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- Author:
- Molina-Franky, Jessica; Plaza, David Fernando; Merali, Carmen; Merali, Salim; Barrero, Carlos; Arévalo-Pinzón, Gabriela; Patarroyo, Manuel Elkin; Patarroyo, Manuel Alfonso
- Source:
- Journal of proteomics 2021 v.231 pp. 104002
- ISSN:
- 1874-3919
- Subject:
- binding proteins, etc ; Plasmodium falciparum; binding capacity; erythrocyte membrane; erythrocytes; ligands; liquid chromatography; membrane proteins; parasites; pathogenesis; receptors; synthetic peptides; tandem mass spectrometry; therapeutics; Show all 14 Subjects
- Abstract:
- ... Successful Plasmodium falciparum invasion of red blood cells includes the orderly execution of highly specific receptor-ligand molecular interactions between the parasite's proteins and the red blood cell membrane proteins. There is a growing need for elucidating receptor-ligand pairings, which will help in understanding the parasite's biology and provide the fundamental basis for developing proph ...
- DOI:
- 10.1016/j.jprot.2020.104002
-
https://dx.doi.org/10.1016/j.jprot.2020.104002
- Author:
- Malik, Ahmed M.; Barmada, Sami J.
- Source:
- Molecular cell 2020 v.79 no.3 pp. 362-364
- ISSN:
- 1097-2765
- Subject:
- RNA-binding proteins, etc ; condensates; granules; stress response; Show all 4 Subjects
- Abstract:
- ... In this issue of Molecular Cell, Wang et al. (2020) investigate stress-induced nuclear condensates of the RNA-binding protein TDP-43, uncovering a protective function for these granules as well as an RNA-dependent mechanism for scaffolding them. ...
- DOI:
- 10.1016/j.molcel.2020.07.018
-
http://dx.doi.org/10.1016/j.molcel.2020.07.018
- Author:
- Guilhas, Baptiste; Walter, Jean-Charles; Rech, Jerome; David, Gabriel; Walliser, Nils Ole; Palmeri, John; Mathieu-Demaziere, Celine; Parmeggiani, Andrea; Bouet, Jean-Yves; Le Gall, Antoine; Nollmann, Marcelo
- Source:
- Molecular cell 2020 v.79 no.2 pp. 293-303.e4
- ISSN:
- 1097-2765
- Subject:
- DNA-binding proteins, etc ; DNA; bacteria; condensates; liquids; Show all 5 Subjects
- Abstract:
- ... Liquid-liquid phase-separated (LLPS) states are key to compartmentalizing components in the absence of membranes; however, it is unclear whether LLPS condensates are actively and specifically organized in the subcellular space and by which mechanisms. Here, we address this question by focusing on the ParABS DNA segregation system, composed of a centromeric-like sequence (parS), a DNA-binding prote ...
- DOI:
- 10.1016/j.molcel.2020.06.034
-
http://dx.doi.org/10.1016/j.molcel.2020.06.034
- Author:
- Shukla, Tarjani N.; Song, Jane; Campbell, Zachary T.
- Source:
- RNA biology 2020 v.17 no.4 pp. 417-424
- ISSN:
- 1555-8584
- Subject:
- RNA-binding proteins, etc ; messenger RNA; oligonucleotides; therapeutics; Show all 4 Subjects
- Abstract:
- ... mRNA function is controlled by RNA-binding proteins. The specificity of RNA-binding factors for their targets is critical in that it enables all subsequent regulation. Despite widespread recognition of the pervasive role RNA-binding proteins play in development and disease, they remain challenging to target with small molecules. A renaissance in RNA therapeutics has led to the identification of mo ...
- DOI:
- 10.1080/15476286.2020.1717059
-
http://dx.doi.org/10.1080/15476286.2020.1717059
- Author:
- Uddin, Mohi; Shibata, Hideshi
- Source:
- Anatomia, histologia, embryologia 2020 v.49 no.1 pp. 150-156
- ISSN:
- 0340-2096
- Subject:
- calcium-binding proteins, etc ; cortex; immunohistochemistry; neurons; rabbits; Show all 5 Subjects
- Abstract:
- ... The rabbit midcingulate cortex that enclosed four cortical areas was immunohistochemically studied using a calcium‐binding protein, parvalbumin, as a neurochemical marker. The distribution of parvalbumin‐immunopositive somata and fibres was similar across all four areas, where they were present mainly in layers 2/3 and 5. However, there were a slightly greater number of the immunopositive structur ...
- DOI:
- 10.1111/ahe.12503
-
http://dx.doi.org/10.1111/ahe.12503
- Author:
- Chen, Fan; Keleş, Sündüz
- Source:
- Genome biology 2020 v.21 no.1 pp. 139
- ISSN:
- 1474-760X
- Subject:
- RNA-binding proteins, etc ; sequence analysis; transcription (genetics); transcriptomics; Show all 4 Subjects
- Abstract:
- ... Advances in high-throughput profiling of RNA-binding proteins (RBPs) have resulted inCLIP-seq datasets coupled with transcriptome profiling by RNA-seq. However, analysis methods that integrate both types of data are lacking. We describe SURF, Statistical Utility for RBP Functions, for integrative analysis of large collections of CLIP-seq and RNA-seq data. We demonstrate SURF’s ability to accuratel ...
- DOI:
- 10.1186/s13059-020-02039-7
-
https://dx.doi.org/10.1186/s13059-020-02039-7
- Author:
- Nagpal, Harsh; Fierz, Beat
- Source:
- Journal of molecular biology 2020 pp. 166676
- ISSN:
- 0022-2836
- Subject:
- binding proteins, etc ; chromosome segregation; epigenetics; eukaryotic cells; kinetochores; mitosis; nucleosomes; Show all 7 Subjects
- Abstract:
- ... The centromere is an essential chromatin domain required for kinetochore recruitment and chromosome segregation in eukaryotes. To perform this role, centro-chromatin adopts a unique structure that provides access to kinetochore proteins and maintains stability under tension during mitosis. This is achieved by the presence of nucleosomes containing the H3 variant CENP-A, which also acts as the epig ...
- DOI:
- 10.1016/j.jmb.2020.10.010
-
https://dx.doi.org/10.1016/j.jmb.2020.10.010
- Author:
- Siemian, Justin N.; Sarsfield, Sarah; Aponte, Yeka
- Source:
- Physiology & behavior 2020 v.221 pp. 112912
- ISSN:
- 0031-9384
- Subject:
- calcium-binding proteins, etc ; electrophysiology; hypothalamus; neurons; neurotransmitters; phenotype; Show all 6 Subjects
- Abstract:
- ... Throughout the central nervous system, neurons expressing the calcium-binding protein parvalbumin have been typically classified as GABAergic with fast-spiking characteristics. However, new methods that allow systematic characterization of the cytoarchitectural organization, connectivity, activity patterns, neurotransmitter nature, and function of genetically-distinct cell types have revealed popu ...
- DOI:
- 10.1016/j.physbeh.2020.112912
-
https://dx.doi.org/10.1016/j.physbeh.2020.112912
- Author:
- Sternburg, Erin L.; Karginov, Fedor V.
- Source:
- Trends in biochemical sciences 2020 v.45 no.7 pp. 593-603
- ISSN:
- 0968-0004
- Subject:
- RNA-binding proteins, etc ; cell biology; computational methodology; messenger RNA; Show all 4 Subjects
- Abstract:
- ... RNA-binding proteins (RBPs) play crucial roles in almost all aspects of cellular biology. RBP binding at specific target sites impacts expression of functionally coordinated sets of mRNAs and involves combinatorial and dynamic interactions with other RBPs. The complexity and principles of these regulatory networks are only beginning to be understood. In recent years, transcriptome-wide experimenta ...
- DOI:
- 10.1016/j.tibs.2020.03.005
-
https://dx.doi.org/10.1016/j.tibs.2020.03.005
- Author:
- Garriga-Canut, Mireia; Yang, Jae-Seong; Preusser, Friedrich; Speroni, Silvia; Gili, Maria; Maurer, Sebastian P.
- Source:
- Methods 2020 v.178 pp. 19-32
- ISSN:
- 1046-2023
- Subject:
- RNA-binding proteins, etc ; RNA; amino acid sequences; genes; mutation; screening; Show all 6 Subjects
- Abstract:
- ... Understanding which proteins and RNAs directly interact is crucial for revealing cellular mechanisms of gene regulation. Efficient methods allowing to detect RNA-protein interactions and dissect the underlying molecular origin for RNA-binding protein (RBP) specificity are in high demand. The recently developed recombination-Y3H screening (rec-Y3H) enabled many-by-many detection of interactions bet ...
- DOI:
- 10.1016/j.ymeth.2019.09.002
-
https://dx.doi.org/10.1016/j.ymeth.2019.09.002
- Author:
- Corley, Meredith; Burns, Margaret C.; Yeo, Gene W.
- Source:
- Molecular cell 2020 v.78 no.1 pp. 9-29
- ISSN:
- 1097-2765
- Subject:
- RNA-binding proteins, etc ; RNA; computer software; hydrogen bonding; prediction; Show all 5 Subjects
- Abstract:
- ... RNA-binding proteins (RBPs) comprise a large class of over 2,000 proteins that interact with transcripts in all manner of RNA-driven processes. The structures and mechanisms that RBPs use to bind and regulate RNA are incredibly diverse. In this review, we take a look at the components of protein-RNA interaction, from the molecular level to multi-component interaction. We first summarize what is kn ...
- DOI:
- 10.1016/j.molcel.2020.03.011
- PubMed:
- 32243832
- PubMed Central:
- PMC7202378
-
https://dx.doi.org/10.1016/j.molcel.2020.03.011
- Author:
- Shinoda, Kouki; Suda, Akiyo; Otonari, Kenko; Futaki, Shiroh; Imanishi, Miki
- Source:
- Chemical communications 2020 v.56 no.9 pp. 1365-1368
- ISSN:
- 1364-548X
- Subject:
- RNA-binding proteins, etc ; RNA; chemical compounds; demethylation; methylation; methyltransferases; Show all 6 Subjects
- Abstract:
- ... New methods to control local RNA methylation are needed to elucidate the function of individual m⁶A. Here, fusion proteins between the programmable RNA binding protein PUF and the m⁶A demethylase FTO or METTL14 methyltransferase were designed. FTO-PUFs and METTL14-PUFs showed sequence-specific RNA demethylation and methylation activities, respectively. ...
- DOI:
- 10.1039/c9cc09298f
-
http://dx.doi.org/10.1039/c9cc09298f
- Author:
- Parfenova, Iuliia; Barral, Yves
- Source:
- Molecular cell 2020 v.77 no.2 pp. 203-204
- ISSN:
- 1097-2765
- Subject:
- RNA-binding proteins, etc ; meiosis; nutrient availability; prions; sporulation; starvation; yeasts; Show all 7 Subjects
- Abstract:
- ... Chakravarty et al. (2019) and Itakura et al. (2019) report that the yeast RNA-binding protein Vts1 can convert into the [SMAUG⁺] prion state and delay meiosis commitment in response to starvation. It enables budding yeast to optimize their sporulation efficiency depending on how quickly nutrient availability fluctuates in their environment. ...
- DOI:
- 10.1016/j.molcel.2019.12.017
-
https://dx.doi.org/10.1016/j.molcel.2019.12.017
- Author:
- Zhang, Minzhe; Wang, Tao; Xiao, Guanghua; Xie, Yang
- Source:
- Genes 2020 v.11 no.1
- ISSN:
- 2073-4425
- Subject:
- RNA-binding proteins, etc ; biogenesis; circular RNA; messenger RNA; Show all 4 Subjects
- Abstract:
- ... Circular RNAs are a special type of RNA that has recently attracted a lot of research interest in studying its formation and function. RNA binding proteins (RBPs) that bind circRNAs are important in these processes, but have been relatively less studied. CLIP-Seq technology has been invented and applied to profile RBP-RNA interactions on the genome-wide scale. While mRNAs are usually the focus of ...
- DOI:
- 10.3390/genes11010054
-
https://dx.doi.org/10.3390/genes11010054
- Author:
- de la Ballina, Laura R.; Munson, Michael J.; Simonsen, Anne
- Source:
- Journal of molecular biology 2020 v.432 no.1 pp. 135-159
- ISSN:
- 0022-2836
- Subject:
- binding proteins, etc ; autophagy; endosomes; eukaryotic cells; lipids; lysosomes; Show all 6 Subjects
- Abstract:
- ... Eukaryotic cells have the capacity to degrade intracellular components through a lysosomal degradation pathway called macroautophagy (henceforth referred to as autophagy) in which superfluous or damaged cytosolic entities are engulfed and separated from the rest of the cell constituents into double membraned vesicles known as autophagosomes. Autophagosomes then fuse with endosomes and lysosomes, w ...
- DOI:
- 10.1016/j.jmb.2019.05.051
-
https://dx.doi.org/10.1016/j.jmb.2019.05.051
- Author:
- Zhang, Jun; Chen, Qingcai; Liu, Bin
- Source:
- Journal of molecular biology 2020 v.432 no.22 pp. 5860-5875
- ISSN:
- 0022-2836
- Subject:
- DNA-binding proteins; RNA-binding proteins, etc ; DNA; RNA; Solanum lycopersicum; artificial intelligence; gene expression; genome; models; prediction; tomatoes; Show all 11 Subjects
- Abstract:
- ... DNA-binding protein (DBP) and RNA-binding protein (RBP) are playing crucial roles in gene expression. Accurate identification of them is of great significance, and accurately computational predictors are highly required. In previous studies, DBP recognition and RBP recognition were treated as two separate tasks. Because the functional and structural similarities between DBPs and RBPs are high, the ...
- DOI:
- 10.1016/j.jmb.2020.09.008
-
https://dx.doi.org/10.1016/j.jmb.2020.09.008
- Author:
- Qiu, Jiajun; Bernhofer, Michael; Heinzinger, Michael; Kemper, Sofie; Norambuena, Tomas; Melo, Francisco; Rost, Burkhard
- Source:
- Journal of molecular biology 2020 v.432 no.7 pp. 2428-2443
- ISSN:
- 0022-2836
- Subject:
- DNA-binding proteins; RNA-binding proteins, etc ; DNA; RNA; amino acid sequences; artificial intelligence; computer simulation; neural networks; prediction; protein content; Show all 10 Subjects
- Abstract:
- ... The intricate details of how proteins bind to proteins, DNA, and RNA are crucial for the understanding of almost all biological processes. Disease-causing sequence variants often affect binding residues. Here, we described a new, comprehensive system of in silico methods that take only protein sequence as input to predict binding of protein to DNA, RNA, and other proteins. Firstly, we needed to de ...
- DOI:
- 10.1016/j.jmb.2020.02.026
-
https://dx.doi.org/10.1016/j.jmb.2020.02.026
- Author:
- Zhou, Yuanyuan; He, Juyun; Su, Ningning; Masagounder, Karthik; Xu, Minglei; Chen, Leling; Liu, Qingying; Ye, Huaqun; Sun, Zhenzhu; Ye, Chaoxia
- Source:
- Aquaculture 2021 v.532 pp. 735962
- ISSN:
- 0044-8486
- Subject:
- binding proteins, etc ; Cyprinus carpio; aspartate-ammonia ligase; bioavailability; blood serum; cysteine; cysteine dioxygenase; diet; essential amino acids; feed conversion; fish; free amino acids; gene expression; genes; growth performance; liver; messenger RNA; methionine; methionine adenosyltransferase; methionine synthase; muscles; protein synthesis; rapamycin; regression analysis; ribosomal proteins; taurine; Show all 26 Subjects
- Abstract:
- ... In this trial, nine diets were formulated to investigate the effects of DL-methionine (DL-Met) and a methionine hydroxy analogue (MHA-Ca) on growth, amino acid profiles and the expression of genes related to taurine and protein synthesis in common carp. The basal diet was prepared without methionine supplementation and the other diets were formulated with 0.1%, 0.2%, 0.3% and 0.4% of DL-Met or MHA ...
- DOI:
- 10.1016/j.aquaculture.2020.735962
-
https://dx.doi.org/10.1016/j.aquaculture.2020.735962
- Author:
- Terawaki, Kiyoshi; Saegusa, Yayoi; Sekiguchi, Kyoji; Shimizu, Tomofumi; Takiyama, Mikina; Matsumoto, Takashi; Iizuka, Seiichi; Matsumoto, Chinami; Motoyama, Fukuhito
- Source:
- Journal of ethnopharmacology 2021 v.265 pp. 113288
- ISSN:
- 0378-8741
- Subject:
- binding proteins, etc ; adenocarcinoma; animal models; antagonists; cell culture; diet; embryo implantation; endometrium; gene expression; human cell lines; human diseases; interleukin-11; leukemia inhibitory factor; liquid chromatography; mechanism of action; messenger RNA; progesterone; prostaglandin synthase; protein synthesis; rats; sesame oil; somatomedins; subcutaneous injection; tandem mass spectrometry; traditional medicine; Japan; Show all 26 Subjects
- Abstract:
- ... Tokishakuyakusan (TSS) is a Kampo medicine that is prescribed for the treatment of infertility in Japan. However, its precise mechanism of action remains unclear.Leukemia inhibitory factor (LIF) in the endometrium plays an indispensable role in embryo implantation and is linked to infertility or implantation failure. Previously, we demonstrated that TSS ameliorated implantation failure induced by ...
- DOI:
- 10.1016/j.jep.2020.113288
-
https://dx.doi.org/10.1016/j.jep.2020.113288
- Author:
- Humphries, Fiachra; Fitzgerald, Katherine A.
- Source:
- Molecular cell 2019 v.76 no.1 pp. 8-10
- ISSN:
- 1097-2765
- Subject:
- DNA-binding proteins, etc ; DNA; immunity; Show all 3 Subjects
- Abstract:
- ... In a recently published article in Science, Cao and colleagues (Wang et al., 2019) identify hnRNPA2B1 as a new DNA-binding protein that initiates and amplifies antiviral immunity, unveiling a new facet of DNA recognition in the nucleus. ...
- DOI:
- 10.1016/j.molcel.2019.09.021
-
https://dx.doi.org/10.1016/j.molcel.2019.09.021