• The observation that ELAVL3 is one of several Hu antigens (neuronal-specific RNA-binding proteins) recognized by the anti-Hu serum antibody present in sera from patients with paraneoplastic encephalomyelitis and sensory neuronopathy (PEM/PSN) suggests it has a role in neurogenesis. (nih.gov)
  • Some binding proteins such as neuronal specific RNA-binding proteins, namely NOVA1, control the alternative splicing of a subset of hnRNA by recognizing and binding to a specific sequence in the RNA (YCAY where Y indicates pyrimidine, U or C). These proteins then recruit splicesomal proteins to this target site. (wikipedia.org)
  • A member of the ELAVL protein family, ELAV-like 3 is a neural-specific RNA-binding protein which contains three RNP-type RNA recognition motifs. (nih.gov)
  • RBPs contain various structural motifs, such as RNA recognition motif (RRM), dsRNA binding domain, zinc finger and others. (wikipedia.org)
  • RNA-immunoprecipitation sequencing (RIP-Seq) of the two eIF4A paralogs revealed that eIF4A1 preferentially binds to mRNAs containing terminal oligopyrimidine (TOP) motifs, whose translation is rapidly repressed upon mTOR inhibition. (biorxiv.org)
  • FAST-iCLIP of Poly-C binding protein 2 (PCBP2) showed that PCBP2-bound CU-rich motifs in different topologies to recognize mRNAs and noncoding RNAs with distinct biological functions. (nih.gov)
  • Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. (embl.de)
  • They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. (embl.de)
  • Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. (embl.de)
  • LIM kinase-1 and LIM kinase-2 belong to a small subfamily with a unique combination of 2 N-terminal LIM motifs and a C-terminal protein kinase domain. (thermofisher.com)
  • N protein contains three dynamic disordered regions that house putative transiently-helical binding motifs. (biorxiv.org)
  • 2015) The SRSF1 RNA Recognition Motifs of are strong inhibitors of HIV-1 replication. (fau.edu)
  • The heterogeneous nuclear ribonucleoprotein (hnRNP) C proteins, among the most abundant pre-mRNA-binding proteins in the eukaryotic nucleus, have a single RNP motif RNA-binding domain. (korea.ac.kr)
  • DEC-205 (CD205), a member of the macrophage mannose receptor protein family, is the prototypic endocytic receptor of dendritic cells, whose ligands include phosphorothioated cytosine-guanosine (CpG) oligonucleotides, a motif often seen in bacterial or viral DNA. (uci.edu)
  • WW domain-mediated interactions reveal a spliceosome-associated protein that binds a third class of proline-rich motif: the proline glycine and methionine-rich motif. (embl.de)
  • Although zinc fingers usually function by binding to DNA or RNA, the LIM motif probably mediates protein-protein interactions. (thermofisher.com)
  • FMRP is an RNA binding protein that binds to G quartet forming RNA using its RGG box motif. (auckland.ac.nz)
  • Our results also indicate that the G quartet RNA recognition is not a general feature of the RGG box motif but rather carries some sequence, protein and/or RNA, specificity. (auckland.ac.nz)
  • Using single-molecule tracking, we show that all three Y-complex proteins exhibit three distinct mobilities, including movement through the cytosol and confined motion, predominantly at membrane-proximal sites but also within the cell center. (uni-marburg.de)
  • In this study we have performed a thermodynamic analysis of the interactions between the FMRP RGG box domain and Sc1, an RNA molecule which had been previously shown to be bound with high affinity by both the full-length FMRP and by its RGG box domain. (auckland.ac.nz)
  • Here we combine single-molecule spectroscopy with all-atom simulations to uncover the molecular details that contribute to N protein function. (biorxiv.org)
  • Two C-shaped structures, each formed by a molecule of tau, bound together to form individual rungs along the filament. (alzforum.org)
  • Small-molecule controlled molecular systems also possess tremendous value in bioengineering and biomedical applications: activation of protein function allows the construction of protein switches and biosensor proteins, whereas inhibition of protein function contributes to the development of novel therapeutic agents. (ku.edu)
  • By utilizing structural information obtained through X-ray crystallography or NMR spectroscopy, these tools allow efficient and affordable examination of large small-molecule databases and provide quantitative evaluation of the likelihood that a given protein-ligand interaction occurs. (ku.edu)
  • The primary focus of this thesis is the development of structure-based computer-aided methodologies for designing small-molecule modulators of protein function. (ku.edu)
  • A gene, the basic unit of heredity, is a segment of DNA containing all the information necessary to synthesize a polypeptide (protein) or a functional RNA molecule. (msdmanuals.com)
  • A gene is a segment of DNA that provides the code to construct a protein or RNA molecule. (msdmanuals.com)
  • RNA-binding proteins (often abbreviated as RBPs) are proteins that bind to the double or single stranded RNA in cells and participate in forming ribonucleoprotein complexes. (wikipedia.org)
  • However, since most mature RNA is exported from the nucleus relatively quickly, most RBPs in the nucleus exist as complexes of protein and pre-mRNA called heterogeneous ribonucleoprotein particles (hnRNPs). (wikipedia.org)
  • NcRNAs almost always function as ribonucleoprotein complexes and not as naked RNAs. (wikipedia.org)
  • We have also made available our software through different web servers, such as pyDockWeb for protein-protein docking, pyDockSAXS for the structural prediction of protein complexes using Small-Angle X-ray Scattering (SAXS) data in collaboration with Pau Bernadó (CBS, Montpellier), or OPRA for the identification of RNA-binding residues in proteins. (bsc.es)
  • More efficient identification of correct docking poses, especially in difficult cases such as weak interactions, multi-protein complexes or membrane proteins. (bsc.es)
  • Characterization of the structure and dynamics of protein-RNA complexes is essential for understanding how they function at the molecular level: how these proteins specifically recognize their target RNAs, what are the structure-function relationships, and assess their biological role in regulating gene expression. (umassmed.edu)
  • Characterization of the structure and dynamics of protein-RNA complexes is essential for understanding how they function at the molecular level: how these proteins specifically recognize their target RNAs, what are the structure-function relationships, and to assess their biological role in regulating gene expression. (umassmed.edu)
  • 2021). I'll also discuss how insights into the specificity of RBP condensation open new doors for understanding of protein-RNA complexes as mediators of signalling, disease and evolution. (canal-u.tv)
  • S487, 478 variants in 56 protein complexes. (lu.se)
  • S4191, 4191 single variants in 265 protein complexes, M1707, 1707 multiple variants in 120 protein complexes. (lu.se)
  • Jemimah S, Sekijima M, Gromiha M, ProAffiMuSeq: sequence-based method to predict the binding free energy change of protein-protein complexes upon mutation using functional classification, Bioinformatics;36(6):1725-1730. (lu.se)
  • They are cytoplasmic and nuclear proteins. (wikipedia.org)
  • Immunofluorescent staining of proteins interacting with mutant FUS were localized to cytoplasmic inclusions. (uky.edu)
  • The autophagic pathway constitutively maintains cellular homeostasis by recycling cytoplasmic organelles and proteins, but it is also stimulated by environmental stress conditions, such as starvation, oxidative stress, and the accumulation of misfolded proteins. (mdpi.com)
  • Perilipin 5 (PLIN5) is a lipid-droplet-associated protein that coordinates intracellular lipolysis in highly oxidative tissues and is thought to regulate lipid metabolism in response to phosphorylation by protein kinase A (PKA). (uci.edu)
  • FUS performs a diverse set of cellular functions, including being a major regulator of RNA metabolism. (uky.edu)
  • To understand how protein synthesis is suppressed by mutant FUS mediated defects in RNA metabolism, we examined changes in a well conserved RNA turnover pathway namely: nonsense mediated decay (NMD). (uky.edu)
  • We found both previously predicted, highly conserved residues as well as additional residues in the RBD to be essential for C1 RNA binding. (korea.ac.kr)
  • These results demonstrate that although the RBD is the primary determinant of C1 RNA binding, residues in the C1-C1 interaction domain also influence the RNA binding activity of the protein. (korea.ac.kr)
  • Among others, we have developed software for prediction of protein-protein complex structure by docking simulations, identification of binding sites on protein surfaces, or prediction of hot-spot residues from energy calculations. (bsc.es)
  • This protein, called DksA, coordinates the expression of numerous genes in response to environmental signals. (infectioncontroltoday.com)
  • Interaction annotations are curated by BioGRID and include physical or genetic interactions observed between at least two genes. (yeastgenome.org)
  • Mutations in many genes encoding RNA-binding proteins (RBPs) cause neurologic diseases, and especially the amyotrophic lateral sclerosis (ALS). (canal-u.tv)
  • His research expanded to the mechanism regulating the transcription of cellular and viral genes and characterized the protein SRSF1 as a strong inhibitor of HIV-1 replication. (fau.edu)
  • Whole exome sequencing of patients who experienced severe influenza reveals several genes, including scaffold protein AHNAK, with predicted loss-of-function variants that are also identified in our proteomic analyses. (cdc.gov)
  • The major part of his production relates to variations ranging from protein engineering to effects and mechanisms of variations in protein structures, genes and diseases. (lu.se)
  • The student will be responsible for improving the annotations, especially for the untranslated regions that lie up and downstream of protein coding genes. (lu.se)
  • The main focus of our research is the development and optimization for High-Performing-Computing (HPC) of computational methodology for the structural and energetic characterization of protein interactions at molecular level. (bsc.es)
  • His fields of research comprise RNA-mediated gene silencing processes with a focus on epigenetic phenomena, including studies on RNA-directed DNA methylation, the characterization of virus silencing suppressor proteins, the development of plant bioreactor platforms and viroid research. (degruyter.com)
  • Fabrication and characterization of gold nano-wires templated on virus-like arrays of tobacco mosaic virus coat proteins. (whiterose.ac.uk)
  • Biophysical characterization of these compounds suggests that the majority of them selectively bind to the engineered ChxR variant. (ku.edu)
  • p class=\'abstract\'>Lin28/LIN-28 is a conserved RNA-binding protein that promotes proliferation and pluripotency and can be oncogenic in mammals. (stanford.edu)
  • Marburg virus (MARV) is a lipid-enveloped virus harboring a negative sense RNA genome, which has caused sporadic outbreaks of viral hemorrhagic fever in Sub-Saharan Africa. (uci.edu)
  • FAST-iCLIP of PCBP2 in hepatitis C virus-infected cells enabled a joint analysis of the PCBP2 interactome with host and viral RNAs and their interplay. (nih.gov)
  • The SARS-CoV-2 nucleocapsid (N) protein is an abundant RNA binding protein critical for viral genome packaging, yet the molecular details that underlie this process are poorly understood. (biorxiv.org)
  • Alfalfa mosaic virus genomic RNAs are infectious only when the viral coat protein binds to the RNA 3' termini. (rcsb.org)
  • The results suggest that a uniform, organized 3' conformation, similar to that found on viral RNAs with transfer RNA-like ends, may be essential for replication. (rcsb.org)
  • 2017) Tat is a multifunctional viral protein that modulates cellular gene expression and functions. (fau.edu)
  • This process effectively changes the RNA sequence from that encoded by the genome and extends the diversity of the gene products. (wikipedia.org)
  • Motion, G.B., Howden, A.J.M., Huitema, E. & Jones, S. DNA-binding protein prediction using plant specific support vector machines: validation and application of a new genome annotation tool. (nature.com)
  • Cross-linking immunoprecipitation (CLIP)-seq is a powerful tool for genome-wide interrogation of RNA-protein interactomes, but current CLIP methods are limited by challenging biochemical steps and fail to detect many classes of noncoding and nonhuman RNAs. (nih.gov)
  • During his tenure at FAU, Dr. Caputi has developed novel techniques to study RNA - RNA binding proteins interactions and made important contributions to our understanding of how cellular proteins modulate the replication of the HIV-1 genome. (fau.edu)
  • He has contributed significantly to the state-of-the-art by frequently presenting novel ideas, methods and results and have pioneered several important proof-of-concepts relevant for the project, including the conceptualization of DNA, RNA and protein variation to Variation Ontology (Vihinen, Genome Res . (lu.se)
  • We have extensive whole genome and RNA sequencing data taken from whole samples of flies at three life stages: larva, pupa and adult. (lu.se)
  • Basic sequence-derived (length, molecular weight, isoelectric point) and experimentally-determined (median abundance, median absolute deviation) protein information. (yeastgenome.org)
  • Small heat shock proteins (sHsps) are molecular chaperones that prevent the aggregation of nonnative proteins. (cipsm.de)
  • Selective activation or inhibition of a particular protein function can help elucidate crucial molecular mechanisms and enables important advances in cell biology. (ku.edu)
  • Mauno Vihinen is well-known for his experience and interest in investigating variations and their effects whether they emerge at molecular levels (DNA, RNA protein), in structural context or in the cellular networks and pathways. (lu.se)
  • Alternative splicing is a mechanism by which different forms of mature mRNAs (messengers RNAs) are generated from the same gene. (wikipedia.org)
  • In the glioma cells, EIF5B promotes cell survival by enhancing the translation of several IRES-containing mRNAs including those encoding anti-apoptotic proteins such as XIAP and Bcl-xL [ 4 ]. (techscience.com)
  • Lin28/LIN-28 also bind and regulate many mRNAs in diverse cell types. (stanford.edu)
  • MicroRNAs (miRNAs) are small, noncoding RNAs that bind to the 3' UTR of target mRNAs, and silence gene expression by inducing degradation of target mRNAs or inhibition of protein translation [ 10 ]. (cdc.gov)
  • The recruitment of this machinery results in the production of viroid-derived small RNAs (vd-sRNAs) that mediate RNA degradation and DNA methylation of cognate sequences. (degruyter.com)
  • This was followed-up in his post-doctoral research at UC Santa Cruz (1996-2001) where he was awarded the prestigious Human Frontier Science Program fellowship and published breakthrough work characterizing the key RNA sequences and the cellular proteins that modulate the alternative splicing of the HIV-1 messenger RNA (mRNA). (fau.edu)
  • It has been previously shown that rbf1 pro-apoptotic activity depends on its ability to decrease the level of anti-apoptotic proteins such as the Bcl-2 family protein Buffy. (sdbonline.org)
  • These non-coding RNAs include microRNAs, small interfering RNAs (siRNA), as well as spliceosomal small nuclear RNAs (snRNA). (wikipedia.org)
  • In this project, I will employ biochemical, cell, systems biology and computational approaches to study the relevance of post-transcriptional regulators such as RNA-binding proteins and microRNAs in DDR. (europa.eu)
  • Mechanistically, it was found that ABHD11-AS1 directly binds SART3 (spliceosome associated factor 3, U4/U6 recycling protein). (cdc.gov)
  • They especially play a major role in post-transcriptional control of RNAs, such as: splicing, polyadenylation, mRNA stabilization, mRNA localization and translation. (wikipedia.org)
  • Although RBPs have a crucial role in post-transcriptional regulation in gene expression, relatively few RBPs have been studied systematically.It has now become clear that RNA-RBP interactions play important roles in many biological processes among organisms. (wikipedia.org)
  • This protein functions through post-transcriptional modification of mRNA transcripts by changing the nucleotide content of the RNA. (wikipedia.org)
  • The proposed project explores a previously uncharacterized link between post-transcriptional RNA operons and DDR. (europa.eu)
  • CLIP enabled us to disentangle the principles driving the condensation of TDP-43 on cellular RNAs, which showed that the IDR selectively fine-tunes the RNA binding properties and functions of the protein (Hallegger et al. (canal-u.tv)
  • Neurons are cells with a complex morphology, which maintain their cellular structure through the compartmentalized expression of proteins essential for growth and plasticity. (canal-u.tv)
  • Mammalian Lin28 and C. elegans LIN-28 have been shown to inhibit biogenesis of the conserved cellular differentiation-promoting microRNA let-7 by directly binding to unprocessed let-7 transcripts. (stanford.edu)
  • The Tel2 (also known as Telo2) and Tti1 proteins control the cellular abundance of mammalian PIKKs and are integral components of mTORC1 and mTORC2. (cipsm.de)
  • Mitochondrial porin , also known as the voltage-dependent anion channel (VDAC), is a multi-functional channel protein that shuttles metabolites between the mitochondria and the cytosol and implicated in cellular life and death decisions. (sdbonline.org)
  • His work on RNA binding proteins and SRSF1 has been continuously funded by the NIH and has recently expanded to the study of the role played by multiple RNA binding proteins on cellular gene transcription and T cell development and functions. (fau.edu)
  • In this first study, we utilized immunoprecipitation of wild-type and mutant FUS in the presence and absence of RNase, followed by LC MS/MS. The identified proteins represent those that directly or indirectly interact with FUS, with relatively high affinity that can be pulled down with immunoprecipitation. (uky.edu)
  • To understand how these mutations act, we developed crosslinking and Immunoprecipitation (CLIP) to obtain transcriptome-wide maps of in vivo protein-RNA interactions. (canal-u.tv)
  • We also identified three mutations in the leucine-rich C1-C1 interaction domain near the carboxyl terminus of the protein that both abolished C1 oligomerization and reduced RNA binding. (korea.ac.kr)
  • 2021). Finally, I will exemplify how these advances helped with studies of mutations in the IDR of TDP-43, a protein that is a central factor in ALS and several other neurodegenerative diseases. (canal-u.tv)
  • While DNA polymerases have read-proof abilities with correction facilities, RNA polymerases do not have such qualities whereby errors, i.e. mutations, occur [ 1 ]. (biomedcentral.com)
  • Some of these mutations may allow RNA virus to cross species like SARS and COVID-19 whereby no vaccination existed. (biomedcentral.com)
  • Pertinent information on the bacterial topoisomerases and DNA gyrases, quinolone binding, DNA/RNA synthesis inhibition, cell death in the absence of protein synthesis, specific mutations within the quinolone resistance-determining region, and mutations that lead to altered access to target enzymes (efflux systems) is also highlighted. (cdc.gov)
  • Rodrigues C, Pires D, Ascher D, mmCSM-PPI: predicting the effects of multiple point mutations on protein-protein interactions, Nucleic Acids Res;49(W1):W417-W424. (lu.se)
  • Li M, Petukh M, Alexov E, Panchenko A, Predicting the Impact of Missense Mutations on Protein-Protein Binding Affinity,J Chem Theory Comput:1770-1780. (lu.se)
  • Rodrigues C, Myung Y, Pires D, Ascher D, mCSM-PPI2: predicting the effects of mutations on protein-protein interactions, Nucleic Acids Res. (lu.se)
  • Huang X, Zheng W, Pearce R, Zhang Y, Huang X, Zheng W, Pearce R, Zhang Y, SSIPe: accurately estimating protein-protein binding affinity change upon mutations using evolutionary profiles in combination with an optimized physical energy function, Bioinformatics;36(8):2429-2437. (lu.se)
  • Our data show that the distinct protein interactions of these highly homologous translation factor paralogs shape protein synthesis during mTORC1 inhibition and provide a unique example of the repressive role of a universal translation activator. (biorxiv.org)
  • Protein synthesis, folding, and tertiary and quaternary structure ultimately determine much of the body's structure and function. (msdmanuals.com)
  • Eukaryotic cells express diverse RBPs with unique RNA-binding activity and protein-protein interaction. (wikipedia.org)
  • Diversity enabled eukaryotic cells to utilize RNA exons in various arrangements, giving rise to a unique RNP (ribonucleoprotein) for each RNA. (wikipedia.org)
  • Eukaryotic translation initiation factor (eIF) 4A - a DEAD-box RNA-binding protein - plays an essential role in translation initiation. (biorxiv.org)
  • The findings, reported in the current issue of the journal Cell , suggest that bacteria rely on a key protein in order to properly regulate gene expression -- a process fundamental to cell survival. (infectioncontroltoday.com)
  • miRNAs are small noncoding RNAs that have broad regulatory functions on gene expression. (lu.se)
  • The student will analyze gene expression in a reference-based pipeline using existing RNA sequencing data from larvae, pupae, and adult flies from each of the two host forms. (lu.se)
  • The effect of Tri-Z on virus binding to its cell surface receptor was evaluated in a hemagglutination inhibition (HAI) assay using chicken red cells. (biomedcentral.com)
  • To this end I explored two parallel paths, one to study activation and one to study inhibition of protein functions. (ku.edu)
  • In parallel to these efforts I carried out studies aimed at inhibition of protein function, as exemplified by my project that uses small molecules to disrupt a protein-RNA interaction. (ku.edu)
  • All RBPs bind RNA, however they do so with different RNA-sequence specificities and affinities, which allows the RBPs to be as diverse as their targets and functions. (wikipedia.org)
  • Other than core splicesome complex, RBPs also bind to the sites of Cis-acting RNA elements that influence exons inclusion or exclusion during splicing. (wikipedia.org)
  • These sites are referred to as exonic splicing enhancers (ESEs), exonic splicing silencers (ESSs), intronic splicing enhancers (ISEs) and intronic splicing silencers (ISSs) and depending on their location of binding, RBPs work as splicing silencers or enhancers. (wikipedia.org)
  • Conventional methods of inhibitor design mostly target RNA-processing enzymes and cannot be generalized to the majority of RNA-binding proteins (RBPs). (ku.edu)
  • A transcriptional arrest leads to a strong change in localization and dynamics of YmcA, YlbF and YaaT, supporting their involvement in global RNA degradation. (uni-marburg.de)
  • It is a regulatory mechanism by which variations in the incorporation of the exons into mRNA leads to the production of more than one related protein, thus expanding possible genomic outputs. (wikipedia.org)
  • Download DNA or protein sequence, view genomic context and coordinates. (yeastgenome.org)
  • Both proteins mediate protein-protein and protein-RNA interactions for cooperative RNA-binding during spliceosome assembly. (cipsm.de)
  • Viroids are pathogenic circular, non-coding, single-stranded RNA molecules. (degruyter.com)
  • Viroids are non-encapsidated, single-stranded (ss), 250-400 nucleotide (nt)-long circular RNA molecules that do not encode proteins (1, 2). (degruyter.com)
  • It leads straight to the active site, and presents a confined area where many proteins and antibiotics that control transcription may bind to carry out their business. (infectioncontroltoday.com)
  • To illustrate our approach, we provide experimental procedures to detect the interaction between plant DNA and two proteins (the AeCRN13 effector from the oomycete Aphanomyces euteiches and the AtWRKY22 defensive transcription factor from Arabidopsis ). (nature.com)
  • A wide variety of interacting proteins were identified and they are involved in a multitude of pathways including: chromosomal organization, transcription, RNA splicing, RNA transport, localized translation, and stress response. (uky.edu)
  • Mammalian lipid homeostasis requires proteolytic activation of membrane-bound sterol regulatory element binding protein (SREBP) transcription factors through sequential action of the Golgi Site-1 and Site-2 proteases. (thebiogrid.org)
  • Moreover, the aberrant expression of three key transcription factors revealed the potential regulatory effects in lipid metabolic disorders, the peroxisomal proliferative agent-activated receptors (PPARs) including PPARα and PPARγ is inhibited, and the activated sterol regulator-binding protein 1 (SREBP1) is overexpressed. (bvsalud.org)
  • the subsequent binding of exogenous indole then reverts this conformational change and restores the native enzyme structure. (ku.edu)
  • The main challenge of generalizing this approach, however, is the difficulty of rationally designing analogous conformational changes in other proteins. (ku.edu)
  • Through collaborative and multidisciplinary efforts, we find that the switchable proteins built via the chemical rescue of structure are frequently controlled indirectly by modulating protein stability, rather than discrete conformational changes. (ku.edu)
  • Since energetic evaluation of protein stability is far more tractable than designing and/or predicting allosteric conformational changes, this finding demonstrates how chemical rescue of structure can be applied to other systems for building a variety of new protein switches. (ku.edu)
  • Li M, Simonetti F, Goncearenco A, Panchenko A, MutaBind estimates and interprets the effects of sequence variants on protein-protein interactions, Nucleic Acids Res. (lu.se)
  • The rod-shaped plant virus tobacco mosaic virus (TMV) is widely used as a nano-fabrication template, and chimeric peptide expression on its major coat protein has extended its potential applications. (whiterose.ac.uk)
  • Here we describe a simple bacterial expression system for production and rapid purification of recombinant chimeric TMV coat protein carrying C-terminal peptide tags. (whiterose.ac.uk)
  • C-terminal peptide tags in such arrays are exposed on the protein surface, allowing interaction with target species. (whiterose.ac.uk)
  • Interestingly, we found that the G quartet recognition is necessary but not sufficient for the FMRP RGG box binding to this RNA target, indicating that additional interactions of the peptide, possibly with the stem and/or stem-G quartet junction region, are required. (auckland.ac.nz)
  • The crystal structure of an alfalfa mosaic virus RNA-peptide complex reveals that conserved AUGC repeats and Pro-Thr-x-Arg-Ser-x-x-Tyr coat protein amino acids cofold upon interacting. (rcsb.org)
  • however, some protein-encoding RNA transcripts have been shown to be subject to editing resulting in a difference in their protein's amino acid sequence. (wikipedia.org)
  • RNA binding proteins can control protein expression by regulating transport, localization, splicing, polyadenylation and turnover of mRNA transcripts. (umassmed.edu)
  • In addition, I will characterize the transcriptome-wide response of existing RNA molecules as well as the newly synthesized transcripts. (europa.eu)
  • We have utilized a C-terminal His-tag to create virus coat protein-templated nano-rods able to bind gold nanoparticles uniformly. (whiterose.ac.uk)
  • Novel tumour-specific RNA-protein interacting partners may serve as candidates to selectively induce cell death in tumour cells. (europa.eu)
  • Click "Protein Details" for further information about the protein such as half-life, abundance, domains, domains shared with other proteins, protein sequence retrieval for various strains, physico-chemical properties, protein modification sites, and external identifiers for the protein. (yeastgenome.org)
  • Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. (embl.de)
  • Sequence-specific RNA-Binding Protein CPEB3 has distinctive isoform-distinct biochemical interactions and neuronal development assembly roles. (aging-us.com)
  • These targets include mRNA, which codes for proteins, as well as a number of functional non-coding RNAs. (wikipedia.org)
  • The CAZy database describes the families of structurally-related catalytic and carbohydrate-binding modules (or functional domains) of enzymes that degrade, modify, or create glycosidic bonds. (lu.se)
  • Nuclear depletion of RNA-binding protein ELAVL3 (HuC) in sporadic and familial amyotrophic lateral sclerosis. (nih.gov)
  • The interaction of ABHD11-AS1 with SART3 promotes USP15 (ubiquitin specific peptidase 15) nuclear localization. (cdc.gov)
  • Nuclear localized USP15 interacts with pre-mRNA processing factor 19 (PRPF19) to increase CD44 RNA alternative splicing activating β-catenin and enhancing cancer stemness. (cdc.gov)
  • We developed an improved individual nucleotide resolution CLIP protocol (iiCLIP), which produces highly sensitive and specific data, and thus enables quantitative comparisons of interactions across conditions (Lee et al. (canal-u.tv)
  • DksA squeezes through this narrow tunnel toward the site where ppGpp binds to the enzyme. (infectioncontroltoday.com)
  • The first project, focused on activation of protein function, is built on an approach developed by our laboratory that designs a de novo allosteric binding site directly into the catalytic domain of an enzyme. (ku.edu)
  • Basically, if miRNA repression is evolutionarily important for a gene, we expect the miRNA binding sites to be shared across closely related species. (lu.se)
  • We will apply this approach to a non-model sparrow study system to answer questions about how hybridization can disrupt evolved miRNA-mRNA interactions, leading to insights about the formation of new species. (lu.se)
  • The student will create a pipeline for identifying conserved miRNA binding sites across several sparrow species using TargetScan as a framework. (lu.se)
  • A prerequisite for rapid adaptations is efficient RNA turnover, with endonuclease RNase Y playing a crucial role in mRNA stability as well as in maturation. (uni-marburg.de)
  • The identified mutants were further tested for binding to poly(U)-Sepharose, a substrate to which wild type hnRNP C1 binds with high affinity. (korea.ac.kr)
  • Using affinity purification-mass spectrometry and global phosphoproteomic and protein abundance analyses using three IAV strains (pH1N1, H3N2, H5N1) in three human cell types (A549, NHBE, THP-1), we map 332 IAV-human protein-protein interactions and identify 13 IAV-modulated kinases. (cdc.gov)
  • Zhang C, Zheng W, Zhang Y, BindProfX: Assessing Mutation-Induced Binding Affinity Change by Protein Interface Profiles with Pseudo-Counts, J Mol Biol. (lu.se)
  • Wang M, Cang Z, Wei G, A topology-based network tree for the prediction of protein-protein binding affinity changes following mutation, Nat Mach Intell):116-123. (lu.se)
  • Lipid-specific oligomerization of the Marburg virus matrix protein VP40 is regulated by two distinct interfaces for virion assembly. (uci.edu)
  • The ssRNA(+), likely transferred into the nucleolus, is finally processed by a type III RNase and a DNA LIGASE into unit-length circular RNAs (8) ( Figure 1 ). (degruyter.com)
  • A hippocampal protein associated with paraneoplastic neurologic syndrome and small cell lung carcinoma. (nih.gov)
  • Consequently, we used iRIP-seq to identify CPEB-binding targets. (aging-us.com)
  • Understanding host proteins essential for IAV infection can identify targets for alternative host-directed therapies (HDTs). (cdc.gov)
  • These findings suggest that combination of trimethoprim and zinc at optimal ratio can be provided as treatment for influenza and possibly other respiratory RNA viruses infection in man. (biomedcentral.com)
  • We identified trimethoprim (TMP) and zinc (Zn) as potential candidates for treatment for RNA virus. (biomedcentral.com)
  • We concluded that mis-localization of these proteins potentially lead to their dysregulation or loss of function, thus contributing to FUS pathogenesis. (uky.edu)
  • At least in plants, DNA regions that become de novo methylated can be defined by homologous RNA molecules in a process termed RNA-directed DNA methylation (RdDM). (degruyter.com)
  • In accordance with its tumor suppressor role, the Retinoblastoma protein pRb can ensure pro-apoptotic functions. (sdbonline.org)
  • 2.0 for positive interactions (epistatic or suppressor interactions) and S score (thebiogrid.org)
  • Quantitative proteomics will be applied to identify the differentially mRNA-bound proteins after the exposure of human cultured cells to ionizing radiation. (europa.eu)
  • These results show that FAST-iCLIP can be used to rapidly discover and decipher mechanisms of RNA-protein recognition across the diversity of human and pathogen RNAs. (nih.gov)
  • Since then, he has been working as a postodoc in Dr. Wassenegger's lab (RLP AgroScience GmbH, AlPlanta) and his main field of interest is RNA-interference (RNAi) and RNA-directed DNA methylation (RdDM) in plants. (degruyter.com)
  • Since then, she has been working as a postodoc in Dr. Wassenegger's lab (RLP AgroScience GmbH, AlPlanta) and her main field of interest is RNA-interference (RNAi) and viroid biology in plants. (degruyter.com)
  • The antiadipogenic mechanism of endostatin lies in its interaction with Sam68 RNA-binding protein in the nuclei of preadipocytes. (diabetesjournals.org)
  • These results provide a mechanism by which Drosophila Bcl-2 family proteins can control apoptosis and shed light on a link between Rbf1 and mitochondrial dynamics, in vivo. (sdbonline.org)
  • The goal of this study is to investigate the mechanism of Cr(VI)-induced lung carcinogenesis focusing on the role of the lncRNA ABHD11 antisense RNA 1 (tail to tail) (ABHD11-AS1). (cdc.gov)
  • The experimental approach we described should be generally applicable for the screening and identification of amino acids that play a role in the binding of proteins to nucleic acid substrates. (korea.ac.kr)
  • MARV assembles and buds from the host cell plasma where MARV matrix protein (mVP40) dimers associate with anionic lipids at the plasma membrane inner leaflet and undergo a dynamic and extensive self-oligomerization into the structural matrix layer. (uci.edu)
  • We aim to develop and optimize computational algorithms for characterizing and understanding protein-protein interactions, which remains one of the most important challenges in Structural Biology. (bsc.es)
  • Her work here is focussed on providing structural and mechanistic insight into the activity of diadenylate cyclase DacA, an essential membrane protein responsible for the production of c-di-AMP in Staphylococcus aureus . (imperial.ac.uk)
  • Luke completed his D.Phil in Clinical Medicine at Oxford University (Merton College), but his research career has predominantly focused on investigating protein function using structural biology as a means to provide a mechanistic understanding in life and in disease. (imperial.ac.uk)
  • Members of the Pospiviroidae family replicate in the nucleus through double-stranded RNA intermediates, attracting the host RNA silencing machinery. (degruyter.com)
  • Upon inoculation, mature Pospiviroidae RNA molecules enter the plant cell nucleus. (degruyter.com)
  • RNA virus requires host cell wall receptors to infect and its nucleus to replicate [ 2 ]. (biomedcentral.com)
  • Click "Interaction Details" to view all interaction annotations and evidence for this locus, including an interaction visualization. (yeastgenome.org)
  • Following TargetScan's approach, students will evaluate conservation of miRNA binding sites across annotations. (lu.se)
  • Znf domains are often found in clusters, where fingers can have different binding specificities. (embl.de)
  • I chose ChxR, a homodimeric response regulator in Chlamydia, as the model protein to examine the feasibility of this strategy. (ku.edu)
  • Taken together, our experiments reveal membrane-associated and membrane-independent activities of Y-complex proteins and a dynamic interplay between them with indirect membrane association of YmcA and YlbF via YaaT. (uni-marburg.de)
  • FLIM-FRET analysis of protein-protein interactions showed that PLIN5 S155 phosphorylation regulates PLIN5 interaction with adipose triglyceride lipase at the lipid droplet, but not with α-β hydrolase domain-containing 5. (uci.edu)