Protein sequences sequence and bind. Medical search. Frequent questions

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)
The cell doesn't need every protein encoded in its genome all the time. (reasons.org)
That is, the nucleotide sequence specifies the digital information of the gene and, at the same time, the higher order architectures of the genome, which in turn influence the expression of the digital information found in the gene. (reasons.org)
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)
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)
Toward this objective, ChIP-Seq data of 14 S/MAR binding proteins were analyzed and the binding site coordinates of these proteins were used to prepare a non-redundant S/MAR dataset of human genome. (researchgate.net)
Recently, genome sequences revealed that in addition to rpoS , an rpoS -like sigma factor was found in V. alginolyticus 12G01. (hindawi.com)
Method for economic evaluation of bacterial whole genome sequencing surveillance compared to standard of care in detecting hospital outbreaks. (cdc.gov)

Sometimes genes are expressed (and the corresponding proteins are produced), and other times they aren't. (reasons.org)
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)

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)
NTA is a tetravalent ligand providing greater specificity but lower yield, while IDA is trivalent-less selective but generally providing more protein. (genengnews.com)
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)
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)
DEELIG: A Deep Learning Approach to Predict Protein-Ligand Binding Affinity. (ncbs.res.in)
Peptide binding of the ligand takes place in an elongated surface groove as an anti-parallel beta-strand interacts with the beta-B strand and the B helix. (embl.de)

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)
Copper shows low specificity and high yield, whereas cobalt is on the other end of the spectrum, generating extremely pure proteins but lower yield. (genengnews.com)
Six to eight histidines are typically used to increase specificity over intrinsic histidine in contaminating proteins. (genengnews.com)
Its substrate specificity suggests that Tsp may contain a substrate recognition domain, which selectively binds to the nonpolar C-termini of substrate proteins, separate from its catalytic site. (embl.de)

Myc proteins are basic helix-loop-helix/ leucine-zipper proteins that bind to specific DNA sequences. (uu.nl)
The laboratory is particularly interested in studying how specific DNA sequences, DNA binding proteins, and chromatin. (rochester.edu)

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)
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)
Collation and analyses of DNA-binding protein domain families from sequence and structural databanks. (ncbs.res.in)

Together these proteins shorten the end of the mRNAs, preparing the molecules for degradation. (elifesciences.org)
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)
Biochemists have long recognized that the nucleotide sequences comprising DNA molecules encode digital information. (reasons.org)
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)

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 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)
Sequence analysis of five tryptic peptides revealed that their sequences matched corresponding sequences of the A2 protein of the heterogeneous nuclear ribonucleoprotein (hnRNP) complex. (jci.org)

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)
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)
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)

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)
Affinity tagging, a popular method for capturing or immobilizing proteins, has several incarnations, none more popular than polyhistidine tagging. (genengnews.com)
After expression, the protein is captured by means of immobilized metal affinity chromatography (IMAC). (genengnews.com)
Oligonucleotide which displays specific binding to a protein or other target, often selected by an iterative cycle of affinity- based enrichment. (genomicglossaries.com)
In most cases, interaction between a PDZ domain and its target is constitutive, with a binding affinity of 1 to 10 microns. (embl.de)

The nucleotide sequences represent a succession of discrete units (i.e., genetic letters), just like the 1's and 0's that encode the digital information on a CD or in an MP3 file. (reasons.org)
2 They note that the nucleotide sequences of DNA not only encode information to make proteins, these sequences also impact the higher order architecture of DNA, which houses the analog information. (reasons.org)
RS_01910 may encode a protein related to creatine transport. (frontiersin.org)

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)
Different PDZs possess different binding specificities. (embl.de)

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

Sequencing of the ZMYND15 gene in a cohort of infertile Chinese men reveals novel mutations in patients with teratozoospermia. (nih.gov)
Bioinformatics analysis of mutations sheds light on the evolution of Dengue NS1 protein with implications in the identification of potential functional and druggable sites. (ncbs.res.in)
Mutations found in methyl CpG binding protein 2(MECP2) are associated with Rett syndrome. (cms.gov)

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)
172 Computational analysis and prediction of proteins that undergo domain swapping. (ncbs.res.in)

This makes them suitable for the purification of proteins from eukaryotic samples, thereby extending the use of polyhistidine proteins from bacterial to more complex expression systems. (genengnews.com)
Botulinum neurotoxins (BoNTs) are bacterial proteins that cause the life-threatening disease botulism 1 . (cdc.gov)

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)

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

In this study, chromatin immunoprecipitation and massively parallel DNA sequencing (ChIP-seq) was performed to identify the AmtR regulon in C. glutamicum ATCC 14067. (frontiersin.org)

Alternative splicing results in multiple transcript variants and protein isoforms. (nih.gov)

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)

Each novel fHbp nucleotide sequence is assigned a numerical identifier in order of submission. (pubmlst.org)
As it turns out, the nucleotide sequence dictates the supercoiling parameters. (reasons.org)
Muskhelishvili and Travers point out that the digital and analog information are coupled intrinsically through the nucleotide sequence. (reasons.org)

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)
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)
Deplancke also worked in advanced bioinformatics to derive predictive models for binding interactions. (genomeweb.com)
In this work, we show that substrate recognition of Tsp is mediated by a PDZ domain, a small protein module that promotes protein-protein interactions by binding to internal or C-terminal sequences of their partner proteins. (embl.de)
The HP model has favorable interactions between adjacent, not directly bound hydrophobic residues. (lu.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)

Amino acid sequence of mouse nidogen, a multidomain basement membrane protein with binding activity for laminin, collagen IV and cells. (unifi.it)
However, according to Dr. Boronowsky, when membrane proteins are being investigated, 10 or even 14 residues might be employed to overcome the masking effects of any detergent that might have been added to improve protein solubilization. (genengnews.com)
PDZ domain proteins are frequently associated with the plasma membrane, a compartment where high concentrations of phosphatidylinositol 4,5-bisphosphate (PIP2) are found. (embl.de)
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)
If the membrane-anchor is missing or defective, Fp and Ip subunits accumulate as soluble proteins in the cytoplasm. (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)
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)
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)

2016. An Approach to Function Annotation for Proteins of Unknown Function (PUFs) in the Transcriptome of Indian Mulberry. . (ncbs.res.in)

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)
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)

this may enable the selective sequestration of c-Cbl from other target proteins. (rcsb.org)
The use of a separate substrate recognition domain such as a PDZ domain may be a general mechanism for achieving selective protein degradation. (embl.de)

Computational tools to study RNA-protein complexes. (ncbs.res.in)

Sigma factors are a class of proteins constituting essential dissociable subunits that confer sequence-specific DNA binding properties to RNA polymerase (RNAP). (hindawi.com)
The Fp and Ip subunits are both very conserved with respect to composition and polypeptide sequence [1]. (lu.se)

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)

Known as "destabilising motifs", these sequences attract the attention of a group of proteins called Ccr4-Not. (elifesciences.org)

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

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)

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)

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)

Control of eukaryotic messenger RNA synthesis by sequence-specific DNA-binding proteins. (wikidata.org)

Cube Biotech offers PureCube resins for the purification of His-tagged proteins. (genengnews.com)
Purification and partial sequencing of the nuclear autoantigen RA33 shows that it is indistinguishable from the A2 protein of the heterogeneous nuclear ribonucleoprotein complex. (jci.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)
Bioinformatics comparisons of RNA-binding proteins of pathogenic and non-pathogenic Escherichia coli strains reveal novel virulence factors. (ncbs.res.in)
2015. Creating a specialist protein resource network: a meeting report for the protein bioinformatics and community resources retreat. . (ncbs.res.in)

Immunoglobulin gene transcription is activated by downstream sequence elements. (wikidata.org)
The assay could help accelerate efforts to map where transcription factors bind the genomes of humans and model organisms, Deplancke said. (genomeweb.com)
Real-time quantitative PCR (RT-qPCR) analysis and sfGFP (superfolder green fluorescent protein) analysis reveal that AmtR directly and negatively regulates the transcription and expression of crn A, cre T, csh A, and hyu B. A growth test shows that C. glutamicum ATCC 14067 can use creatine or creatinine as a sole nitrogen source. (frontiersin.org)

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)

Thus, the principle of protein or peptide haptenation could be used in in vitro assays to predict the sensitization potential of a new chemical entity. (cdc.gov)

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)
In summary, these data strongly indicate that RA33 and A2 are the same protein, and thus identify on a molecular level a new autoantigen. (jci.org)
One of the key molecular events in skin sensitization is protein haptenation, i.e. the chemical modification of self-skin protein(s) thus forming macromolecular immunogens. (cdc.gov)
The basis of hapten- molecular mechanisms of the sensitization pro- protein binding work is the hypothesis that upon cess will result in novel opportunities for the skin absorption, only protein-reactive chemicals development of alternative methods for assessing (or those that can be metabolically or chemically skin sensitization hazard and relative potency of converted to protein-reactive species) are able to chemicals. (cdc.gov)

Photoaffinity labeling with a fluorescent nonpolar peptide caused the covalent attachment of the peptide to a single site on the Tsp protein. (embl.de)
The covalent bond to FAD in SQR is essential for enzyme activity and the main reason for this is that the bond raises the midpoint redox potential of the flavin by more than 80 mV compared to non-covalently bound flavin. (lu.se)

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

We show that this conserved RNA interactome harbours many proteins without previously assigned roles in RNA biology (enigmRBPs), including surprisingly many metabolic enzymes. (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)

Binding sites for laminin and collagen IV are present on the C-terminal globule but not yet precisely localized. (unifi.it)

The protein consists of some 1217 amino acid residues and a 28-residue signal peptide. (unifi.it)

In this framework, a gene consists of an isolated piece of code specifying the digital information (i.e., amino acid sequence) used by the cell's machinery to build a particular protein . (reasons.org)

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)

A control mutant of dMax that contains a proline residue in the leucinezipper region was unable to bind to N-Myc and did not revert the N-Myc-induced changes in cellular gene expression. (uu.nl)

2020. Distinct Evolutionary Origins of Intron Retention Splicing Events in Antiporter Transcripts Relate to Sequence Specific Distinctions in Species. . (ncbs.res.in)

Cleavage of polyhistidine from the protein is normally not attempted unless the protein is used as a drug in humans or animals. (genengnews.com)
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)

Deepened knowledge on the biophysical chemistry of proteins with emphasis on properties rather than methods. (lu.se)

Weak sequence homologies (25%) were detected between some regions of nidogen, the LDL receptor, thyroglobulin and the EGF precursor. (unifi.it)

Anatomy10

Organisms22

Chemicals and Drugs58

Analytical, Diagnostic and Therapeutic Techniques and Equipment47

Phenomena and Processes92

Disciplines and Occupations6

Technology, Industry, Agriculture2

Information Science35

Health Care10

Genome9

Genes2

Ligand6

Specificity6

Specific DNA sequences2

Structural6

Molecules6

Peptide sequences1

Peptides3

MRNA10

Affinity5

Encode3

Specificities3

Distribution of proteins2

Mutations3

Prediction4

Bacterial2

RNAs3

Genetic1

Chromatin1

Transcript1

Gene ontology2

Nucleotide sequence3

Interactions7

Membrane12

Transcriptome1

RBPs3

Selective2

Complexes1

Subunits2

Ubiquitination1

Motifs1

Vivo2

Bacteria1

Soluble1

Tyrosine1

Eukaryotic1

Purification2

Bioinformatics3

Transcription3

Assay1

Vitro1

Molecular4

Covalent2

Datasets1

Previously assigned1

Alignment1

Laminin1

Residues1

Amino acid1

Identification3

Cellular1

Species1

Cleavage2

Chemistry1

Receptor1