusions

2020 ◽  
Vol 11 ◽  
Author(s):  
Yuan-Ke Zhou ◽  
Jie Hu ◽  
Zi-Ang Shen ◽  
Wen-Ya Zhang ◽  
Pu-Feng Du
Keyword(s):  
Protein Interactions ◽  
Biological Activities ◽  
Receiver Operating Curve ◽  
Cellular Regulation ◽  
Novel Proteins ◽  
Kernel Fusion ◽  
Laplacian Regularized Least Squares ◽  
Functional Mechanisms ◽  
Potential Interactions ◽  
Novel Model

Long non-coding RNAs (lncRNAs) play an important role in serval biological activities, including transcription, splicing, translation, and some other cellular regulation processes. lncRNAs perform their biological functions by interacting with various proteins. The studies on lncRNA-protein interactions are of great value to the understanding of lncRNA functional mechanisms. In this paper, we proposed a novel model to predict potential lncRNA-protein interactions using the SKF (similarity kernel fusion) and LapRLS (Laplacian regularized least squares) algorithms. We named this method the LPI-SKF. Various similarities of both lncRNAs and proteins were integrated into the LPI-SKF. LPI-SKF can be applied in predicting potential interactions involving novel proteins or lncRNAs. We obtained an AUROC (area under receiver operating curve) of 0.909 in a 5-fold cross-validation, which outperforms other state-of-the-art methods. A total of 19 out of the top 20 ranked interaction predictions were verified by existing data, which implied that the LPI-SKF had great potential in discovering unknown lncRNA-protein interactions accurately. All data and codes of this work can be downloaded from a GitHub repository (https://github.com/zyk2118216069/LPI-SKF).

scholarly journals Novel Roles of SH2 and SH3 Domains in Lipid Binding

Cells ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 1191
Author(s):  
Szabolcs Sipeki ◽  
Kitti Koprivanacz ◽  
Tamás Takács ◽  
Anita Kurilla ◽  
Loretta László ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Specific Protein ◽  
Lipid Binding ◽  
Sh2 Domain ◽  
Essential Property ◽  
Cellular Regulation ◽  
Sh3 Domains ◽  
Protein Partners ◽  
Interaction Domains ◽  
Central Paradigm

Signal transduction, the ability of cells to perceive information from the surroundings and alter behavior in response, is an essential property of life. Studies on tyrosine kinase action fundamentally changed our concept of cellular regulation. The induced assembly of subcellular hubs via the recognition of local protein or lipid modifications by modular protein interactions is now a central paradigm in signaling. Such molecular interactions are mediated by specific protein interaction domains. The first such domain identified was the SH2 domain, which was postulated to be a reader capable of finding and binding protein partners displaying phosphorylated tyrosine side chains. The SH3 domain was found to be involved in the formation of stable protein sub-complexes by constitutively attaching to proline-rich surfaces on its binding partners. The SH2 and SH3 domains have thus served as the prototypes for a diverse collection of interaction domains that recognize not only proteins but also lipids, nucleic acids, and small molecules. It has also been found that particular SH2 and SH3 domains themselves might also bind to and rely on lipids to modulate complex assembly. Some lipid-binding properties of SH2 and SH3 domains are reviewed here.

20. Discovery of Novel Proteins Involved the Insulin/IGF-1 Signalling Pathway

2018 ◽  
Author(s):  
David (Wen Xiao) Wei
Keyword(s):  
Protein Interactions ◽  
Mutant Form ◽  
Yeast Two Hybrid ◽  
C Elegans ◽  
Insulin Growth Factor ◽  
Novel Proteins ◽  
Similar Phenotype ◽  
Two Hybrid ◽  
Hsp90 Protein ◽  
Novel Protein

The insulin/insulin growth factor-1 (IGF-1) signalling (IIS) pathway plays a key role in metabolism, growth and development. Though research has elucidated aspects of this pathway, it is not fully characterized or understood. A better understanding of the pathway will give insight into related diseases such as cancer. To discover novel proteins involved in the IIS pathway, the C. elegans worm was used due to the homology its insulin/IGF-1 receptor shares with that of humans.  To identify novel protein interactions with the insulin/IGF-1 receptor, we performed a yeast two-hybrid screen using a library of worm proteins. We found several separate interactions with the worm homolog of the HSP90 protein. To support the involvement of HSP90 in the IIS pathway, we studied the phenotypes of worm strains with a mutant form of HSP90. They showed a similar phenotype to those that have a mutant form of the insulin/IGF-1 receptor, inappropriately entering a developmental stage known as dauer. This strongly suggests the involvement of HSP90 in the IIS pathway. Based on previous research, we hypothesized the interaction between HSP90 and the insulin/IGF-1 receptor may allow it to bind other proteins. Thus, we performed a modified yeast two-hybrid screen to identify proteins which interact with the receptor in the presence of HSP90. The screen identified 15 interactions, many more than with the insulin/IGF-1 receptor alone, supporting this hypothesis. Overall, we provide evidence of a novel interaction with insulin/IGF-1 receptor, suggesting HSP90 may be a potential target for developing therapies for IIS pathway related diseases.

scholarly journals A Bibliometric Analysis of Researches on Flap Endonuclease 1 From 2005 to 2019

2021 ◽  
Author(s):  
Qiaochu Wei ◽  
Jiming Shen ◽  
Dongni Wang ◽  
Xu Han ◽  
Jing Shi ◽  
...  
Keyword(s):  
Bibliometric Analysis ◽  
Protein Interactions ◽  
Cell Biology ◽  
Biological Activities ◽  
The United States ◽  
Dna Metabolism ◽  
Flap Endonuclease 1 ◽  
The Past ◽  
Oncology Research ◽  
Research Frontiers

Abstract Background: Flap endonuclease 1 (FEN1) is a structure-specific nuclease that plays a role in a variety of DNA metabolism processes. FEN1 is important for maintaining genomic stability and regulating cell growth and development. It is associated with the occurrence and development of several diseases, especially cancers. There is a lack of systematic bibliometric analyses focusing on research trends and knowledge structures related to FEN1.Purpose: To analyze hotspots, the current state and research frontiers performed for FEN1 over the past 15 years. Methods: Publications were retrieved from the Web of Science Core Collection (WoSCC) database, analyzing publication dates ranging from 2005 to 2019. VOSviewer1.6.15 and Citespace5.7 R1 were used to perform a bibliometric analysis in terms of countries, institutions, authors, journals and research areas related to FEN1. A total of 421 publications were included in this analysis. Results: Our findings indicated that FEN1 has received more attention and interest from researchers in the past 15 years. Institutes in the United States, specifically the Beckman Research Institute of City of Hope published the most research related to FEN1. SHEN BH，ZHENG L and BAMBARA RA were the most active researchers investigating this endonuclease and most of this research was published in the Journal of Biological Chemistry. The main scientific areas of FEN1 were related to biochemistry, molecular biology，cell biology，genetics and oncology. Research hotspots included biological activities, DNA metabolism mechanisms, protein-protein interactions and gene mutations. Research frontiers included oxidative stress, phosphorylation and tumor progression and treatment. Conclusion: This bibliometric study may aid researchers in the understanding of the knowledge base and research frontiers associated with FEN1. In addition, emerging hotspots for research can be used as the subjects of future studies.

scholarly journals Proanthocyanidins: Oligomeric Structures with Unique Biochemical Properties and Great Therapeutic Promise

2012 ◽  
Vol 7 (3) ◽  
pp. 1934578X1200700 ◽  
Author(s):  
Zhanjie Xu ◽  
Peng Du ◽  
Peter Meiser ◽  
Claus Jacob
Keyword(s):  
Protein Interactions ◽  
Biological Activities ◽  
Antioxidant Properties ◽  
Chemical Properties ◽  
Cancer Chemoprevention ◽  
Biochemical Properties ◽  
Synthetic Methods ◽  
Practical Applications ◽  
Wide Range ◽  
Physical And Chemical

Proanthocyanidins represent a unique class of oligomeric and polymeric secondary metabolites found ubiquitously and in considerable amounts in plants and some algae. These substances exhibit a range of rather surprising physical and chemical properties which, once applied to living organisms, are translated into a multitude of biological activities. The latter include antioxidant properties, cancer chemoprevention, anti-inflammatory and anti-diabetic effects as well as some exceptional, yet highly interesting activities, such as anti-nutritional and antimicrobial activity. Despite the wide range of activities and possible medical/agricultural applications of proanthocyanidins, many questions still remain, including issues related to bioavailability, metabolism and the precise biochemical, extra- and intracellular targets and mode(s) of action of these highly potent materials. Among the various physical and chemical interactions of such substances, strong binding to proteins appears to form the basis of many of their biological activities. Once easy-to-use synthetic methods to produce appropriate quantities of pure proanthocyanidins are available, it will be possible to identify the prime biological targets of these oligomers, study oligomer-protein interactions in more detail and develop possible practical applications in medicine and agriculture.

scholarly journals A review of protein adsorption on bioceramics

2012 ◽  
Vol 2 (3) ◽  
pp. 259-277 ◽  
Author(s):  
Kefeng Wang ◽  
Changchun Zhou ◽  
Youliang Hong ◽  
Xingdong Zhang
Keyword(s):  
Tissue Regeneration ◽  
Protein Interactions ◽  
Tissue Repair ◽  
Cellular Response ◽  
Biological Activities ◽  
Biological Mechanisms ◽  
Hard Tissue ◽  
Coated Layer ◽  
Sense And Respond

Bioceramics, because of its excellent biocompatible and mechanical properties, has always been considered as the most promising materials for hard tissue repair. It is well know that an appropriate cellular response to bioceramics surfaces is essential for tissue regeneration and integration. As the in vivo implants, the implanted bioceramics are immediately coated with proteins from blood and body fluids, and it is through this coated layer that cells sense and respond to foreign implants. Hence, the adsorption of proteins is critical within the sequence of biological activities. However, the biological mechanisms of the interactions of bioceramics and proteins are still not well understood. In this review, we will recapitulate the recent studies on the bioceramic–protein interactions.

scholarly journals Distinct p53 acetylation cassettes differentially influence gene-expression patterns and cell fate

2006 ◽  
Vol 173 (4) ◽  
pp. 533-544 ◽  
Author(s):  
Chad D. Knights ◽  
Jason Catania ◽  
Simone Di Giovanni ◽  
Selen Muratoglu ◽  
Ricardo Perez ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Fate ◽  
Protein Interactions ◽  
Posttranslational Modifications ◽  
Biological Activities ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Gene Expression Profiles ◽  
P53 Gene ◽  
Protein Protein Interactions

The activity of the p53 gene product is regulated by a plethora of posttranslational modifications. An open question is whether such posttranslational changes act redundantly or dependently upon one another. We show that a functional interference between specific acetylated and phosphorylated residues of p53 influences cell fate. Acetylation of lysine 320 (K320) prevents phosphorylation of crucial serines in the NH2-terminal region of p53; only allows activation of genes containing high-affinity p53 binding sites, such as p21/WAF; and promotes cell survival after DNA damage. In contrast, acetylation of K373 leads to hyperphosphorylation of p53 NH2-terminal residues and enhances the interaction with promoters for which p53 possesses low DNA binding affinity, such as those contained in proapoptotic genes, leading to cell death. Further, acetylation of each of these two lysine clusters differentially regulates the interaction of p53 with coactivators and corepressors and produces distinct gene-expression profiles. By analogy with the “histone code” hypothesis, we propose that the multiple biological activities of p53 are orchestrated and deciphered by different “p53 cassettes,” each containing combination patterns of posttranslational modifications and protein–protein interactions.

scholarly journals Proximal Protein Interaction Landscape of RAS Paralogs

Cancers ◽  
2020 ◽  
Vol 12 (11) ◽  
pp. 3326 ◽  
Author(s):  
Benoît Béganton ◽  
Etienne Coyaud ◽  
Estelle M. N. Laurent ◽  
Alain Mangé ◽  
Julien Jacquemetton ◽  
...  
Keyword(s):  
Protein Interaction ◽  
Protein Interactions ◽  
Biological Activities ◽  
Mammalian Species ◽  
Variable Region ◽  
Specific Protein ◽  
Protein Networks ◽  
Ras Proteins ◽  
Wild Type ◽  
Protein Protein Interaction

RAS proteins (KRAS, NRAS and HRAS) are frequently activated in different cancer types (e.g., non-small cell lung cancer, colorectal cancer, melanoma and bladder cancer). For many years, their activities were considered redundant due to their high degree of sequence homology (80% identity) and their shared upstream and downstream protein partners. However, the high conservation of the Hyper-Variable-Region across mammalian species, the preferential activation of different RAS proteins in specific tumor types and the specific post-translational modifications and plasma membrane-localization of each paralog suggest they could ensure discrete functions. To gain insights into RAS proteins specificities, we explored their proximal protein–protein interaction landscapes using the proximity-dependent biotin identification technology (BioID) in Flp-In T-REx 293 cell lines stably transfected and inducibly expressing wild type KRAS4B, NRAS or HRAS. We identified more than 800 high-confidence proximal interactors, allowing us to propose an unprecedented comparative analysis of wild type RAS paralogs protein networks. These data bring novel information on poorly characterized RAS functions, e.g., its putative involvement in metabolic pathways, and on shared as well as paralog-specific protein networks that could partially explain the complexity of RAS functions. These networks of protein interactions open numerous avenues to better understand RAS paralogs biological activities.

scholarly journals A bibliometric analysis of researches on flap endonuclease 1 from 2005 to 2019

BMC Cancer ◽  
2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Qiaochu Wei ◽  
Jiming Shen ◽  
Dongni Wang ◽  
Xu Han ◽  
Jing Shi ◽  
...  
Keyword(s):  
Bibliometric Analysis ◽  
Protein Interactions ◽  
Cell Biology ◽  
Biological Activities ◽  
The United States ◽  
Dna Metabolism ◽  
Flap Endonuclease 1 ◽  
The Past ◽  
Oncology Research ◽  
Research Frontiers

Abstract Background Flap endonuclease 1 (FEN1) is a structure-specific nuclease that plays a role in a variety of DNA metabolism processes. FEN1 is important for maintaining genomic stability and regulating cell growth and development. It is associated with the occurrence and development of several diseases, especially cancers. There is a lack of systematic bibliometric analyses focusing on research trends and knowledge structures related to FEN1. Purpose To analyze hotspots, the current state and research frontiers performed for FEN1 over the past 15 years. Methods Publications were retrieved from the Web of Science Core Collection (WoSCC) database, analyzing publication dates ranging from 2005 to 2019. VOSviewer1.6.15 and Citespace5.7 R1 were used to perform a bibliometric analysis in terms of countries, institutions, authors, journals and research areas related to FEN1. A total of 421 publications were included in this analysis. Results Our findings indicated that FEN1 has received more attention and interest from researchers in the past 15 years. Institutes in the United States, specifically the Beckman Research Institute of City of Hope published the most research related to FEN1. Shen BH, Zheng L and Bambara Ra were the most active researchers investigating this endonuclease and most of this research was published in the Journal of Biological Chemistry. The main scientific areas of FEN1 were related to biochemistry, molecular biology, cell biology, genetics and oncology. Research hotspots included biological activities, DNA metabolism mechanisms, protein-protein interactions and gene mutations. Research frontiers included oxidative stress, phosphorylation and tumor progression and treatment. Conclusion This bibliometric study may aid researchers in the understanding of the knowledge base and research frontiers associated with FEN1. In addition, emerging hotspots for research can be used as the subjects of future studies.

KASH-domain proteins and the cytoskeletal landscapes of the nuclear envelope

2008 ◽  
Vol 36 (6) ◽  
pp. 1368-1372 ◽  
Author(s):  
Maria Schneider ◽  
Angelika A. Noegel ◽  
Iakowos Karakesisoglou
Keyword(s):  
Nuclear Envelope ◽  
Nuclear Membrane ◽  
Mammalian Cells ◽  
Molecular Mechanisms ◽  
Nuclear Architecture ◽  
Membrane Interface ◽  
Novel Proteins ◽  
Evolutionarily Conserved ◽  
Membrane Tethering ◽  
Novel Model

Over the last few years, several novel proteins have been identified that facilitate the physical integration of the nucleus with the cytoplasmic compartment. The majority belong to the evolutionarily conserved KASH [klarsicht/ANC-1 (anchorage 1)/SYNE (synaptic nuclear envelope protein) homology]-domain family, which function primarily as exclusive outer nuclear membrane scaffolds that associate with the cytoskeleton, the centrosome and the motor protein apparatus. In the present paper, we propose a novel model, which may explain why these proteins also determine nuclear architecture. Moreover, we discuss further nuclear membrane-tethering devices, which indicate collectively the presence of specific molecular mechanisms that organize the cytoplasmic–nuclear membrane interface in mammalian cells.

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