Protein sequence binding protein. Medical search. Frequent questions

The 3'-OH terminal insertions were used to create fusion proteins and develop the use of MBP as an affinity handle for the purification of foreign proteins and peptides by affinity chromatography on cross-linked amylose and elution with maltose in mild physico-chemical conditions. (wikipedia.org)
The whole amino acid sequence of nidogen was deduced from cDNA clones isolated from expression libraries and confirmed to approximately 50% by Edman degradation of peptides. (unifi.it)
Cysteine-Selective Modification of Peptides and Proteins via Desulfurative C-C Bond Formation CHEMISTRY-A EUROPEAN JOURNAL. (nottingham.ac.uk)
Time scales of water dynamics at biological interfaces: peptides, proteins and cells. (lu.se)

Positional cloning of lymphopenia ( lyp ) in the BB rat revealed a frameshift mutation in Gimap5 , a member of at least seven related GTPase Immune Associated Protein genes located on rat chromosome 4q24. (hindawi.com)
Our aim was to clone and sequence the cDNA of the BB diabetes prone (DP) and diabetes resistant (DR) alleles of all seven Gimap genes in the congenic DR. lyp rat line with 2 Mb of BB DP DNA introgressed onto the DR genetic background. (hindawi.com)
Gimap5 is a member of at least seven related GTPase Immune Associated Protein ( Gimap ) genes located within 150 Kilobases (Kb) on rat chromosome (RNO) 4 [ 2 , 3 ]. (hindawi.com)
The fact that the Gimap genes are located together in a tight cluster on RNO4 (and in conserved synteny with many other species), combined with their sequence similarities, suggests the possibility that the proteins carry out similar function. (hindawi.com)
Here, we present evidence that the promoter regions of intellectual disability-associated genes are uniquely enriched in LTR sequences of the MER41 HERVs. (biorxiv.org)
Interestingly, ID-associated genes exhibit promoter-localized MER41 LTRs that harbor TF binding sites (TFBSs) for not only STAT1 but also other immune TFs such as, in particular, NFKB1 (Nuclear Factor Kappa B Subunit 1) and STAT3 (Signal Transducer And Activator Of Transcription 3). (biorxiv.org)
Of note, functionally-relevant differences between humans and chimpanzees are observed regarding the 3 main components of this pathway: i) the protein sequences of immunes TFs binding MER41 LTRs, ii) the insertion sites of MER41 LTRs in the promoter regions of ID-associated genes and iii) the protein sequences of the targeted ID-associated genes. (biorxiv.org)
Alvarez JD, Yasui DH, Niida H, Joh T, Loh DY, Kohwi-Shigematsu T. The MAR-binding protein SATB1 orchestrates temporal and spatial expression of multiple genes during T-cell development. (bdbiosciences.com)
We have learned that genes in mammalian cells are transcribed into messenger RNAs (mRNAs), which are to be translated into polypeptides (proteins). (intechopen.com)
For example, steroid and thyroid hormones directly bind to nuclear receptors, which induce expression of specific genes. (intechopen.com)
Synthetic antisense DNAs are used to hybridize to complementary sequences in target RNAs or DNAs to effect the functioning of specific genes for investigative or therapeutic purposes. (genomicglossaries.com)

In terms of predicting where in the genome the transcription factors bind, the models we're able to derive seem to be, in general, actually better than the other assays. (genomeweb.com)
WGS, whole-genome sequencing. (cdc.gov)
Note: CDC may perform conventional microbiological methods, slide agglutination, and whole genome sequencing as needed to resolve any discrepancies. (cdc.gov)
1 WGS: Whole genome sequencing - a process that determines the complete DNA sequence of an organism's genome at one time. (cdc.gov)
The S. cerevisiae Reference Genome sequence is derived from laboratory strain S288C . (yeastgenome.org)
This study provides the first genome-wide captures of the dynamics of in vivo AmtR binding events and the regulatory network they define. (frontiersin.org)
Method for economic evaluation of bacterial whole genome sequencing surveillance compared to standard of care in detecting hospital outbreaks. (cdc.gov)

When a cell needs to make a particular protein, it first copies the instructions from the matching gene into a molecule known as a messenger RNA (or an mRNA for short). (elifesciences.org)
The more mRNA copies it makes, the more protein it can produce. (elifesciences.org)
A simple way to control protein production is to raise or lower the number of these mRNA messages, and living cells have lots of ways to make this happen. (elifesciences.org)
RNA binding proteins (RBPs) play a vital role in post-transcriptional processes in all eukaryotes, such as splicing regulation, mRNA transport, and modulation of mRNA translation and decay. (biomedcentral.com)
Proteins shown in red (FDR 0.01) represent the mRNA interactome. (nature.com)
c ) Overlap of mRNA interactome proteins in yeast and HuH-7. (nature.com)
d ) Validation of the yeast mRNA interactome using western blotting of input samples and eluate after interactome capture with specific antibodies (ADH1, alcohol dehydrogenase 1, PUB1) or against TAP-tagged proteins (PGK1, phosphoglycerate kinase 1, TDH1, triose phosphate dehydrogenase, TRX2, thioredoxine 2, SHE2, Swi5p-dependent HO Expression 2). (nature.com)
mRNA localisation requires primary sequences and secondary structures often localised in their 3'UTR (3). (europa.eu)
RNA binding proteins recognize these sequences and assemble with their mRNA target into mRNPs. (europa.eu)
Mutations affecting zipcodes, RBPs or motor-proteins required for neuronal mRNA localization were shown to lead to severe neurodegenerative diseases as ALS, FXTAS and FXS (7), underlining the need to understand the mechanisms that drive neuronal mRNA transport. (europa.eu)
Dendritic localisation of CaMKIIa-mRNA requires its 3'UTR harbouring binding sites for RBPs as FMRP and Staufen2, which are required for its correct localisation. (europa.eu)
Inhibiting the localisation of this mRNA leads to a significant reduction of CamKIIa protein at postsynaptic densities and a strong reduction of cognitive abilities in animal models (12). (europa.eu)
Also in this specific case, it is not understood how RBPs, potential adaptors and motor proteins, which are essential for the transport of CaMKIIa-mRNA are mechanistically contributing to its correct localisation. (europa.eu)
The regulation of expression of X-box-binding protein-1 (XBP1), a transcriptional factor, involves an unconventional mRNA splicing that removes the 26 nucleotides intron. (mdpi.com)
Furthermore, the team discovered that each time an mRNA molecule is translated, the GFP gets knocked off, and when translation is finished, another GFP binds to it, enhancing the overall fluorescent signal. (genengnews.com)
Moreover, as the word 'coding' refers to the relationship between nucleic acids and proteins, rather than the mere transcription of DNA into RNA, it is logical to call the strand with the mRNA sequence the coding strand, as in the first example. (genomicglossaries.com)
The sense strand has the same sequence as the mRNA transcript. (genomicglossaries.com)

Together these proteins shorten the end of the mRNAs, preparing the molecules for degradation. (elifesciences.org)
Deep sequencing of RNA molecules cross-linked to immunoprecipitated protein particles (CLIP-seq) revealed. (shengsci.com)
By physically restraining bound molecules against an antibody array, they capture both transient interactions, which yeast two-hybrid or tandem mass spectrometry methods don't, and weak interactions, which are usually obliterated by the wash in protein-DNA microarrays. (genomeweb.com)
Recognizing similarities and deriving relationships among protein molecules is a fundamental requirement in present-day biology. (nih.gov)
Inferring functional similarities between protein molecules by comparing their binding sites is still largely exploratory and not as yet a routine protocol. (nih.gov)
When both proteins find their target sequence, the GFP molecules join and become fluorescent-a signal to the researchers that the target RNA is present. (genengnews.com)
His research spans a wide range, from the quantum chemistry of small molecules and the spectroscopic properties of proteins, to the application of state-of-the-art statistical and computer science methodology to problems in bioinformatics, drug design and sustainable chemistry. (nottingham.ac.uk)
A synthetic, specially- designed oligonucleotide with the ability to recognize and bind a protein ligand molecule or molecules with high affinity and specificity. (genomicglossaries.com)
Biologics are large, very complex protein molecules. (medscape.com)
Nanosecond to microsecond protein dynamics probed by magnetic relaxation dispersion of buried water molecules. (lu.se)

The protein consists of some 1217 amino acid residues and a 28-residue signal peptide. (unifi.it)
DNA-binding hot spots are dominant and fundamental residues that contribute most of the binding free energy yet accounting for a small portion of protein-DNA interfaces. (biomedcentral.com)
The HP model has favorable interactions between adjacent, not directly bound hydrophobic residues. (lu.se)

Recently developed unbiased high content techniques to identify RBPs in vivo yielded information on differences in cell type-specific expression and/or RNA-binding activity of RBPs in mammalian cells 2 , 3 . (nature.com)
Distinct structural bases for sequence-specific DNA binding by mammalian BEN domain proteins. (bvsalud.org)
Here, we characterize several mammalian BEN domain (BD) factors, including from two NACC family BTB-BEN proteins and from BEND3, which has four BDs. (bvsalud.org)
Together, these studies expand the DNA recognition activities of BEN factors and provide structural insights into sequence-specific DNA binding by mammalian BEN proteins . (bvsalud.org)
Identification of binding sites of EVI1 in mammalian cells. (rochester.edu)

report the molecular cloning of Painting of fourth (Pof), which encodes a protein that specifically paints chromosome 4 (Proc Natl Acad Sci USA 2001, 98:6273-6278). (the-scientist.com)
Basic sequence-derived (length, molecular weight, isoelectric point) and experimentally-determined (median abundance, median absolute deviation) protein information. (yeastgenome.org)
These RNA-binding proteins could also be used to build molecular assembly lines that would bring together enzymes needed to perform a series of reactions that produce a drug or another molecule of interest. (genengnews.com)
Another aspect of Hirst's research focuses on the study of protein-ligand interactions, using techniques including QSAR, machine learning, neural networks, docking, molecular dynamics (MD) simulations and quantum chemistry. (nottingham.ac.uk)
The communication between molecular motors and double-stranded DNA binding proteins is a common feature in DNA replication, repair, recombination and transcription and also in instances where conflict occurs between these processes. (sciencedaily.com)
Molecular biologists describing DNA sequences or referring to one of the two strands of double- stranded DNA frequently use complementary pairs of terms, such as coding/ non- coding, sense/ nonsense or transcribing/ non- transcribing. (genomicglossaries.com)
Results: We present ZEAL, an interactive tool to superpose global and local protein structures based on their shape resemblance using 3D (Zernike-Canterakis) functions to represent the molecular surface. (lu.se)

MBP is used to increase the solubility of recombinant proteins expressed in E. coli. (wikipedia.org)
In addition, MBP can itself be used as an affinity tag for purification of recombinant proteins. (wikipedia.org)

Especially, deep learning is increasingly used in the bioinformatics field by virtue of its ability to learn generalized representations from DNA and protein sequences. (biomedcentral.com)
Deplancke also worked in advanced bioinformatics to derive predictive models for binding interactions. (genomeweb.com)
Objective: The aim of this study was to identify DA-associated functional genetic variants through next-generation sequencing (NGS), bioinformatics, and functional assays. (cdc.gov)

RNA-binding proteins contribute to specificity by interacting with both Ccr4-Not and target mRNAs, but this is not fully understood. (elifesciences.org)
Analyses of the mitochondrial hydroxysteroid dehydrogenase (HSD17B10) uncover the RNA-binding specificity of an enigmRBP. (nature.com)
We also determined the RNA targets of an RNA-binding mitochondrial enzyme and show its specificity in RNA binding. (nature.com)

As is shown in Table 1 , these methods mostly employ RNA sequence and structural information to predict protein-RNA interactions. (biomedcentral.com)
Only 60% of yeast and 73% of the human RBPs have functions assigned to RNA biology or structural motifs known to convey RNA binding, and many intensively studied proteins surprisingly emerge as RBPs (termed 'enigmRBPs'), including almost all glycolytic enzymes, pointing to emerging connections between gene regulation and metabolism. (nature.com)
Finally, comparison with our previous invertebrate BEN structures, along with additional structural predictions using AlphaFold2 and RoseTTAFold, reveal distinct strategies for target DNA recognition by different types of BEN domain proteins . (bvsalud.org)
Similarities can be present at various levels which can be detected through comparison of protein sequences or their structural folds. (nih.gov)
To benefit from the enormous amount of structural data that is being rapidly accumulated, it is essential to have high throughput tools that enable large scale binding site comparison. (nih.gov)
His calculations on protein circular dichroism spectroscopy, a key technique in structural biology, are the most accurate to be published. (nottingham.ac.uk)

Sequencing of the ZMYND15 gene in a cohort of infertile Chinese men reveals novel mutations in patients with teratozoospermia. (nih.gov)
Mutations in the norrin protein interfere with its ability to bind to frizzled-4, resulting in the signs and symptoms of Norrie disease. (medlineplus.gov)

Our analysis also demonstrates that shape information alone is insufficient to discriminate between diverse binding sites, unless combined with chemical nature of amino acids. (nih.gov)
We performed a pair-wise analysis of 48 surface-exposed amino acids involved in interacting with factor H, among 383 fHbp variant group 1 sequences. (ox.ac.uk)
At the fH-binding site, ID pairs differed by a maximum of 13 (27%) amino acids. (ox.ac.uk)
ID 9 shared an amino acid sequence common to 83 ID types. (ox.ac.uk)
The selected ID types differed by up to 6 amino acids, in the fH-binding site. (ox.ac.uk)
Amino acid sequence of mouse nidogen, a multidomain basement membrane protein with binding activity for laminin, collagen IV and cells. (unifi.it)
Pumby adapts naturally occurring proteins called Pumilio homology domains (PumHDs), which consist of amino acids that bind to each of the four different ribonucleotide bases that make up RNA sequences. (genengnews.com)
Hoping to make the assembly of RNA-binding proteins less of a trial-and-error and more programmable task, the MIT researchers tested many amino acid combinations. (genengnews.com)
Ultimately, the researchers found a particular set of amino acids that will bind each of the four bases at any position in the target sequence. (genengnews.com)

Using a two-color assay to simultaneously monitor poly(A) tail removal from different RNAs, we demonstrate that Puf3 can distinguish between RNAs of very similar sequence. (elifesciences.org)
To address the second, we investigated RNAs bound by the metabolic enzyme hydroxysteroid dehydrogenase 17-β 10 (HSD17B10). (nature.com)
After cell lysis, polyadenylated RNAs were captured on oligo d(T) beads followed by stringent washes to remove non-crosslinked proteins. (nature.com)
Modular, programmable proteins can be used to track RNAs of interest in living cells. (genengnews.com)
The article described how Pumby modules can be "concatenated in chains of varying composition and length to bind desired target RNAs. (genengnews.com)
We validate that the Pumby architecture can perform RNA-directed protein assembly and enhancement of translation of RNAs," the article's authors continued. (genengnews.com)

Selective microfluidics-based ligand enrichment followed by sequencing, or SMiLE-seq, combines antibody arrays, mechanical trapping, and next-generation sequencing readouts to provide a new platform for characterizing DNA-protein interactions. (genomeweb.com)
A dry ligand-binding cavity in a solvated protein. (lu.se)

POF complexes may function like the Male Lethal Specific proteins, which regulate dosage-compensation of the X chromosome. (the-scientist.com)
It is a complex regulatory and transport system involving many proteins and protein complexes. (wikipedia.org)

Known as "destabilising motifs", these sequences attract the attention of a group of proteins called Ccr4-Not. (elifesciences.org)
The transcription factors bind to any number of DNA motifs in the library, those interactions are trapped, and then the readout matches up each motif with the transcription factor via the barcode. (genomeweb.com)
The predicted structures of the Gimap proteins show common sequences and motifs, such as GTP-binding domains in the N-terminal half, but with differing C-terminal ends [ 2 , 3 ]. (hindawi.com)

The mRNAs can carry short sequences of genetic letters that can trigger their own destruction. (elifesciences.org)

That year, the two published a paper in Science describing a method to trap low-affinity DNA-protein interactions, specifically those of transcription factors. (genomeweb.com)
Once the fusion protein is obtained in purified form, the protein of interest is often cleaved from MBP with a specific protease and can then be separated from MBP by affinity chromatography. (wikipedia.org)
Stereospecific Effects of Oxygen-to-Sulfur Substitution in DNA Phosphate on Ion Pair Dynamics and Protein-DNA Affinity. (utmb.edu)
Tissue culture supernatant is purified by either protein A/G or affinity purification methods. (bdbiosciences.com)
fMT]] is a metallothionein, binding Arsenite(III) and Arsenate(V), it has higher affinity for As(III). (igem.org)
Oligonucleotide which displays specific binding to a protein or other target, often selected by an iterative cycle of affinity- based enrichment. (genomicglossaries.com)
It's going to bind to that target with the same binding affinity to within a narrow range, possibly an even narrower range than for one of the batches of the innovator. (medscape.com)
DNA affinity precipitation and mass spectroscopy of rs147978008 revealed allele-dependent binding of H1 histones, which was confirmed by using Western blotting. (cdc.gov)

Alternative splicing results in multiple transcript variants and protein isoforms. (nih.gov)
Similarly, how the mechanisms by which reduced Gimap5 transcript levels and the absence of the Gimap5 protein [ 2 , 7 , 8 ] contribute to lymphopenia and T1D are still being elucidated [ 9 - 13 ]. (hindawi.com)

You are seeking a database of transcription factor binding specificities. (stackexchange.com)
In a paper published in Nature Methods this week, a Switzerland-based team of researchers, led by bioengineer Bart Deplancke of the École Polytechnique Fédérale de Lausanne (EPFL), showcased the assay's ability to determine DNA-binding specificities for transcription factors. (genomeweb.com)

This is also done for the corresponding peptide sequence. (pubmlst.org)
PLEASE NOTE: as some nucleotide (allele) sequences encode previously assigned peptide sequences, due to synonymous substitutions, the allele sequence and peptide sequence identifiers do not necessarily correspond. (pubmlst.org)
The database enables the allele and peptide sequence identifiers to be related to each other and to any alternative names. (pubmlst.org)
The defective exports of the mutant MBPs are consistent with the alpha-helical conformation and hydrophobic interactions of the signal peptide in its interaction with the translocon motor protein SecA. (wikipedia.org)
An obligatory, intrapeptidyl H-bond between the phosphotyrosine and the conserved asparagine or adjacent arginine is essential for binding and orients the peptide into a positively charged pocket on c-Cbl. (rcsb.org)
Each serotype of BoNT hydrolyzes their protein substrates at different peptide bonds. (cdc.gov)

Specifically, we used word embedding algorithm to extract features of RNA sequences and secondary structures, i.e., distributed representation of k-mers sequence rather than traditional one-hot encoding. (biomedcentral.com)
The distributed representations of RNA sequences and secondary structures can effectively detect the latent relationship and similarity between k-mers, and thus improve the predictive performance. (biomedcentral.com)
Comparison of the structures of the liganded and unliganded forms of MBP has shown that the binding of maltose induces a major conformational change that closes the groove by a rigid motion of the two domains around the linking polypeptide hinge. (wikipedia.org)

RNA-binding proteins (RBPs) exert a broad range of biological functions. (nature.com)
RNA-binding proteins (RBPs) mediate pivotal cellular functions such as RNA transport, degradation or translation and represent key effectors of post-transcriptional gene regulation. (nature.com)
It is still not known which RBPs or adaptor proteins are essential to recruit microtubule-binding motor proteins to mRNPs and to which extend this varies between different transported mRNAs. (europa.eu)

Sodium azide may be removed by washing stained cells or plate-bound antibody or dialyzing soluble antibody in sodium azide-free buffer. (bdbiosciences.com)
Both methods yield antibody in solution that is free of most other soluble proteins, lipids, etc. (bdbiosciences.com)
These toxins inhibit the release of neurotransmitters at the neuromuscular junction by cleaving soluble NSF attachment protein receptor (SNARE) complex proteins in nerve cells, which prevents the fusion of neurotransmitter containing vesicles to cell membranes 2 . (cdc.gov)
If the membrane-anchor is missing or defective, Fp and Ip subunits accumulate as soluble proteins in the cytoplasm. (lu.se)

Antifreeze proteins (AFPs) are a group of proteins that inhibit body fluids from growing to ice crystals and thus improve biological antifreeze ability. (biomedcentral.com)

Single-molecule kinetics reveal microscopic mechanism by which High-Mobility Group B proteins alter DNA flexibility. (shengsci.com)
Each protein is also attached to half of a green fluorescent protein (GFP) molecule. (genengnews.com)

First, they designed two Pumby proteins that would bind to adjacent RNA sequences. (genengnews.com)

Nucleotide-binding oligomerization domain-containing protein 1 (NOD1) is an intracellular pattern recognition receptor that recognizes bacterial peptidoglycan (PG) containing meso-diaminopimelic acid (mesoDAP) and activates the innate immune system. (amrita.edu)
Botulinum neurotoxins (BoNTs) are bacterial proteins that cause the life-threatening disease botulism 1 . (cdc.gov)

Positive damage modulation at some ETS transcription factor binding sites coincided at base level with melanoma somatic mutation hotspots. (scilifelab.se)
Gimap5 was identified as the lyp gene in the BBDP rat through a frameshift mutation and premature truncation of the Gimap5 protein [ 2 , 6 ] and can be rescued in a P1-derived artificial chromosome (PAC) transgenic rat [ 7 ]. (hindawi.com)

In this article, we reconcile this inconsistency by showing that, in a defined in vitro system with plasmid DNA templates, a variety of sequence-specific DNA-binding proteins, such as the bacteriophage λ O replication initiator or the E. coli lactose or galactose repressors, strikingly stimulate transcription-coupled DNA supercoiling. (johnshopkins.edu)
Bacteria often can't support over-expression needed to get workable quantities of protein for an assay, and in vitro expression often can't synthesize a fully functional transcription factor. (genomeweb.com)
In vitro selection data revealed sequence-specific binding activities of isolated BEN domains from all of these factors. (bvsalud.org)

It has also been demonstrated that STAT1 (Signal Transducer And Activator Of Transcription 1), a transcription factor (TF) crucially involved in the IFNγ pathway, binds consensus sequences that, in humans, are located with a high frequency in the LTRs (Long Terminal Repeats) of the MER41 family of primate-specific HERVs (Human Endogenous Retrovirus). (biorxiv.org)

The details appeared online the week of April 25 in PNAS, in an article entitled, "A Programmable RNA Binding Protein Composed of Repeats of a Single Modular Unit. (genengnews.com)

All models were trained, tested, and evaluated on 145 SAM binding protein chains where no two chains have more than 40\% sequence similarity. (edu.in)
We demonstrate further that this stimulation requires the presence in the DNA template of a recognition sequence for the relevant DNA-binding protein and depends on the production of long RNA chains by an RNA polymerase. (johnshopkins.edu)
Changes in conformational dynamics of basic side chains upon protein-DNA association. (utmb.edu)

Is the Subject Area "Protein structure prediction" applicable to this article? (plos.org)
With the increasing volume of verified RBP binding sites, quite a few studies focused on developing computational prediction models based on the known RBP binding sites. (biomedcentral.com)
I am a computer scientist and we are working on protein function prediction algorithms. (stackexchange.com)

Both precursor and mature forms of MBP are functional for the binding of maltose. (wikipedia.org)
Because X-inactivation leads to some cells that produce functional norrin protein and some cells that do not, females can have some features of Norrie disease. (medlineplus.gov)
It is unexpected that B. subtilis SQR without covalently bound FAD is not assembled in the E. coli membrane provided that all other aspects of assembly, including iron-sulfur cluster biogenesis, are functional in the heterologous system. (lu.se)

We find that the fission yeast homologues of Tristetraprolin/TTP and Pumilio/Puf (Zfs1 and Puf3) interact with Ccr4-Not via multiple regions within low-complexity sequences, suggestive of a multipartite interface that extends beyond previously defined interactions. (elifesciences.org)
Oli [ 16 ] uses k-mer frequency as input feature into an SVM classifier to predict RNA-protein interactions. (biomedcentral.com)
Deciphering protein–protein interactions. (crossref.org)
Our work provides proof of concept for the study of protein-DNA interactions at individual loci using light and sequencing, and reveals widespread and potent modulation of UV damage in regulatory regions. (scilifelab.se)
Protein folding, going from sequence to structure by mini- a quadratic Hamiltonian requires additional spin variables and mizing an energy function, represents a difficult optimization implementing interactions such as self-avoidance becomes problem. (lu.se)

The malEp and malKp promoters are synergistically activated by protein MalT, the activator of the Mal regulon and by the cAMP receptor protein CRP. (wikipedia.org)
Weak sequence homologies (25%) were detected between some regions of nidogen, the LDL receptor, thyroglobulin and the EGF precursor. (unifi.it)

These data support the hypothesis that N-Myc affects neuroblastoma gene expression through the formation of a DNA-binding heterodimeric complex with Max in vivo. (uu.nl)
First, the general TFs (GTFs), including preinitiation complex components TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and THIIH, are the primary protein factors that are required for the initiation of transcription from the TATA box (or TATA element), then elongation is executed by RNA polymerase II (RNA pol II) [ 1 ]. (intechopen.com)
The physical basis of model-free analysis of NMR relaxation data from proteins and complex fluids. (lu.se)
The light chain is a zinc-metalloprotease which is responsible for the cleavage of three SNARE complex proteins including SNAP-25 (Synaptosome-associated protein of 25 kDa), synaptobrevin-2 (also termed VAMP-2) and syntaxin. (cdc.gov)

Contribution of factor H-Binding protein sequence to the cross-reactivity of meningococcal native outer membrane vesicle vaccines with over-expressed fHbp variant group 1. (ox.ac.uk)
SQR consists of a membrane-peripheral heterodimer domain (often called succinate dehydrogenase) which is tightly bound to a membrane-spanning anchor, which is a cytochrome with one or two heme groups depending on the organism. (lu.se)
The flavin together with the iron-sulfur clusters function to mediate electron transfer from the dicarboxylate binding site on the Fp subunit to the membrane-anchor domain where quinone is reduced to quinol. (lu.se)
With the full complement of prosthetic groups they are then bound to the heme-containing membrane-anchor to form the active SQR. (lu.se)
Flavinylation of Fp in B. subtilis does not require the Ip subunit or the membrane anchor but depends on folding of the Fp polypeptide into a state that can bind FAD and subsequent mediate covalent binding of the FAD [3, 4]. (lu.se)
In the Fp subunit of SQR, and the closely related membrane-associated fumarate reductase of anaerobic organisms, FAD is covalently attached via an 8α-N(3)-histidyl linkage to a histidine (His) in a conserved sequence in the N-terminal part of the polypeptide. (lu.se)
SQR in E. coli and B. subtilis can be assembled in the membrane without covalently bound FAD but are enzymatically inactive [3, 4, 6]. (lu.se)
Notably, certain B. subtilis mutants with mutated Fp lack covalently bound flavin and do not assemble the SQR polypeptides in the membrane [3]. (lu.se)

IONMF [ 15 ] proposes a feature representation method of orthogonal matrix eigendecomposition, which integrates the k-mer sequence, secondary structure, gene ontology (GO) information and region type as input into a machine learning model to predict binding sites. (biomedcentral.com)
I was looking on Gene Ontology and Protein Databank where I'd expect such informations, but I was unable to find it. (stackexchange.com)

Cells continuously monitor protein synthesis to prevent accumulation of aberrant polypeptides. (shengsci.com)

It is thought that motor or adaptor proteins recognise different features on the surface of mRNPs with different affinities. (europa.eu)
Yet, much of biology happens on the surface of proteins, which is why proteins with shared ancestry and similar function often have comparable surface shapes. (lu.se)
Superposition of proteins based on surface shape can enable comparison of highly divergent proteins, identify convergent evolution and enable detailed comparison of surface features and binding sites. (lu.se)
For comparisons of proteins with limited sequence and backbone-fold similarity, where coordinate-based methods typically fail, ZEAL can often find alignments with substantial surface-shape correspondence. (lu.se)
In particular, we find that global surface shape similarity is particular common among DNA binding proteins. (lu.se)
High water mobility on the ice-binding surface of a hyperactive antifreeze protein. (lu.se)

NEW YORK (GenomeWeb) - A new microfluidics-driven DNA-protein binding assay has its creators dreaming of launching a startup to cash in on several potential applications. (genomeweb.com)
The assay could help accelerate efforts to map where transcription factors bind the genomes of humans and model organisms, Deplancke said. (genomeweb.com)

POF protein decorates chromosome 4 by spreading out from an initiation site in the proximal region of the chromosome. (the-scientist.com)

For this, we would make use of datasets about containing DNA-binding proteins and the DNA sequences they bind to. (stackexchange.com)

The identification of RBP binding sites is a crucial step in understanding the biological mechanism of post-transcriptional gene regulation. (biomedcentral.com)
Therefore, the identification of RBP binding sites is crucial to understanding the mechanism of biological processes. (biomedcentral.com)
In addition, the effectiveness of antitoxin treatment may vary depending on circulating toxin levels, so that rapid identification and quantification of BoNT proteins in clinical specimens and food is desirable for optimization of treatment. (cdc.gov)

This gene encodes a MYND-containing zinc-binding protein with a nuclear localization sequence. (nih.gov)

Our data are most consistent with a model in which specific DNA-binding proteins facilitate a twin-domain mechanism to enhance DNA supercoiling during transcription. (johnshopkins.edu)

We generated isogenic NOMV-producing meningococcal strains from an African serogroup W isolate, each over-expressing one of four fHbp variant group 1 sequences (ID 1, 5, 9, or 74), including those most common among invasive African meningococcal isolates. (ox.ac.uk)
Sequencing was conducted on 23 influenza (H1N1)pdm09 isolates that were recovered from positive samples. (who.int)
There were two different mismatches in the probe target sites of the HA gene sequences of all isolates ( n = 23) with additional mismatches only at position 7 (template binding site) identified for all eight negative real-time RT-PCR isolates. (who.int)

Download DNA or protein sequence, view genomic context and coordinates. (yeastgenome.org)

The miniF plasmid C protein: sequence, purification and DNA binding. (shengsci.com)
The C protein has been purified from cells carrying the Ptrp-C plasmid, and a preliminary study of C protein-DNA binding properties has been carried out. (shengsci.com)
Several plasmid vectors were developed to facilitate the expression and purification of such fusion proteins. (wikipedia.org)

Thermodynamic Additivity for Impacts of Base-Pair Substitutions on Association of the Egr-1 Zinc-Finger Protein with DNA. (utmb.edu)

Nidogen contains two consensus sequences for tyrosine sulfation and for asparagine beta-hydroxylation, two N-linked carbohydrate acceptor sites and, within one of the EGF-like repeats an Arg-Gly-Asp sequence. (unifi.it)

Each novel fHbp nucleotide sequence is assigned a numerical identifier in order of submission. (pubmlst.org)
We have determined the nucleotide sequence of the C gene. (shengsci.com)

A new algorithm has been developed to compare binding sites in accurate, efficient and high-throughput manner. (nih.gov)

Breadth of killing was mostly due to anti-fHbp antibodies, with some restriction according to ID type sequence differences. (ox.ac.uk)
Sera from residual specimens from NHANES 2001-2002 participants were tested for levels of IgG antibodies against cancer antigen (CA) 125, CA15.3 and human epididymal secretory protein 4 (HE4). (cdc.gov)

The c-Cbl tyrosine kinase binding domain (Cbl-TKB), essentially an 'embedded' SH2 domain, has a critical role in targeting proteins for ubiquitination. (rcsb.org)

As TMV has a stoichiometry of three nucleotides per protein subunit, the sequence of TMV RNA suggested to be the nucleation site for self-assembly of the virus has three possible binding frames. (nature.com)

Though the representation used is conceptually simplistic, we demonstrate that along with the new alignment strategy used, it is sufficient to enable binding comparison with high sensitivity. (nih.gov)

In this paper, we implemented a novel deep neural network model, DeepRKE, which combines primary RNA sequence and secondary structure information to effectively predict RBP binding sites. (biomedcentral.com)
The distributed representations are taken as input of convolutional neural networks (CNN) and bidirectional long-term short-term memory networks (BiLSTM) to identify RBP binding sites. (biomedcentral.com)

DNA-Binding Proteins (DBP) plays a pivotal role in biological system. (biomedcentral.com)

b ) Volcano plot showing the distribution of proteins according to their enrichment in crosslinked (CL) over non-CL samples. (nature.com)

In vivo, Myc proteins have been found associated with Max, another basic helix4oop-helix/leucine-zipper protein. (uu.nl)

Anatomy4

Organisms6

Chemicals and Drugs59

Analytical, Diagnostic and Therapeutic Techniques and Equipment23

Phenomena and Processes47

Disciplines and Occupations3

Information Science21

Health Care3

Peptides4

Genes11

Genome7

MRNA17

Molecules10

Residues3

Mammalian5

Molecular7

Recombinant proteins2

Bioinformatics3

Specificity3

Structural6

Mutations2

Amino9

RNAs6

Ligand2

Complexes2

Motifs3

Genetic1

Affinity8

Transcript2

Specificities2

Peptide6

Structures3

RBPs3

Soluble4

Group of proteins1

Molecule2

Adjacent1

Bacterial2

Mutation2

Vitro3

Transcription factor1

PNAS1

Chains3

Prediction3

Functional3

Interactions5

Receptor2

Complex4

Membrane8

Gene ontology2

Polypeptides1

Surface6

Assay2

Chromosome1

Datasets1

Identification3

Localization1

Mechanism1

Isolates3

Genomic1

Plasmid3

Zinc-Finger1

Consensus1

Nucleotide sequence2

High-throughput1

Antibodies2

Ubiquitination1

Subunit1

Alignment1

Neural2

Pivotal1

Enrichment1

Vivo1