Binding sites of proteins. Medical search. Frequent questions

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)
Structural analysis of their complexes with rRNA requires identification of their binding sites in the 5S rRNA. (unboundmedicine.com)
Insulin-like growth factor-binding proteins (IGFBPs) control bioavailability, activity, and distribution of insulin-like growth factor (IGF)1 and -2 through high-affinity IGFBP/IGF complexes. (rcsb.org)
Although the C-terminal domains do not form stable binary complexes with either IGF1 or the N-terminal domain of IGFBP4, in the ternary complex, the C-terminal domain contacts both and contributes to blocking of the IGF1 receptor-binding region of IGF1. (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)

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)
D614G is potently neutralized by antibodies targeting the receptor binding domain D614G shifts S protein conformation towards an ACE2-binding fusion-competent state. (cdc.gov)

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)
The coat protein can bind helices with bulged adenines at either position, but the 3'-proximal site binds with greater affinity. (rcsb.org)
A high-affinity IGF1-binding site is located in a globular structure between residues 39 and 82. (rcsb.org)
We previously reported the development of high affinity Zn2+ FRET sensors based on the Zn2+-mediated interaction between the CXXC motifs present in the copper chaperone proteins ATOX1 and WD4. (tue.nl)
Here we used an affinity-purification mass spectrometry-based (AP-MS) approach to identify novel and particularly intracellular sGAG-interacting proteins in human bone marrow stromal cells (hBMSC). (degruyter.com)
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)

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)
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)
Matching of structural motifs using hashing on residue labels and geometric filtering for protein function prediction. (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)
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)
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)
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)
Introduction to Protein-DNA Interactions: Structure, Thermodynamics, and Bioinformatics describes what we know about protein-DNA interactions from the complementary perspectives of molecular and structural biology and bioinformatics and how each perspective informs the others. (cshlpress.com)
Structural and biochemical characterization of two heme binding sites on α1-microglobulin using site directed mutagenesis and molecular simulation. (lu.se)
Proteins that contain linked binding sites are called allosteric proteins and can be of various types, such as enzymes, receptors, structural proteins, and motor proteins. (jove.com)

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)
Methods for the assessment of ligand poses in protein binding sites are also used in the early phase of drug development within docking programs. (uni-marburg.de)
How to Measure the Similarity Between Protein Ligand-binding Sites. (uni-marburg.de)
The Automatic Search for Ligand Binding Sites in Proteins of Known Three-dimensional Structure Using only Geometric Criteria. (uni-marburg.de)
Pocketome via Comprehensive Identification and Classification of Ligand Binding Envelopes. (uni-marburg.de)
A simple and fuzzy method to align and compare druggable ligand-binding sites. (uni-marburg.de)
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)
An investigation of the ligand-binding site of the glutamine-binding protein of Escherichia coli using rotational-echo double-resonance NMR. (bionmr.com)
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)
These results have unambiguously determined the ligand orientation with respect to the imidazole ring of His156, which is an important first step in refining the ligand-binding-site model of GlnBP in general. (bionmr.com)
SeeSAR automatically detects the binding site of a ligand for you. (biosolveit.de)
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)
Using tert-butyl groups in a ligand to identify its binding site on a protein. (cipps.org.au)
Identifying ligand-binding sites on proteins is key to understanding how the protein functions and finding new drugs. (drugdiscoverynews.com)
Several algorithms have been developed to look for binding clefts in protein surfaces, but none of them into account a key identifier of protein-ligand binding, the clustering of specific amino acids. (drugdiscoverynews.com)
They found specific amino acids tended to be found within concavities more often than others, and they used this information to develop an index called propensity for ligand binding (PLB). (drugdiscoverynews.com)
When they looked at the highest scoring concavities on a given protein, they found 79% represented known ligand binding sites. (drugdiscoverynews.com)
The PLB index would also be useful for identifying ligand-binding sites on novel target molecules with unknown ligands. (drugdiscoverynews.com)
A longstanding effort to do so is by exploiting protein structures to predict new reagents and therapeutic leads (structure-based ligand discovery). (ucsf.edu)
In Reversible Ligand Binding (eds A. Bellelli and J. Carey). (jove.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)
Two non-consecutive sets of zinc-binding residues form two separate metal-binding sites. (nih.gov)
VH is derived from a single protein domain of 35 residues [ 9 ]. (hindawi.com)
In IGFBP4, residues 1-38 form a rigid disulphide bond ladder-like structure, and the first five N-terminal residues bind to IGF and partially mask IGF residues responsible for the type 1 IGF receptor binding. (rcsb.org)
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)

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)
The interaction of sGAG with α2-macroglobulin receptor-associated protein (LRPAP1), exportin-1 (XPO1), and serine protease HTRA1 (HTRA1) was confirmed in reverse assays. (degruyter.com)
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)

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)

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)
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)
The identification of RBP binding sites is a crucial step in understanding the biological mechanism of post-transcriptional gene regulation. (biomedcentral.com)
The structures reveal the mechanisms of IGF signaling regulation via IGFBP binding. (rcsb.org)
Shepard, AR, Zhang, W & Eberhardt, NL 1994, ' Two CGTCA motifs and a GHF1/Pit1 binding site mediate cAMP-dependent protein kinase A regulation of human growth hormone gene expression in rat anterior pituitary GC cells ', Journal of Biological Chemistry , vol. 269, no. 3, pp. 1804-1814. (elsevierpure.com)
The involvement of viral DNA-binding proteins in the regulation of virulence genes, transcription, DNA replication, and repair make them significant targets. (mdpi.com)
Intriguingly, human Hu proteins can substitute for ELAV in a Drosophila model for alternative splicing regulation. (findaphd.com)

As they report in the Journal of Chemical Information and Modeling , the researchers started with X-ray structures of proteins bound by drugs or druglike ligands, the latter defined by 14 molecular descriptors. (drugdiscoverynews.com)
Developing computational methods to relate receptors by the similarity of their ligands, rather than by protein sequence or structure. (ucsf.edu)

Koay, MST, Janssen, BMG & Merkx, M 2013, ' Tuning the metal binding site specificity of a fluorescent sensor protein: from copper to zinc and back ', Dalton Transactions , vol. 42, pp. 3230-3232. (tue.nl)
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)
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)

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)

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)
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)
By identifying many sGAG-specific interacting proteins, our data provide a resource for upcoming studies aimed at molecular mechanisms and understanding of sGAG cellular effects. (degruyter.com)
One of the foundations of molecular biology is how the interactions of proteins with DNA control many aspects of gene expression. (cshlpress.com)
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)

abstract = "Cry1Fa insecticidal protein was successfully radiolabeled with (125)I-Na. (bath.ac.uk)

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)
We show that SARS-CoV-2 spike protein interacts with both cellular heparan sulfate and angiotensin converting enzyme 2 (ACE2) through its Receptor Binding Domain (RBD). (cdc.gov)

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)
Antibody binding sites are not black and white, and interactions between influenza and antibodies are wildly complicated. (stackexchange.com)
Since the mid-20th century, from discoveries of the lac repressor and operator and the competition between the cI and cro proteins for the same segment of DNA, we have learned an enormous amount about the interactions of proteins with DNA and their control of fundamental processes in the cell. (cshlpress.com)
A particular emphasis is on how insights from experimental work can be translated into specific computational approaches to create a unified view of the field and a fuller understanding of protein-DNA interactions. (cshlpress.com)

The 14-3-3 proteins are highly conserved in all eukaryotes. (elifesciences.org)
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)

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)

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)
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)
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)

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)

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)
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)

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)
Gel shift analyses indicated that similar, ubiquitous, thermostable protein(s) specifically bound the pCRE and dCRE motifs. (elsevierpure.com)

CRISPR-Cas (clustered regularly interspaced short palindromic repeats and CRISPR-associated proteins) adaptive immune systems defend microbes against foreign nucleic acids via RNA-guided endonucleases. (nih.gov)
Consecutive pathway and cluster analysis led to the identification of biological processes, namely processes involving binding and processing of nucleic acids, LRP1-dependent endocytosis, and exosome formation. (degruyter.com)

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)
Tests the new methods in well-controlled systems, determining x-ray crystal structures and measuring binding thermodynamics. (ucsf.edu)

I would like a list of all very important AA substitutions (that are near the receptor binding site) to involve in a bioinformatics project. (stackexchange.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)

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)

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)
Amino acid substitutions near the receptor binding site HA protein in type A H3N2 influenza strains? (stackexchange.com)
The special emphasis amino acid sites list does not include all amino acids that are near the binding site. (stackexchange.com)
begingroup$ I may provide a more substantial answer after reading the paper but right now I just want to point out that an amino acid substitution can affect sites that are far from it (on the sequence) because it can affect the folding. (stackexchange.com)
How does one predict how large of an effect on antigenic drift a substitution in the amino acid sequence of a surface protein of influenza has? (stackexchange.com)
Using the Alpha Site Finder function of MOE , they identified concavities in the proteins' surfaces and characterized the composition of amino acids in these concavities, as well as more general placement on protein surfaces. (drugdiscoverynews.com)
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)

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)
Enrichment analysis for protein localization showed that mainly intracellular and cell-associated interacting proteins were identified. (degruyter.com)
Localization of binding sites in the central nervous system for leptin (OB protein) in normal, obese (ob/ob), and diabetic (db/db) C57BL/6J mice. (bvsalud.org)

The identification of the intracellular sGAG-interacting proteins could help to unravel these functions. (degruyter.com)
Intracellular trafficking of the human Wilson protein: the role of the six N-terminal metal-binding sites. (medlineplus.gov)

DNA FOOTPRINTING utilizes this technique to analyze the DNA contact sites of DNA-BINDING PROTEINS. (bvsalud.org)
The browser features both a phylogenetic-tree-based view and a genomic-coordinate, track-based view in which users can analyze the sequence features of viral genomes, sequence diversity among viral strains, genomic sites of diagnostic tests, predicted immunogenic epitopes and a continuously updated repository of publicly available genomic datasets. (cdc.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)
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)
Annexin VI has been identified as a major membrane-associated protein capable of directly binding α 2 M* at acidic pH. (tmu.edu.tw)
Specific binding to brush border membrane vesicles was shown for the lepidopteran species Ostrinia nubilalis, Spodoptera frugiperda, Spodoptera exigua, Helicoverpa armigera, Heliothis virescens, and Plutella xylostella. (bath.ac.uk)
They have been defined as monotropic integral membrane proteins located primarily in the endoplasmic reticulum (COX-1) and the perinuclear envelope (COX-2). (medscape.com)

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, the identification of RBP binding sites is crucial to understanding the mechanism of biological processes. (biomedcentral.com)

It also has six additional regulatory subunits, each with a site that can bind both pyrimidines and purines, the building blocks of DNA and RNA. (jove.com)
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)

Applying these to G-Protein Coupled Receptors (GPCRs), which are the single largest family of signaling receptors in human cells. (ucsf.edu)

Study of Functional and Allosteric Sites in Protein Superfamilies. (jove.com)

Binding sites linkages can regulate a protein's function. (jove.com)

The normal EWS gene encodes an RNA binding protein closely related to FUS (gene) and TAF15, all of which have been associated to amyotrophic lateral sclerosis. (wikipedia.org)
The transcription of COX-1 yields a 2.7-kilobase (kb) messenger ribonucleic acid (mRNA) that encodes a 576-residue, 65-kd protein. (medscape.com)
Conversely, the transcription of COX-2 yields a 4.5-kb mRNA that encodes a 70-kd protein with roughly 70-75% homology to the COX-1 protein. (medscape.com)

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

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)
Within the Cas13a (also called C2c2) subfamily, the active site is functionally diverse in terms of both nucleotide cleavage preference and turnover efficiency. (nih.gov)

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)

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)
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)

To address this problem, researchers at Astellas Pharma and Tokai University developed a new algorithm that allowed them to predict drug and druglike molecule binding. (drugdiscoverynews.com)
This protein is part of the P-type ATPase family, a group of proteins that transport metals into and out of cells by using energy stored in the molecule adenosine triphosphate (ATP). (medlineplus.gov)

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

Methods: ZDEC oxidation/reduction products and sites of protein binding were assessed using high-performance liquid chromatography and mass spectrometry. (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)

Docking studies suggest a heparin/heparan sulfate-binding site adjacent to the ACE2 binding site. (cdc.gov)
Both ACE2 and heparin can bind independently to spike protein in vitro. (cdc.gov)

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

Arabidopsis ethylene-responsive element binding factors act as transcriptional activators or repressors of GCC box-mediated gene expression. (ugent.be)

The expression of a chimeric protein with the EWS transactivation domain fused to the DNA binding region of a transcription factor generates a powerful oncogenic protein causing Ewing sarcoma and other members of the Ewing family of tumors. (wikipedia.org)
pCRE) and a pituitary-specific transcription factor (GHF1/Pit1) binding site at nucleotides -123/-112 (dGHF1) which were required for cAMP responsiveness. (elsevierpure.com)

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)

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)
In patients multiple myeloma, the globulin concentration is often increased, leading to excessive binding of calcium to the monoclonal paraprotein and occasional elevation of the total serum calcium concentration, yet the ionized calcium level may be normal in these individuals. (medscape.com)

Our extensive experimental results show that DeepRKE is an efficacious tool for predicting RBP binding sites. (biomedcentral.com)

Within liver cells, copper-transporting ATPase 2 is found in a structure called the Golgi apparatus, which modifies newly produced enzymes and other proteins. (medlineplus.gov)

One of the methods that have been proposed is a multiobjective optimization, in which protein stability and catalytic activity are simultaneously optimized [ 4 , 5 ]. (hindawi.com)
For example, aspartate transcarbamoylase, also known as ATCase, is a large enzyme containing six catalytic subunits, each with a substrate binding site. (jove.com)
Binding of UTP and CTP to the enzyme negatively regulates the linked catalytic site when the concentration of pyrimidines is high, relative to the concentration of purines in the cell. (jove.com)

Biology Stack Exchange is a question and answer site for biology researchers, academics, and students. (stackexchange.com)

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)

They are typically trained from a set of input features, which can be generally divided into three categories: protein sequence information, protein structure information and a combination of the two categories. (nature.com)
Previously, a TL5-binding site has been identified, a TL5-RNA complex crystallized, and its structure determined to 2.3 A. The sites for L5 and L18 were characterized, and two corresponding 5S rRNA fragments constructed. (unboundmedicine.com)
For instance, RNAcontext [ 12 ] uses position weight matrix (PWM) of RNA sequence and secondary structure profile to predict the binding preference of RBP. (biomedcentral.com)
GraphProt [ 14 ] adopts the form of graph coding to integrate RNA sequence and structure into the graph kernel to generate a feature vector of more than 3,000 dimensions, which is subsequently used as the input of an SVM model to predict RBP binding preference. (biomedcentral.com)
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)
There are no general rules but some approximations can be made if we know the protein structure. (stackexchange.com)
A1M binds heme and the crystal structure suggests that C34 and H123 participate in a heme binding site. (lu.se)

PKC and CaMKII phosphorylate the synprint site and inhibit SNARE protein binding in vitro . (bvsalud.org)

Anatomy18

Organisms13

Chemicals and Drugs101

Analytical, Diagnostic and Therapeutic Techniques and Equipment36

Phenomena and Processes84

Disciplines and Occupations3

Technology, Industry, Agriculture1

Information Science9

Health Care1

Complexes8

Conformation2

Affinity7

Structural14

Ligand20

Residues7

Interaction9

Prediction1

Regulation8

Ligands2

Specificity3

Mutations3

Molecular6

Abstract1

Interacts3

Interactions9

Highly conserved2

Computational2

Phosphorylation5

Drosophila2

Sequences2

Motifs2

Nucleic2

Structures2

Bioinformatics1

Molecules2

Motif3

Amino8

Localization3

Intracellular2

Analyze2

Membrane5

Identification2

Regulatory2

Receptors1

Allosteric1

Regulate1

Encodes3

Chains1

Nucleotide2

Chromosomes1

Mutation2

Molecule2

Characterization1

Mass spectrometry1

Functional2

Heparin2

Annotation1

Arabidopsis1

Transcription2

Residue1

Monoclonal3

Predicting1

Enzymes1

Catalytic3

Biology1

Virulence1

Structure7

Vitro1