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1. A novel platform for peptide-mediated affinity capture and LC-MS/MS identification of host receptors involved in Plasmodium invasion

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

2. TDP-43 Nuclear Bodies: A NEAT Response to Stress?

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

3. ATP-Driven Separation of Liquid Phase Condensates in Bacteria

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

4. Molecular entrapment by RNA: an emerging tool for disrupting protein–RNA interactions in vivo

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

5. Distribution of neuronal structures immunoreactive for parvalbumin in the midcingulate cortex of the rabbit

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

6. SURF: integrative analysis of a compendium of RNA-seq and CLIP-seq datasets highlights complex governing of alternative transcriptional regulation by RNA-binding proteins

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

7. The Elusive Structure of Centro-Chromatin: Molecular Order or Dynamic Heterogenetity?

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

8. Glutamatergic fast-spiking parvalbumin neurons in the lateral hypothalamus: Electrophysiological properties to behavior

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

9. Global Approaches in Studying RNA-Binding Protein Interaction Networks

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

10. rec-Y3H screening allows the detection of simultaneous RNA-protein interface mutations

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

11. How RNA-Binding Proteins Interact with RNA: Molecules and Mechanisms

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

12. Programmable RNA methylation and demethylation using PUF RNA binding proteins

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

13. Yeast Sporulation and [SMAUG+] Prion: Faster Is Not Always Better

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

14. Large-Scale Profiling of RBP-circRNA Interactions from Public CLIP-Seq Datasets

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

15. Lipids and Lipid-Binding Proteins in Selective Autophagy

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

16. iDRBP_MMC: Identifying DNA-Binding Proteins and RNA-Binding Proteins Based on Multi-Label Learning Model and Motif-Based Convolutional Neural Network

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

17. ProNA2020 predicts protein–DNA, protein–RNA, and protein–protein binding proteins and residues from sequence

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

18. Effects of DL-methionine 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 (Cyprinus carpio)

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

19. The ameliorating effects of tokishakuyakusan in a rat model of implantation failure involves endometrial gland leukemia inhibitory factor and decidualization

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

20. hnRNPA2B1: Fueling Antiviral Immunity from the Nucleus

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