Protein binding site. Medical search. Frequent questions

These programs are utilized to screen entire libraries of molecules for a possible ligand of a binding site and to furthermore estimate in which conformation the ligand will most likely bind. (uni-marburg.de)

Similarities can be present at various levels which can be detected through comparison of protein sequences or their structural folds. (nih.gov)
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)
Although there is an appreciable amount of divergence in the sequences of all these proteins, the copper ligand sites are conserved. (wikipedia.org)
Protein design methods use trial and error or more sophisticated methods like directed evolution or inverse folding to generate novel scaffolds or to find novel protein sequences folding into a defined scaffold, respectively. (hindawi.com)
Given the intimate relationship between a protein's structure and function, a way to design proteins with targeted properties is to start from a desired structure and find sequences able to fold into it, imposing additional constraints in the process [ 1 ]. (hindawi.com)
One of the methods that does seem to work well is TargetScan, which relies on both pairing of seed sequences (a subset of the 18-23 bp that make up a miRNA) and phylogenetic conservation of sites. (lu.se)

Matching of structural motifs using hashing on residue labels and geometric filtering for protein function prediction. (uni-marburg.de)
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)

The knowledge about DNA-binding residues, binding specificity and binding affinity helps to not only understand the recognition mechanism of protein-DNA complex, but also give clues for protein function annotation. (nature.com)
Bullock and Fersht 8 have shown that mutations of DNA-binding residues, such as those on the tumor repressor protein P53, may predispose individuals to cancer. (nature.com)
Protein sequence information mainly consists of amino acid residue composition, biochemical features of amino acid residues and evolutionary information in terms of position-specific scoring matrices (PSSM). (nature.com)
VH is derived from a single protein domain of 35 residues [ 9 ]. (hindawi.com)
Two non-consecutive sets of zinc-binding residues form two separate metal-binding sites. (nih.gov)
In addition, you can precisely expand it by adding individual residues - or with a single click to find empty pockets in your protein. (biosolveit.de)
Occasionally, the site 2 residues of two YfeA molecules will cooperate with the histidine tag of a third YfeA molecule in coordinating the same metal and lead to metal-dependent crystallographic packing. (uky.edu)

Mutations in the cardiac MyBP-C gene likely cause chromosome 11-linked hypertrophic cardiomyopathy, further supporting the hypothesis that hypertrophic cardiomyopathy results from mutations in genes encoding contractile proteins. (nih.gov)
Phosphorylation-resistant site mutations in PIF7 result in increased nuclear localization and shade-induced gene expression, and consequently augment hypocotyl elongation. (elifesciences.org)
About half the mutations change one of the protein building blocks (amino acids) used to make copper-transporting ATPase 2. (medlineplus.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)
TY - JOUR T1 - Structural characterization of Escherichia coli ribosomal protein S8 and its binding site in 16S ribosomal RNA. (unboundmedicine.com)
The structural comparison of binding sites is especially useful when applied on distantly related proteins as a comparison solely based on the amino acid sequence is not sufficient in such cases. (uni-marburg.de)
As is shown in Table 1 , these methods mostly employ RNA sequence and structural information to predict protein-RNA interactions. (biomedcentral.com)
However, analogous proteins may have structural homology although this is not a prerequisite. (hindawi.com)
However, a new structural paradigm has recently been proposed, in which aluminum interacts directly with the backbone of the proteins, provoking drastic changes in their secondary structure and leading ultimately to their denaturation. (worktribe.com)
REDOR, combined with strategically placed isotopic labels, is effective in obtaining model-independent internuclear distances and thus detailed structural information on the ligand-binding site of GlnBP. (bionmr.com)
In a collaborative effort, the Lund Protein Production Platform (LP3) , the FragMAX platform at the BioMAX beamline of the MAX IV laboratory, the Deuteration and Macromolecular Crystallization (DEMAX) of the European Spallation Source ESS and the group of Professor F. Kozielski at University College London published new results on non-structural protein from SARS-CoV-2. (lu.se)
Structural and biochemical characterization of two heme binding sites on α1-microglobulin using site directed mutagenesis and molecular simulation. (lu.se)
His calculations on protein circular dichroism spectroscopy, a key technique in structural biology, are the most accurate to be published. (nottingham.ac.uk)
To obtain mechanistic insights into how phosphorylation impacts on alternative splicing regulation we will combine available structural information for molecular modelling of ELAV multimerization and RNA binding to instruct experimental validation. (findaphd.com)
Further, this project will apply statistical analysis of data and we willl use molecular modelling of available structural information to make predictions how phosphorylations impacts on ELAV multimerization and RNA binding. (findaphd.com)

Several experimental techniques have been proposed to identify the DNA-binding sites and investigate the interaction modes between proteins and DNAs. (nature.com)
Here we use the topographic and recognition (TREC) mode of an atomic force microscope to visualize UCP1 reconstituted into lipid bilayers and to analyze the ATP-protein interaction at a single molecule level. (uni-linz.ac.at)
We have utilized the interaction between the erythroid-specific enhancer in hypersensitivity site 2 (HS2) of the human β-globin locus control region and the globin gene promoters as a model to elucidate the mechanisms governing promoter/enhancer interactions. (monash.edu)
Various drastic effects have been attributed to aluminum in its interaction with polypeptides and proteins. (worktribe.com)
Mechanism of SNARE protein binding and regulation of Cav2 channels by phosphorylation of the synaptic protein interaction site. (bvsalud.org)
Ca(v)2.1 and Ca(v)2.2 channels conduct P/Q-type and N-type Ca(2+) currents that initiate neurotransmission and bind SNARE proteins through a synaptic protein interaction (synprint) site. (bvsalud.org)
Blocking the interaction between PIF7 and 14-3-3 proteins or reducing the expression of 14-3-3 proteins accelerates shade-induced nuclear localization and de-phosphorylation of PIF7, and enhances the shade phenotype. (elifesciences.org)
Techniques for measuring specific nucleic acid interaction with another nucleic acid or with a protein by digestion of the non-interacting nucleic acid by various nucleases. (bvsalud.org)

Thus, while the adenine site preferences of the spliceosome and of phage GA may be due to protein factors, the preferred adenine is predisposed in the free RNA to conformational rearrangement involved in formation of the active complexes. (rcsb.org)
Binding site identification and structure determination of protein-ligand complexes by NMR a semiautomated approach. (bionmr.com)
Cell surface annexin VI is also capable of mediating internalization and degradation of cell surface-bound 125 -TGF-β 1 and 125 I-α 2 M* at pH 6 and of forming ternary complexes with 125 I-α 2 M* and LRP-1 at neutral pH as demonstrated by co-immunoprecipitation. (tmu.edu.tw)
Of the resulting antigen/antibody complexes, the T3 analogue/antibody complexes are bound to the streptavidin coated solid phase. (cdc.gov)
Separation in a magnetic field and washing removes the sample T3/antibody complexes and other materials not bound to the solid phase. (cdc.gov)

Indeed, MyBP-C is a substantial component of the myofibrils that interacts with several proteins of the thick filament of the sarcomere. (nih.gov)
PIF7 interacts with 14-3-3 proteins. (elifesciences.org)
It interacts also with anticoagulant protein S and with serum amyloid P component. (lu.se)

ELAV/Hu proteins comprise a family of highly conserved neuronal RNA binding proteins important for the development of the nervous system and for neuronal functions. (findaphd.com)
The 14-3-3 proteins are highly conserved in all eukaryotes. (elifesciences.org)

Here we identify two separate microdomains that each bind syntaxin 1A and SNAP-25 in vitro and are regulated by PKC phosphorylation at serines 774 and 898 and CaMKII phosphorylation at serines 784 and 896. (bvsalud.org)
Chimeric Ca(V)2.1a channels containing the synprint site of Ca(v)2.2 gain modulation by syntaxin 1A , which is blocked by PKC phosphorylation at the sites identified above. (bvsalud.org)
Our results support a bipartite model for the synprint site in which each SNARE -binding microdomain is controlled by a separate PKC and CaMKII phosphorylation site that regulates channel modulation by SNARE proteins . (bvsalud.org)
From initial studies on human Hu proteins, we anticipate that altering phosphorylation will impact dramatically on ELAV function and will generate neurological phenotypes. (findaphd.com)
These studies demonstrate a phosphorylation-dependent translocation of PIF7 when plants are in shade and a novel mechanism involving 14-3-3 proteins, mediated by the retention of PIF7 in the cytoplasm that suppresses the shade response. (elifesciences.org)

The Additional sex combs gene of Drosophila encodes a chromatin protein that binds to shared and unique Polycomb group sites on polytene chromosomes. (ox.ac.uk)
This group contains uncharacterized proteins including Drosophila melanogaster GM13116p and Caenorhabditis elegans hypothetical protein R11G1.4, both of which contain C2 (a calcium-binding domain) and C1 domains. (nih.gov)
Intriguingly, human Hu proteins can substitute for ELAV in a Drosophila model for alternative splicing regulation. (findaphd.com)

abstract = "Cry1Fa insecticidal protein was successfully radiolabeled with (125)I-Na. (bath.ac.uk)
abstract = "The substrate-binding protein YfeA (also known as YPO2439 or y1897) is a polyspecific metal-binding protein that is crucial for nutrient acquisition and virulence in Yersinia pestis, the causative microbe of plague. (uky.edu)

The coat protein can bind helices with bulged adenines at either position, but the 3'-proximal site binds with greater affinity. (rcsb.org)
The identification of novel, high affinity AQP9 inhibitors in an intracellular binding site. (lu.se)
Affinity tags can reduce merohedral twinning of membrane protein crystals. (lu.se)

Purification and characterization of two protein kinases acting on the aquaporin SoPIP2;1. (lu.se)

The comparison between our proposed PDNAsite method and the existing methods indicate that PDNAsite outperforms most of the existing methods and is a useful tool for DNA-binding site identification. (nature.com)
Therefore, a reliable identification of DNA-binding sites in DNA-binding protein is important for protein function annotation, in silico modeling of transcription regulation and site-directed mutagenesis. (nature.com)
Pocketome via Comprehensive Identification and Classification of Ligand Binding Envelopes. (uni-marburg.de)
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)
Furthermore, this resource has allowed the identification of cis -regulatory sites in previously unexplored regions of the genome and the cooperating transcription factors underlying estrogen signaling in breast cancer. (nature.com)
Figure 4: Identification of enriched motifs within the estrogen receptor binding sites and validation of transcription factor binding. (nature.com)

Wang and his coworkers 12 investigated the discriminative power of three sequence features from protein sequence, including the side chain pKa value, the hydrophobicity index and the molecular mass of an amino acid. (nature.com)
However, molecular weight is also important due to potential steric incompatibilities within protein cores. (hindawi.com)
Discrete neuronal populations in brain express relaxin and relaxin-3, and molecular studies have identified former-orphan, G-protein-coupled receptors LGR7 and GPCR135 as their native receptors. (wiley.com)
In this study, we provide the first evidence that MucR from Brucella abortus binds more than one target site in the promoter region of its own gene, suggesting a molecular mechanism by which this protein represses its own expression. (cnr.it)
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 main aim of our research is to understand the molecular details and physiological roles of the multitude of water channel-like proteins present in plants and animals. (lu.se)

There is an urgent need for computational tools that can rapidly and reliably identify DNA-binding sites in DNA-binding proteins. (nature.com)
Computational design of novel proteins with well-defined functions is an ongoing topic in computational biology. (hindawi.com)

Protein-DNA interactions are involved in many fundamental biological processes essential for cellular function. (nature.com)
An analysis of the number of binding sites in the spatial context of the target site indicates that the interactions between binding sites next to each other are important for protein-DNA recognition and their binding ability. (nature.com)
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)
Hydrophobicity was one of the most important physicochemical properties, due to the fact that it is involved in protein interactions, for example, by forming hydrophobic cores. (hindawi.com)
These interactions are thought to be established mainly through the binding of aluminum to phosphorylated and non-phosphorylated amino acid sidechains. (worktribe.com)

We have studied this RNA motif in a 21 nucleotide hairpin containing a GA coat protein-binding site whose four nucleotide loop has been replaced by a more stable loop from the related phage Ms2. (rcsb.org)
We have compared the enhancer activity of this core element with a synthetic enhancer lacking the factor binding sites flanking the AP1/NF-E2 motif (HS2(M)). In fetal/erythroid K562 cells, enhancement of a linked γ-promoter was significantly greater with wild-type HS2 than with HS2(M). In contrast, the increase in β-promoter activity in these cells was equivalent with either enhancer fragment. (monash.edu)
Taken together, this data suggests that the stage-specific factors binding the proximal globin promoters and the factors flanking the AP1/NF-E2 motif of HS2 act in synergy. (monash.edu)
We have successfully combined two unrelated naturally occurring binding sites, the immunoglobin Fc-binding site of the Z domain and the DNA-binding motif of MyoD bHLH, into a novel stable protein. (hindawi.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)
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)

DNA FOOTPRINTING utilizes this technique to analyze the DNA contact sites of DNA-BINDING PROTEINS. (bvsalud.org)

A tight regulation of proton transport in the inner mitochondrial membrane is crucial for physiological processes such as ATP synthesis, heat production, or regulation of the reactive oxygen species as proposed for the uncoupling protein family members (UCP). (uni-linz.ac.at)
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)

Furthermore, a circular dichroism analysis reveals that MucR is a heat-stable protein. (cnr.it)
Insights from the work on formamide and other small amides have been applied to studies of proteins and have led to significant improvements in the calculation of the circular dichroism of proteins from first principles. (nottingham.ac.uk)

Human TSH is one of several glycoprotein hormones consisting of two non-covalently bound peptide chains: an a-chain, which is nearly identical in all, and a ß-chain, which is responsible for immunological and biological specificity. (cdc.gov)

Using cantilever tips with different cross-linker lengths, we determined the location of the nucleotide binding site inside the membrane with 1 precision. (uni-linz.ac.at)
Nature, 2011, 476, 109-113), our data provide a valuable insight into the mechanism of the nucleotide binding and pave the way for new pharmacological approaches against the diseases mentioned above. (uni-linz.ac.at)
Figure 1: Summary of estrogen receptor and RNA PolII binding sites and correlation with nucleotide and gene number. (nature.com)

HS2 contains a 400-base pair core element consisting of tandem AP1/NF-E2 motifs flanked by binding sites for multiple ubiquitous and erythroid-specific factors. (monash.edu)
Since ELAV/Hu proteins bind short U-rich motifs embedded in a highly degenerate sequence context, it is thought that multimerization of ELAV/Hu proteins is key to generate target specificity and that this step is highly regulated by cellular signaling. (findaphd.com)

Hepatic vesicular ion-trapping, intrinsic elimination clearance, permeability-surface area product, and intracellular binding were derived using a physiologically based pharmacokinetic model. (aspetjournals.org)
Lipophilicity and p K a determined hepatic drug retention: a drug with low p K a and low lipophilicity (e.g., antipyrine) distributes as unbound drug, a drug with high p K a and low lipophilicity (e.g., atenolol) by ion-trapping, and a drug with a high p K a and high lipophilicity (e.g., propranolol) is retained by ion-trapping and intracellular binding. (aspetjournals.org)
Intracellular trafficking of the human Wilson protein: the role of the six N-terminal metal-binding sites. (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)
Asx was cloned by transposon tagging and encodes a protein of 1668 amino acids containing an unusual cysteine cluster at the carboxy terminus. (ox.ac.uk)
A common amino acid substitution replaces the amino acid histidine with the amino acid glutamine at position 1069 in the protein (written as His1069Gln or H1069Q). (medlineplus.gov)

We mapped all estrogen receptor and RNA polymerase II binding sites on a genome-wide scale, identifying the authentic cis binding sites and target genes, in breast cancer cells. (nature.com)
Forkhead box protein M1 (FOXM1) is a key transcription factor (TF) that regulates a common set of genes related to the cell cycle in various cell types. (mdpi.com)
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)

ASX binds to multiple sites on polytene chromosomes, 70% of which overlap those of Polycomb, polyhomeotic and Polycomblike, and 30% of which are unique. (ox.ac.uk)

Each fiber contains hundreds to thousands of rodlike myofibrils, which are bundles of thin and thick protein chains termed myofilaments. (medscape.com)

Protein binding site comparisons are frequently used receptor-based techniques in early stages of the drug development process. (uni-marburg.de)
Figure 2: Estrogen-mediated transcript changes and correlation with estrogen receptor binding. (nature.com)
Figure 3: Estrogen receptor and RNA PolII binding relative to specific gene targets. (nature.com)
Figure 5: Involvement of cooperating transcription factors at estrogen receptor binding sites. (nature.com)
Figure 7: Assessment of estrogen receptor binding properties in different cell systems. (nature.com)
In the version of this article initially published online, the estrogen receptor and RNA PolII binding data were aligned incorrectly in the top panel of Figure 3, which represents estrogen receptor binding at the ESR1 gene region. (nature.com)
Trifluoperazine and fluphenazine, which inhibit ligand binding to the acidic pH binding sites, block degradation after internalization of cell surface-bound 125 I-TGF- β 1 or 125 I-α 2 M*. These results suggest that cell surface annexin VI may function as an acidic pH binding site or receptor and may also function as a co-receptor with LRP-1 at neutral pH. (tmu.edu.tw)

Two proteins (hemagglutinin and neuraminidase) on the surface of influenza viruses contain the major antigens targeted by antibodies (see Figure 1). (cdc.gov)
The above image shows the different features of an influenza virus, including the main surface proteins, hemagglutinin (HA) and neuraminidase (NA). (cdc.gov)

Annexin VI has been identified as a major membrane-associated protein capable of directly binding α 2 M* at acidic pH. (tmu.edu.tw)

By fragment screening using x-ray crystallography we identified four ligands revealing ligand-binding sites in conserved interfaces between SARS-CoV-2 nsp10 and nsp14/nsp16. (lu.se)

Annotation of Selaginella moellendorffii major intrinsic proteins and the evolution of the protein family in terrestrial plants. (lu.se)

A comparison of the structures reveals that the metal can be displaced at five different locations ranging from ∼4 to ∼16 Å away from the canonical site 2. (uky.edu)

Acts upstream of or within lipid metabolic process and protein import into nucleus. (nih.gov)

Recently the human cardiac myosin binding protein-C (MyBP-C) gene was mapped to chromosome 11p11.2 (ref. 8), making this gene a good candidate for the fourth locus, CMH4 (ref. 5). (nih.gov)

Perturbation studies where the geometry of a given site was retained but the residue types were changed randomly, indicated that chance similarities were virtually non-existent. (nih.gov)
The existence of a single histidine residue (His156) in the binding site has provided an excellent probe for distance measurements between protein and ligand. (bionmr.com)

A sample is added to a reaction vessel with goat anti-hTSH-alkaline phosphatase conjugate, buffered protein solution, and paramagnetic particles coated with immobilized mouse monoclonal anti-hTSH antibody. (cdc.gov)
The hTSH binds to the immobilized monoclonal anti-hTSH on the solid phase while the goat anti-hTSH-alkaline phosphatase conjugate reacts with a different antigenic site on the hTSH. (cdc.gov)

E7 from human papil omavirus type 16 cooperate to cancer: the European prospective investigation into doi:10.1093/carcin/bgp321 PMID:20047954 target the PDZ protein Na/H exchange regulatory cancer and nutrition study. (who.int)

These studies have revealed that 14-3-3 proteins can interact with the phosphorylated forms of their client proteins in response to certain signals, and that this binding finalizes the signaling event by enabling a change in the subcellular localization, protein stability or intrinsic enzymatic activity of the client, or by promoting an association between the client and other proteins. (elifesciences.org)

In two unrelated French families linked to CMH4, we found a mutation in a splice acceptor site of the MyBP-C gene, which causes the skipping of the associated exon and could produce truncated cardiac MyBP-Cs. (nih.gov)
Hypomorphic mutation in the site-1 protease Mbtps1 endows resistance to persistent viral infection in a cell-specific manner. (nih.gov)
This type of mutation alters the 3-dimensional structure of the protein or its stability, preventing copper-transporting ATPase 2 from functioning properly. (medlineplus.gov)

Orthologous to human MBTPS1 (membrane bound transcription factor peptidase, site 1). (nih.gov)

The comparison of recognition patterns obtained with anti-UCP1 antibody and ATP led to the conclusion that the ATP binding site can be accessed from both sides of the membrane. (uni-linz.ac.at)
Unoccupied binding sites on the anti-T3 antibody are bridged to the particle through the T3 analog. (cdc.gov)
A sample is added to a reaction vessel with anti-thyroxine antibody, thyroxine-alkaline phosphatase conjugate, and paramagnetic particles coated with goat anti-mouse capture antibody and a stripping agent to dissociate all T4 from binding proteins. (cdc.gov)

Moreover, binding site comparisons are used as an idea generator for bioisosteric replacements of individual functional groups of the newly developed drug and to unravel the function of hitherto orphan proteins. (uni-marburg.de)
With a shortage of functional protein, removal of excess copper from the body is impaired. (medlineplus.gov)

However, no changes induced by monensin treatment were observed in intrinsic clearance, permeability, or binding for the three model drugs. (aspetjournals.org)
Phylogeny of major intrinsic proteins. (lu.se)

Following influenza virus infection or receipt of a flu vaccine, the body's immune system develops antibodies that recognize and bind to "antigenic sites," which are regions found on an influenza virus' surface proteins. (cdc.gov)
By binding to the HA antigenic sites, antibodies can neutralize influenza viruses, which prevents them from causing further infection. (cdc.gov)
Antibodies that bind to the NA antigenic sites can also reduce further spread. (cdc.gov)

In the present work, accelerated methods for the comparison of protein binding sites as well as an extended procedure for the assessment of ligand poses in protein binding sites are presented. (uni-marburg.de)

Monensin did not affect binding or metabolic activity in vitro for the drugs. (aspetjournals.org)

Anatomy15

Organisms13

Chemicals and Drugs98

Analytical, Diagnostic and Therapeutic Techniques and Equipment42

Phenomena and Processes87

Disciplines and Occupations1

Technology, Industry, Agriculture1

Information Science9

Health Care3

Conformation1

Sequences6

Prediction2

Residues7

Mutations3

Structural12

Interaction8

Complexes5

Interacts3

Highly conserved2

Phosphorylation5

Drosophila3

Abstract2

Affinity3

Characterization1

Identification7

Molecular6

Computational2

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Motif4

Molecules3

Analyze1

Regulation2

Circular dichroism2

Peptide1

Nucleotide3

Motifs2

Intracellular3

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Genes3

Chromosomes1

Chains1

Receptor7

Hemagglutinin2

Membrane-associated1

Ligands1

Annotation1

Structures1

Lipid metabolic process1

Myosin1

Residue2

Monoclonal2

PMID1

Localization1

Mutation3

Transcription factor1

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Functional2

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Comparison of protein1

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