Protein section describes binding. Medical search. Frequent questions

The overall objective of the MM-PBSA method and it's complementary MM-GBSA method is to calculate the free energy difference between two states which most often represent the bound and unbound state of two solvated molecules or alternatively to compare the free energy of two different solvated conformations of the same molecule. (ambermd.org)
Lipoid proteinosis is a condition that results from the formation of numerous small clumps (deposits) of proteins and other molecules in various tissues throughout the body. (medlineplus.gov)
Ligands entering a protein binding pocket essentially compete with water molecules for binding to the protein. (acs.org)
Hence, the location and thermodynamic properties of water molecules in protein structures have gained increased attention in the drug design community. (acs.org)
The implemented routines analyze the protein environment of water molecules in molecular dynamics (MD) simulations and can differentiate between hydrogen bonded waters as well as waters in a protein environment of hydrophobic, charged, or aromatic atom groups. (acs.org)
PyRod adds a new perspective to structure-based screening campaigns by providing easy-to-interpret dMIFs and purely protein-based pharmacophores that are solely based on tracing water molecules in MD simulations. (acs.org)
When separating out molecules or proteins of different charges at a certain pH. (flashcardmachine.com)
These 'Interaction' records describe the binding event between two molecules. (biomedcentral.com)

Binding of a miRNA to a complementary sequence in a target mRNA is mediated by Argonaute proteins leading to degradation of the mRNA or translational inhibition, thereby lowering protein levels in cells [ 7 ]. (researchsquare.com)
The novel switch was found in Arabidopsis plants to control splicing of mRNA transcripts that encode signaling protein regulators of the plant immune response. (phys.org)
To turn immune defenses on, the researchers say, a simple chemical modification of the RNA-binding protein reverses mRNA splicing that normally keeps immune responses deactivated. (phys.org)
To turn the immune response back off, a second chemical modification of the RNA-binding protein returns mRNA splicing to "normal," and the immune response is back to being held in check. (phys.org)
In this study, at the mRNA and/or protein level, the expression patterns were similar for renal FXYD12 and NKA in the two medakas. (ijbs.com)

Intrinsically disordered regions (IDRs) lacking a fixed three-dimensional protein structure are widespread and play a central role in cell regulation. (iucr.org)
Extending outward from the hexameric core, Hfq presents a C-terminal region, described as intrinsically disordered in solution. (bvsalud.org)

The entropy contribution can be found by performing normal mode analysis on the three species but in practice entropy contributions can be neglected if only a comparison of states of similar entropy is desired such as two ligands binding to the same protein. (ambermd.org)
In this article, we describe a simple computational approach, based on the effect allosteric ligands exert on protein flexibility upon binding, to predict the existence and position of allosteric sites on a given protein structure. (biomedcentral.com)
We also analyzed four biological examples in detail, revealing that this simple coarse-grained methodology is able to capture the effects triggered by allosteric ligands already described in the literature. (biomedcentral.com)

In the interaction with proteins, lead binds with virtually every available functional group, including sulfhydryl, amine, phosphate, and carboxyl groups, with sulfhydryl having the highest affinity. (cdc.gov)
For chemokines binding with high affinity to sugar residues, immobilization can even lead to the formation of stable solid phase gradients, which induce a variant of haptotaxis 9 . (nature.com)
After having captured antigen in non-lymphoid tissues, DCs migrate along immobilized gradients of the high affinity sugar-binding chemokine (C-C motif) ligand21 (CCL21) towards lymphatic vessels, from where they are flushed into the sinus of lymph nodes. (nature.com)
Doxycycline has a high degree of lipoid solubility and a low affinity for calcium binding. (nih.gov)
When the molecule has a binding affinity that can be taken advantage of. (flashcardmachine.com)
Although the molecular significance of levetiracetam binding to SV2A is not understood, levetiracetam and related analogs showed rank order of affinity for SV2A which correlated with the potency of their antiseizure activity in audiogenic seizure-prone mice. (drugcentral.org)
FluoTag®-X2 anti-TagFP is derived from an in-house developed single-domain antibody (sdAb) that recognizes fluorescent proteins deriving from Entacmaea quadricolor, such as mTagBFP, mTagRFP, mTagRFP657 and mKate with high affinity and specificity. (nano-tag.com)
The strength of interaction between antibody and antigen at single antigenic sites can be described by the affinity of the antibody for the antigen. (sigmaaldrich.com)
The affinity constant for antibody-antigen binding can span a wide range, extending from below 105/mol to above 1012/mol. (sigmaaldrich.com)
A term used to describe the combined strength of multiple bond interactions [as opposed to affinity, which is a term used to describe the strength of a single bond]. (cdc.gov)

Pull-down assays between PRPF31 and PRPF6 proteins showed a stronger interaction for the mutant than wild type, suggesting a mechanism for the negative effect. (molvis.org)
The Biomolecular Interaction Network Database (BIND) was developed to undertake the mammoth task of providing a public database of all known biomolecular interactions. (biomedcentral.com)
The Pathway record describes a cellular process as a sequential list of Interaction records, and provides associated data such as phenotype. (biomedcentral.com)
The 'visualize interaction' feature in the search results is entertaining - clicking on a protein unleashes a series of connecting boxes identifying all the proteins known (to BIND) to interact with it. (biomedcentral.com)
These findings suggest that the interaction of levetiracetam with the SV2A protein may contribute to the antiepileptic mechanism of action of the drug. (drugcentral.org)
Our results demonstrated that NIMA-related kinase 2 (Nek2) binds β-catenin, blocking the interaction between this protein and the destruction complex, and ultimately contributing to sorafenib resistance for HCC. (biomedcentral.com)

Doxycycline inhibits bacterial protein synthesis by binding to the 30S ribosomal subunit. (nih.gov)
Synthesis of these structures is energy intensive and, while extensive transcriptional regulation has been described, little is known about the posttranscriptional regulation. (bvsalud.org)
Unlike most sRNAs, MotR and FliX base pair within the coding sequences of target mRNAs and act on ribosomal protein mRNAs connecting ribosome production and flagella synthesis. (bvsalud.org)
The sole site of synthesis of the FXI plasma protein is the liver. (medscape.com)
This system separates mutations that (1) result in decreased synthesis of the protein (Glu117Stop or Type II) producing no measurable FXI in the homozygous state, (2) abnormal dimerization of the protein (Phe283Leu or Type III) producing approximately 10% of FXI in the homozygous state, or (3) dimerization that results in the FXI protein to be poorly secreted (Ser225Phe and Cys398Tyr). (medscape.com)

Doxycycline has been shown to be active against most isolates of the following microorganisms, both in vitro and in clinical infections as described in the INDICATIONS AND USAGE section of the package insert for DOXYCYCLINE HYCLATE CAPSULES. (nih.gov)

By screening for proteins that colocalize with NHR-67 punctae, we identified new regulators of uterine cell fate maintenance: homologs of the transcriptional co-repressor Groucho (UNC-37 and LSY-22), as well as the TCF/LEF homolog POP-1. (elifesciences.org)
The Trithorax group (TrxG) is composed of diverse, evolutionary conserved proteins that form chromatin-associated complexes accounting for epigenetic transcriptional memory. (silverchair.com)
In the last decades, HOX proteins have been extensively studied due to their pivotal role in transcriptional events. (mdpi.com)

Dr. Cochran's translational interests span protein-based drug discovery and development for applications in oncology and regenerative medicine, and the development of new technologies for high-throughput protein analysis and engineering. (stanford.edu)

The "well" inthe free energy diagram where the native folded protein exists. (flashcardmachine.com)
This Product is not recommended to be used to detect proteins in Western Blott, sdAbs tend to recognize mainly native/folded proteins. (nano-tag.com)

Avidity is a term that can be used to describe antibody-antigen interactions, where multiple, weak bonds form between antigen and antibody. (cdc.gov)

By querying the literature and a recently available database of allosteric sites, we gathered 213 allosteric proteins with structural information that we further filtered into a non-redundant set of 91 proteins. (biomedcentral.com)
Furthermore, we implemented an approach that achieves 65% positive predictive value in identifying allosteric sites within the set of predicted cavities of a protein (stricter parameters set, 0.22 sensitivity), by combining the current analysis on dynamics with previous results on structural conservation of allosteric sites. (biomedcentral.com)
To explain this briefly, if the pathogen's active site is very well conserved in nature it may share important structural features with the human homologue, which could be then bound and inhibited as well by the antimicrobial drug causing toxic side-effects on the patient. (biomedcentral.com)
This gene provides instructions for making a protein that is found in most tissues within the extracellular matrix, which is an intricate lattice that forms in the space between cells and provides structural support. (medlineplus.gov)
The ECM1 protein can attach (bind) to numerous structural proteins to provide strength to tissues. (medlineplus.gov)
These characteristics correlate with a distinct nuclear architecture, epigenetic signatures enriched for active chromatin marks and hyperdynamic binding of structural chromatin proteins. (biomedcentral.com)
Geneticists have described many interesting connections between chromatin components and transcription, but they have lacked a system to investigate the structural basis of the connections. (nih.gov)

In its binding with sulfhydryl groups, lead may interfere with the activity of zinc metalloenzymes, as zinc binds to a sulfhydryl group at the active site. (cdc.gov)
Lead also binds to metallothionein, a sulfhydryl-rich protein, but does not appear to displace cadmium or zinc. (cdc.gov)

Mechanistically, FSH, via binding to hepatic FSHRs, activates the Gi2α/β-arrestin-2/Akt pathway and subsequently inhibits the binding of FoxO1 with the SREBP-2 promoter, thus preventing FoxO1 from repressing SREBP-2 gene transcription. (nature.com)
One would be to analyze other genes affected by this process of DNA methylation that inhibits CREB1 binding, with the aim of seeing what role they play in the organism, as well as their possible association with diseases. (fapesp.br)

Particle-enhanced assays are based on the reaction between a soluble analyte and the corresponding antigen or antibody bound to polystyrene particles. (cdc.gov)
Ultimately these factors define the specificity of the antibody, that is, the likelihood that the particular antibody is binding to a precise antigen epitope. (sigmaaldrich.com)
Cross-reactivity is sometimes desirable when one wants general binding to a related group of antigens or when attempting cross-species labeling when the antigen epitope sequence is not highly conserved during evolution. (sigmaaldrich.com)
Usually there are multiple bond formations observed, ensuring relatively tight binding between antibody and antigen. (sigmaaldrich.com)
however when multiple individual bonds are present at the same time, the overall effect is strong binding of antigen to antibody. (cdc.gov)

Missense mutations in PRPF31 have previously been shown to cause reduced protein solubility, suggesting insufficiency of functional protein as the disease mechanism. (molvis.org)
Proteins can be regarded as the functional building blocks of life, carrying out and coordinating almost all biological processes. (biomedcentral.com)
A lack of functional ECM1 protein reduces binding between ECM1 and other proteins, leading to an unstable extracellular matrix. (medlineplus.gov)

These mechanisms include the ability of lead to inhibit or mimic the action of calcium and to interact with proteins. (cdc.gov)

The hydrophobic sections are attracted nonpolar patches on the chaperone. (flashcardmachine.com)

The unstable extracellular matrix may cause neighboring cells to overproduce proteins and other materials. (medlineplus.gov)

Cross-reactivity refers to an antibody or population of antibodies binding to epitopes on other antigens. (sigmaaldrich.com)

In this tutorial we will demonstrate the use of the MM/PB(GB)SA scripts included with Amber and AmberTools to automatically perform all the necessary steps to estimate the binding free energy of a protein-protein complex (RAS and RAF) and a protein-ligand complex (Estrogen Receptor and Raloxifene) using both MM-GBSA and MM-PBSA methods in serial and parallel. (ambermd.org)
We performed normal-mode analysis and observed significant changes in protein flexibility upon allosteric-ligand binding in 70% of the cases. (biomedcentral.com)
These results agree with the current view that allosteric mechanisms are in many cases governed by changes in protein dynamics caused by ligand binding. (biomedcentral.com)
We introduce a simple computational approach to predict the presence and position of allosteric sites in a protein based on the analysis of changes in protein normal modes upon the binding of a coarse-grained ligand at predicted cavities. (biomedcentral.com)
Thus, lower levels of evolutionary conservation at ligand-binding sites may allow for more selective drugs. (biomedcentral.com)
Here, we present PyRod, a free and open-source Python software that allows for visualization of pharmacophoric binding pocket characteristics, identification of hot spots for ligand binding, and subsequent generation of pharmacophore features for virtual screening. (acs.org)
We previously described that peripheral administration to neonatal mice of the TLR2 ligand PAM3CSK4 (P3C), a prototypic Gram-positive bacterial lipopeptide, induces the migration of innate immune cells to the CSF. (biomedcentral.com)

Alternatively spliced variants that encode different protein isoforms have been described but the full-length nature of only one has been determined. (wikipedia.org)

saturable and stereoselective neuronal binding site in rat brain tissue has been described for levetiracetam. (drugcentral.org)
In a cross-sectional study of 48 AD patients without diabetes, 20 cognitively normal diabetic patients, 16 patients with frontotemporal dementia, and 84 cognitively normal controls, researchers found that dysfunctionally phosphorylated insulin receptor substrate-1 (IRS-1), a neuronal protein, is detectable in blood using exosome-based technology and may be able to predict AD up to 10 years before the appearance of symptoms. (medscape.com)

This paper, and the accompanying Diagram, describe many aspects of the influenza vaccine process including important similarities and differences in how seasonal human influenza viruses and H5N1 viruses are handled. (who.int)

The book discusses the essential components of a balanced diet such as carbohydrates, fats, proteins, vitamins, calcium, iron, and other minerals along with the information about dietary elements that may need to be limited, such as sodium, sugar, and fat. (omnigraphics.com)

In non-fixed brain sections these antibodies gave labeling patterns similar to autoradiographic distributions with particularly high levels in the hippocampus. (jneurosci.org)

C57BL/KaLwRij mice were implanted subcutaneously with unilateral murine green fluorescent protein-expressing 5TGM1 tumors and divided into 3 independent groups: untreated, treated beginning week 2 after tumor implantation, and treated beginning week 3 after tumor implantation. (snmjournals.org)
Amytracker 480 is our blue fluorescent optotracer for labeling protein aggregates with repetitive arrangement of β-sheets. (ebbabiotech.com)

Allostery can be defined as the regulation of a protein's function by binding of an effector molecule at a site which is not the active site. (biomedcentral.com)
Although BIND currently only accepts protein-protein and protein-nucleic acid interactions, tools are being developed for the site to accept small-molecule data. (biomedcentral.com)
A proposed classification system for factor XI deficiency is based on the patterns of protein production or dimerization of the FXI molecule. (medscape.com)

AMPA receptor variants were identified with a polyclonal antibody recognizing the conserved extracellular loop region of all four AMPA receptor subunits (GluR1-4, both flip and flop ), whereas NMDA receptors were immunolabeled with a polyclonal antibody that binds to an extracellular N-terminal epitope of the NR1 subunit, common to all splice variants. (jneurosci.org)
Receptor binding studies on guinea-pig pulmonary macrophages, rabbit neutrophils, and human neutrophils utilizing tritium labeled fMLP were undertaken to investigate the possibility they could be used to develop a competitive binding assay. (cdc.gov)
The receptor binding patterns indicated the presence of at least three fMLP receptors that would interfere with measuring fMLP in a competitive assay. (cdc.gov)
19 normal healthy in- receptor protein (CD117) that is structurally dividuals were recruited as a control group. (who.int)

Hfq is an RNA-binding protein that is ubiquitous and highly conserved in bacterial species. (bvsalud.org)

Initially, lead is distributed to the blood plasma and soft tissues, but under steady state conditions 99% of the lead in blood is found in the erythrocyte, where much of it is bound to hemoglobin. (cdc.gov)
BIND-related tools include BIND BLAST (for BLASTing against the proteins found in the BIND database) and PreBIND, a tool that searches the scientific literature for possible interactions and then submits bona fide interactions to BIND. (biomedcentral.com)
By screening β-catenin-interacting proteins, we found that Nek2 could bind β-catenin in sorafenib-treated HCC cell lines. (biomedcentral.com)
Moreover, the FXYD protein family was found to be a regulator of NKA. (ijbs.com)
Proteins that are found in blood or other bodily fluids of vertebrates. (cdc.gov)
Below is a list of the main nomenclatures found in the literature to describe BrS. (bvsalud.org)

The DNA-binding motif suggest this protein is involved in the regulation of transcription and chromatin remodeling. (wikipedia.org)
Recently, several chromatin-related proteins have been shown to regulate ESC pluripotency and/or differentiation, yet the role of the major heterochromatin proteins in pluripotency is unknown. (biomedcentral.com)
The minor fraction of HP1β that is chromatin-bound in ESCs is enriched within exons, unlike the situation in differentiated cells, where it binds heterochromatic satellite repeats and chromocenters. (biomedcentral.com)

However, typically one makes the approximation that no significant conformational changes occur upon binding so that the snapshots for all three species can be obtained from a single trajectory. (ambermd.org)

When separating out proteins of different molecular weights. (flashcardmachine.com)
at the same time developing protein and peptide-based tools that will allow us to manipulate cellular processes on a molecular level. (stanford.edu)
Plasma FXI complexes with high-molecular-weight kininogen, which then aids in the binding of FXI to negatively charged surfaces. (medscape.com)

After six months it is available under a Creative Commons License (Attribution-Noncommercial-Share Alike 4.0 International license, as described at https://creativecommons.org/licenses/by-nc-sa/4.0/ ). (rupress.org)

Insoluble protein aggregates associated with Alzheimer's and Prion disease. (flashcardmachine.com)
It labels Aβ plaques and neurofibrillary tangles in tissue sections with AD pathology and α-synuclein aggregates in tissue sections with PD pathology. (ebbabiotech.com)

Small noncoding RNAs called microRNAs (miRNA) negatively regulate gene expression by sequence-specific targeting of protein-coding transcripts [ 6 ]. (researchsquare.com)

Have a look at our specificity chart in our Resource Section . (nano-tag.com)
Look at detailed protocols and our specificity chart in our Resource Section . (nano-tag.com)

Rosenthal and colleagues first described factor XI deficiency in 1953. (medscape.com)

Allostery is one of the most powerful and common ways of regulation of protein activity. (biomedcentral.com)
Tight regulation of these processes is fundamental in all kingdoms of life and allostery represents one of the most commmon and powerful means of modulating protein activity[ 1 ]. (biomedcentral.com)
Experimental data indicate that this binding site is the synaptic vesicle protein SV2A, thought to be involved in the regulation of vesicle exocytosis. (drugcentral.org)
in the second, we are addressing the role of a sequence-specific DNA-binding histone acetylase, Spt10p, in the cell cycle-dependent regulation of the histone genes. (nih.gov)

Neurological disorders such Alzheimer's disease, as well as depression and aging, correlate with reduced levels of this protein in the brain. (fapesp.br)

In the poster section, Joanna Shisler (University of Illinois at Urbana-Champaign [UIUC], Urbana) reported that the modified virus, Ankara, activates nuclear factor κB through the mitogen-activated protein kinase, extracellular signal-regulated kinase (MEK)/extracellular signal-regulated kinase (ERK) pathway, possibly facilitating the host immune response. (cdc.gov)
In the poster section, Joanna Shisler (University of Illinois at Urbana-Champaign [UIUC], Urbana) reported that the modified virus, Ankara, activates nuclear factor κB through the mitogen-activated protein kinase, extracellular signal–regulated kinase (MEK)/extracellular signal–regulated kinase (ERK) pathway, possibly facilitating the host immune response. (cdc.gov)

Describe the basice disulfide exchange mechanism. (flashcardmachine.com)
If the expression of other genes besides PKMzeta is affected by this pattern of DNA methylation, it must be particularly relevant to brain alterations possibly associated with pathologies, and the authors showed that the mechanism is not confined to the protein PKMzeta. (fapesp.br)
As described July 20 in their report published in Nature Plants , they identified a new regulatory switching mechanism-an RNA-binding protein-that helps turn on immune responses a few minutes after attack. (phys.org)
These findings provide clues to the mechanism of host-bacteria interactions which may not be defined solely by protein-protein and protein-outer membrane contacts, but also by the exchange of RNAs, and in particular sRNAs. (bvsalud.org)

The study showed, however, that hypermethylation of this piece of the gene resulted in significantly lower levels of the protein PKMzeta. (fapesp.br)

An epigenetic technique often used by researchers is gene silencing by DNA methylation, in which methyl groups are added to a specific section of a gene to prevent its transcription. (fapesp.br)

Estrogens are important regulators of growth and differentiation in (range, 0 -9 fmol/mg protein, median 0.7). (lu.se)

In clinical depression, however, a transition occurs to sensitization of immuno-inflammatory pathways, progressive damage by oxidative and nitrosative stress to lipids, proteins, and DNA, and autoimmune responses directed against self-epitopes. (biomedcentral.com)
In this context, there is abundant evidence that clinical depression is an immuno-inflammatory disorder characterized by among other things increased levels of PICs and acute phase proteins, including C-reactive protein and haptoglobin [ 11 - 20 ]. (biomedcentral.com)
ER protein determinations were performed using two-thirds of all breast cancers are ER at the time of diagnosis, the standard methods in the routine clinical laboratory (9). (lu.se)

PreBIND-searches and direct submission of experimental data are the two primary mechanisms of importing new data into BIND. (biomedcentral.com)

He also showed that double-stranded (ds)RNA- and ZDNA binding proteins had a role in poxvirus pathogenesis. (cdc.gov)
Here, based on genetic analyses in zebrafish, we identify the multidomain protein Brpf1 as a novel TrxG member with a central role during development. (silverchair.com)
The authors also analyzed the role of other genes in the central nervous system to see if they were inhibited by this process of DNA hypermethylation that prevented CREB1 binding. (fapesp.br)

En outre, il y avait une aug- mentation significative de la forme soluble du c-kit dans le sérum des patients atteints de pemphigus vulgaire actif par rapport aux témoins. (who.int)

Here we identify Heterochromatin Protein 1β (HP1β) as an essential protein for proper differentiation, and, unexpectedly, for the maintenance of pluripotency in ESCs. (biomedcentral.com)

To my mind this greatly increases the chances of BIND avoiding 'orphan database' syndrome and instead maturing into a highly useful online tool. (biomedcentral.com)

In 2008 after further mutagenesis and the exchange of ~12 amino acid residues, this red-emitting protein turned into a blue-emitting protein TagBFP. (nano-tag.com)

It is a 160,000-d protein composed of a disulfide-linked dimer with identical polypeptide chains. (medscape.com)

In this work we show, by using a combination of infrared and circular dichroism spectroscopies, that Hfq, after interacting with the inner membrane, can be translocated into the periplasm, and then be exported in OMVs, with the possibility to be bound to sRNAs. (bvsalud.org)

Rosenthal first described this bleeding disorder in 1953. (medscape.com)

BIND was originally designed by researchers at the University of Toronto (a list of key people is available at the site), but has since been passed into the hands of blueprint WORLDWIDE Inc., a non-profit organization specializing in biomolecular data management. (biomedcentral.com)

In this section, we will use 'R' to simulate a simple constitutive gene expression model. (openwetware.org)

How is crystal structure resolution influenced by protein dynamics? (flashcardmachine.com)

Anatomy45

Organisms17

Diseases28

Chemicals and Drugs38

Analytical, Diagnostic and Therapeutic Techniques and Equipment89

Phenomena and Processes31

Disciplines and Occupations11

Anthropology, Education, Sociology and Social Phenomena1

Technology, Industry, Agriculture1

Information Science8

Named Groups1

Health Care11

Geographicals1

Molecules8

MRNA5

Intrinsically disordered2

Ligands3

Affinity10

Interaction6

Synthesis5

Microorganisms1

Transcriptional3

High-throughput protein1

Native folded2

Antibody-antigen1

Structural7

Sulfhydryl2

Inhibits2

Antigen5

Functional3

Interact1

Hydrophobic1

Extracellular matrix1

Antigens1

Ligand7

Isoforms1

Neuronal2

Diagram1

Calcium1

Antibodies1

Fluorescent2

Molecule3

Receptor4

Bacterial1

Found6

Chromatin3

Conformational1

Molecular3

Https1

Aggregates2

Transcripts1

Specificity2

Factor XI deficie1

Regulation4

Alzheimer's1

Immune response2

Mechanism4

Significantly1

Epigenetic1

Regulators1

Clinical3

Experimental1

Role3

Soluble1

Differentiation1

Syndrome1

Residues1

Polypeptide1

Possibility1

Rosenthal1

Researchers1

Gene expression1

Dynamics1