The largest database of trusted experimental protocols

Imidazole

Imidazole is a heterocyclic aromatic organic compound with the chemical formula C3H4N2.
It is a five-membered ring containing two nitrogen atoms at position 1 and 3.
Imidazole and its derivatives play a crucial role in various biological processes, including protein structure, enzyme catalysis, and pH regulation.
They are commonly found in biomolecules such as histidine, a key amino acid, and are also used in the synthesis of pharmaceuticals, agrochemicals, and other industrial chemicals.
Imidazole research is essential for understanding and advancing fields like biochemistry, medicinal chemistry, and materials science.
PubCompare.ai's AI-driven tools can help optimize Imidazole research by identifying the best protocols, products, and methods from literature, preprints, and patents, boosting productivity and research outcomes.

Most cited protocols related to «Imidazole»

Input PDB files can contain numerous errors and format inconsistencies, such as missing heavy atoms, suboptimal residue conformations and non-standard atom names. H++ attempts to make automatic, albeit conservative corrections for many of these problems when possible. Otherwise the errors are identified for possible manual correction. For example, the N and O atoms in the amide groups of ASN and GLN, and the N and C atoms in the imidazole ring of HIS cannot be easily distinguished from electron density maps. Thus, the assignment of these atoms in the PDB file may be (optionally) ‘flipped’ using the reduce algorithm that is based on an analysis of van der Waals contacts and H-bonding (26 (link)). An example of errors that are identified for manual correction are missing residues in the middle of protein chains. Input PDB files may also contain HETATM entries for solvent and ligand molecules; H++ removes these entries. Solvent molecules are removed by default because they are treated implicitly by the continuum solvent methodology used. Non-protein ligands are removed by default, but an option is now available to manually include many ligands and specific buried water molecules for processing, as described on the H++ site. Inclusion of buried waters has been shown to improve the accuracy of computed pK of nearby groups (27 (link)). For peptide, protein, DNA and RNA ligands, current AMBER force field parameters are used to add H atoms and assign atomic partial charges. For other organic ligands, H++ uses OpenBabel (28 ) to add H atoms, and atomic partial charges are assigned using the antechamber module from AmberTools (29 (link)) and the generalized AMBER force field (GAFF) parameter set. PDB structures may also contain residues with partial occupancy representing multiple possible conformations. Without manual intervention from the user, H++ selects the ‘A’ conformation and ignores all others.
An input PQR file, on the other hand, is assumed to have already been validated (e.g. in order to compute the atomic charges and radii included in the PQR file). Therefore, most error and consistency checks are bypassed for input PQR files. In addition, H++ requires AMBER compatible atom and residue names in the input PQR file.
Publication 2012
Amber Amides Electrons Imidazoles Ligands Microtubule-Associated Proteins Peptides Proteins Radius Solvents
The K206A mutation was introduced by mutagenesis in SCFP3A, mTurquoise and mTurquoise2 on the pRSET vector (primers listed in Supplementary Table S6). After verification by sequencing, the coding sequence of the CFP variants was transferred into pQE60–Cerulean7 (link), using the NcoI and BsrGI restriction sites to replace Cerulean. His-tagged recombinant proteins meant for crystallization were expressed in E. coli BL21 CodonPlus (DE3) RIL cells (Stratagene) in autoinduction medium, at 27 °C for 24 h on the RoBioMol platform of the Institut de Biologie Structurale. Cells were lysed by sonication in the presence of 20 mM Tris (pH 8.0) and 500 mM NaCl with EDTA-free protease inhibitors (Complete, Roche). His-tagged proteins were purified on a Ni-NTA Superflow column (Qiagen) and eluted with 100 mM imidazole in the buffer described above. Fractions containing purified proteins were pooled, dialysed against 20 mM Tris (pH 8.0), and concentrated to 38–85 mg ml−1. Site-directed mutagenesis of pRSET-mTurquoise on position 146, 165 or 220 were performed using the primers listed in Supplementary Table S6. For spectroscopic characterization, proteins were expressed using the pRSET vectors expressed in BL21 (DE3) cells and purified as described10 (link).
Publication 2012
Buffers Cells Cloning Vectors Crystallization Edetic Acid Escherichia coli imidazole Mutagenesis Mutagenesis, Site-Directed Mutation Oligonucleotide Primers Open Reading Frames Protease Inhibitors Proteins Recombinant Proteins Sodium Chloride Spectrum Analysis Tromethamine
Wild type arnA was PCR amplified from E. coli genomic DNA with NdeI and XhoI restriction site overhangs on the 5’ and 3’ ends, respectively, using primers 1F and 1R (See all primer details in Table S1), and cloned into the bacterial expression vector pColaDuet (EMD Millipore). Two serine point mutations were introduced at site 1 (H359S and H361S) using primers 2F and 2R. Two additional serine point mutations were introduced at site 2 (H592S and H593S) using primers 3F and 3R to generate the final arnA mutant containing a total of four histidine to serine mutations.
The arnA knockout strain was generated with the E. coli recombineering technique10 (link), using the pKD4 plasmid as a template for the selectable marker and BL21(DE3) as the parental strain. The forward and reverse primers, 4F and 4R, were designed to maintain the reading frame of arnB, which shares its start codon with the stop codon of arnA within the arn operon11 (link) (also called pmrHFIJKLM operon12 (link)). A slightly modified scheme was used to introduce the arnA mutant back into the arnA knockout strain at the original locus (Fig. S1). First, mutant arnA was amplified and combined with the amplified selectable marker in a second PCR step. The resulting PCR product containing mutated arnA and the selectable marker was transformed into the arnA knockout strain for recombination using the λ Red recombinase plasmid (pKD46). The selectable marker was eliminated using the FLP plasmid (pCP20). For the modification in slyD, the arnA mutant strain was transformed with a PCR product (generated using primers 5F and 5R) containing a selectable marker flanked by homologous overhangs that, after recombination, result in the elimination of the 46-residue C-terminal, histidine-rich segment of SlyD. Again, the selectable marker was later removed using pCP20. Proper genomic integration was confirmed by PCR and sequencing. The RIL plasmid (Agilent Technologies) encoding rare tRNAs was transformed into the final expression strain to improve the expression of our eukaryotic target proteins.
The binding affinity of wild type and mutant ArnA were assessed by immobilizing purified protein onto a 1 ml His-Trap FF column (GE Healthcare) equilibrated in 50 mM potassium phosphate pH 8.0, 300 mM NaCl, and 5 mM beta-mercaptoethanol. Protein was eluted with a linear gradient of 0–150 mM imidazole. The imidazole concentration at the elution peak of each protein was recorded and compared.
Growth analysis was performed at 18, 25 and 37°C for both LOBSTR and the BL21(DE3) strains carrying the same test expression plasmid (See table S2 for a list of all test constructs). Cultures of 1L were grown in LB medium supplemented with 0.4% (w/v) glucose and antibiotic selection at 37°C to OD600 ~0.7. Protein expression was induced with 0.2 mM IPTG 20 minutes after the cultures were shifted to the desired expression temperature. OD600 was measured from the initial synchronization time and until the cells were harvested ~20–22 hours after induction.
To test protein purification, BL21(DE3) and LOBSTR cultures were started at 37°C in LB medium supplemented with 0.4% (w/v) glucose and appropriate antibiotic selection. At OD600 ~0.7, cultures were shifted to 18°C and induced with 0.2 mM IPTG ~20 min later. Cultures were harvested after 18–20 hours. For each strain and construct tested, a total of ~3.5g of cells were resuspended in 50 mL of resuspension buffer (40 mM potassium phosphate pH 8.0, 150 mM NaCl, 40 mM imidazole, and 3mM beta-mercaptoethanol) and lysed with a cell disrupter (Constant Systems). Lysates were cleared for 25 min at 9500×g and the soluble fraction was incubated with 400 µl bed volume of Ni Sepharose 6 Fast Flow (GE Healthcare) resin for 1 hour while stirring at 4°C. The resin was collected and washed with 6 mL of resuspension buffer and eluted with 2 mL of elution buffer (40 mM potassium phosphate pH 8.0, 150 mM NaCl, 250 mM imidazole, and 3 mM beta-mercaptoethanol). Elution fractions were analyzed on a 4–15 % SDS-PAGE gradient gel (Bio-RAD) and stained with Coomassie Blue R250. Purifications using Ni-NTA (Qiagen) and Talon (Clontech) resins were performed using resuspension buffer containing 20 mM or 5 mM imidazole, respectively, following manufacturer’s recommendations.
Publication 2013
2-Mercaptoethanol Antibiotics Autosomal Recessive Polycystic Kidney Disease Bacteria Buffers Cells Claw Cloning Vectors Codon, Initiator Coomassie blue Escherichia coli Eukaryotic Cells Genome Glucose Histidine imidazole Isopropyl Thiogalactoside Mutation Oligonucleotide Primers Parent Plasmids Point Mutation potassium phosphate Proteins Protein Targeting, Cellular Reading Frames Recombinase Recombination, Genetic Resins, Plant SDS-PAGE Sepharose Serine Sodium Chloride Strains Transfer RNA
Proteins that could accommodate backbone grafting of the V1/V2 stub from HIV-1 gp120 were identified using the Multigraft Match algorithm48 (link) implemented in Rosetta. Potential V1/V2 scaffolds were examined manually and, if necessary, optimizations were made to accommodate full-length V1/V2 loops (residues 126–196) or to alter scaffold properties (for example, mutating the intrinsic immunoglobulin affinity of 1FD6; ref. 49 (link)). For each V1/V2 scaffold, protein-A-purified PG9, altered to remove light-chain glycosylation and to introduce an HRV3C cleavage site in the hinge, was bound to Protein A Plus agarose, and the V1/V2 scaffold added. After washing away unbound scaffold, HRV3C protease was added to elute the PG9 Fab–V1/V2 scaffold complex. Complexes of PG9 Fab bound to 1FD6-CAP45 or 1FD6-ZM109 crystallized in similar conditions50 (link) (8–17% (w/v) PEG 3350, 5–10% (v/v) 2-methyl-2,4-pentanediol, 0.2 M lithium sulphate, 0.1 M imidazole pH 6.5). Crystals were cryoprotected with 15% (v/v) 2R,3R-butanediol, diffraction data were collected to 2.19 and 1.80 Å for PG9–1FD6-CAP45 and PG9–1FD6-ZM109, respectively, and structures solved by molecular replacement.
Publication 2011
Antibody Affinity Butylene Glycols Cytokinesis HIV Envelope Protein gp120 imidazole lithium sulfate Peptide Hydrolases polyethylene glycol 3350 Protein Glycosylation Proteins Sepharose Staphylococcal Protein A TNFSF14 protein, human Vertebral Column
All fluorescent protein coding sequences were inserted between BamHI and EcoRI sites in the constitutive expression vector pNCS which encodes an N-terminal 6×His tag and linker. Sequences for all primers used in this study are listed in Supplementary Table 4. Fluorescent proteins were expressed in E. coli strain NEBTurbo (New England Biolabs) or Mach1 (Invitrogen) by growing cultures in 2×YT medium supplemented with ampicillin overnight at 37 °C and shaking at 250 rpm. Fluorescent proteins were purified by Ni2+-affinity chromatography as previously described9 (link). Proteins were eluted in 50 mM Tris pH 7.5 or 50 mM sodium phosphate buffer pH 7.5 containing 250 mM imidazole. For all further characterization experiments, eluted fluorescent proteins were buffer-exchanged using Amicon Ultra0.5 10 kD MWCO ultrafiltration units (Millipore) into the same buffer without imidazole. Proteins were found to be stable when stored at 4°C indefinitely or when frozen at −20 °C or −80 °C.
Publication 2013
Ampicillin Buffers Chromatography, Affinity Cloning Vectors Culture Media Deoxyribonuclease EcoRI Escherichia coli Freezing imidazole Oligonucleotide Primers Open Reading Frames Proteins sodium phosphate Strains Tromethamine Ultrafiltration

Most recents protocols related to «Imidazole»

The 2-fluorophenyl-imidazole used in this study was synthesized and provided by Dr. Thais Rossa, supervised by Professor Dr. Marcus Mandolesi Sá of the Department of Chemistry at the Universidade Federal de Santa Catarina (UFSC). The substituted fluorophenyl-imidazole (Figure 1) was synthesized by a reaction involving an azirine, a primary amine and an aldehyde [18 (link)]. The imidazole tested has a purity greater than 99% and was dissolved in 1% dimethyl sulfoxide (DMSO), following the predefined concentrations. After that, fluorophenyl-imidazole was aliquoted and stored at −80°C until the experiments, when it was properly dissolved in a cell culture medium.
Full text: Click here
Publication 2024
Imidazole (2.0 g, 29.3 mmol),
dimethyl sulfoxide (30 mL), and 1.5
equiv KOH (2.47 g, 44 mmol) were placed in a round-bottom flask and
stirred in a water-containing beaker for 30 min. One equivalent of
1-bromo-3-methylbutane (4.43 g, 29.3 mmol) was added dropwise, as
the reaction is exothermic, so cool water was added to a stirring
beaker to maintain the reaction media’s temperature. N-Alkylated compound (1-isopentyl-1H-imidazole)
having a yield of 92.30% was synthesized. In the next step, in a round-bottom
flask, an N-alkylated compound (2.0 g, 14.4 mmol)
was taken and dissolved in 1,4-dioxane (30 mL). While being constantly
stirred, 1-bromopentane (2.18 g, 13.24 mmol) was added drop by drop
in the solution. At 100 °C, the reaction mixture was refluxed
for 22 h. N-Hexane was used twice to wash the product
solution; an oily, brownish product was obtained. Yield: 86.53%.
Publication 2024

Protocol full text hidden due to copyright restrictions

Open the protocol to access the free full text link

Publication 2024

Example 2

Ten rubber compositions were prepared as indicated above. Their formulations (in phr) and properties have been summarised in Table 2 below.

TABLE 2
C.4C.5C.6C.7C.8C.9C.10C.11C.12C.13
NR (1)100100100100100100100100100100
Carbon black (2)60606060606060606060
ZnO (3)8888888888
6PPD (4)2222222222
Stearic acid (5)0.60.60.60.60.60.60.60.60.60.6
Sulfur6666666666
CBS (6)1111111111
Epoxy resin (7)16161612121616121216
Hardener (8)1.93.61.91.41.4
Hardener (9)3.63.62.72.7
Imidazole (10)0.50.50.50.50.5
Cured properties
MAS10% 23° C. (MPa)10010611680911261329093102
MAS10% 100° C. (MPa)10010113185123173202133146108
(1) Natural rubber
(2) Carbon black N347 (name according to standard ASTM D-1765)
(3) Zinc oxide (industrial grade - Umicore)
(4) N-1,3-dimethylbutyl-N-phenyl-para-phenylenediamine (Santoflex 6-PPD from Flexsys)
(5) Stearin (Pristerene 4931 from Uniqema)
(6) N-Cyclohexylbenzothiazolesulfenamide (Santocure CBS from Flexsys)
(7) Epoxy cresol novolac resin, Poly[(o-cresyl glycidyl ether)-co-formaldehyde], ref. 408042 from Sigma-Aldrich
(8) Aromatic diamine hardener, Ethacure 100 from Albemarle (CAS 68479-98-1)
(9) Aromatic diamine hardener, Ethacure 300 from Albemarle (CAS 106264-79-3)
(10) Imidazole, Aradur 3123 from Huntsman (CAS 185554-99-8)

These tests illustrate that the addition of an imidazole makes it possible to improve the stiffness at high temperature. Test C.5 shows that solely increasing the amount of hardener makes it possible to increase the stiffness at low temperature but not the stiffness at high temperature. Test C.13 shows that the imidazole used without hardener does not make it possible to improve the stiffness at high temperature. It is therefore clearly the combination of the hardener and the imidazole that makes it possible to obtain both a satisfactory stiffness at ambient temperature and at high temperature.

Full text: Click here
Patent 2024
Isolation of imidazole standards was
reported before.10 (link) Lepidilines A–E
(15) were obtained in sufficient
amounts (10–20 mg).
Structure elucidation was performed by means of extensive spectroscopic
and computational techniques using the published protocol of the authors.20 (link) Standard purity was determined by means of the
total intensity method applied to the 1H NMR spectrum of
the purified compounds. Briefly, the total integration (area) of all 1H signals belonging to a lepidiline is compared to the total
integration of all signals observed in its 1H NMR spectrum.
Publication 2024

Top products related to «Imidazole»

Sourced in United States, Germany, Spain, United Kingdom, France, India, Italy, Switzerland, Sweden
Imidazole is a heterocyclic organic compound with the chemical formula C3H4N2. It is a five-membered aromatic ring containing two nitrogen atoms. Imidazole serves as a core functional group in various chemical and biological applications.
Sourced in Germany, United States, United Kingdom, Netherlands, China, Switzerland, Italy, Canada, Spain, India
Ni-NTA agarose is a solid-phase affinity chromatography resin designed for the purification of recombinant proteins containing a histidine-tag. It consists of nickel-nitrilotriacetic acid (Ni-NTA) coupled to agarose beads, which selectively bind to the histidine-tagged proteins.
Sourced in Germany, United States, United Kingdom, Canada, Netherlands, India
Ni-NTA resin is a nickel-nitrilotriacetic acid (Ni-NTA) affinity chromatography medium used for the purification of recombinant proteins containing a histidine-tag (His-tag) sequence. The resin binds to the His-tag and allows the target protein to be isolated from complex mixtures.
Sourced in United States, United Kingdom, Sweden, Germany, China
The HisTrap HP column is a pre-packed chromatography column designed for the purification of recombinant proteins containing a histidine tag. The column is filled with a matrix that selectively binds to the histidine tag, allowing the target protein to be separated from other components in the sample.
Sourced in Germany, United States, United Kingdom, Netherlands, Italy
Ni-NTA agarose beads are a chromatography resin used for the purification of His-tagged proteins. The beads consist of a nickel-nitrilotriacetic acid (Ni-NTA) complex immobilized on an agarose matrix. These beads can selectively bind and capture proteins with a polyhistidine (His-tag) affinity tag, allowing for their efficient separation and purification from complex mixtures.
Sourced in United States, United Kingdom, Sweden, France
The HisTrap column is a versatile affinity chromatography tool designed for the purification of histidine-tagged recombinant proteins. It features a prepacked matrix that selectively binds to the histidine-tag, allowing for efficient capture and purification of the target protein.
Sourced in Germany, United States, Netherlands, France
Ni-NTA beads are a type of agarose-based affinity resin used for the purification of recombinant proteins that contain a polyhistidine (His) tag. The Ni-NTA (Nickel-Nitrilotriacetic Acid) moiety on the beads binds to the His-tagged proteins, allowing them to be separated from other cellular components during the purification process.
Sourced in United States, Switzerland, Germany, China, United Kingdom, France, Canada, Japan, Italy, Australia, Austria, Sweden, Spain, Cameroon, India, Macao, Belgium, Israel
Protease inhibitor cocktail is a laboratory reagent used to inhibit the activity of proteases, which are enzymes that break down proteins. It is commonly used in protein extraction and purification procedures to prevent protein degradation.
Sourced in United States, United Kingdom, Sweden, Germany, France, Japan, Switzerland
Superdex 200 is a size-exclusion chromatography medium used for the separation and purification of proteins, peptides, and other biomolecules. It is composed of highly cross-linked agarose beads that allow for efficient separation based on molecular size. The Superdex 200 matrix provides a wide fractionation range and high resolution, making it a versatile tool for a variety of applications in biotechnology and life science research.
Sourced in United States, United Kingdom, Germany, Sweden, Japan, Canada, Belgium
The PD-10 column is a size-exclusion chromatography column designed for desalting and buffer exchange of protein samples. It is commonly used to separate low molecular weight substances from high molecular weight compounds, such as proteins, in a rapid and efficient manner.

More about "Imidazole"

Imidazole is a vital heterocyclic organic compound with the chemical formula C3H4N2.
This five-membered ring contains two nitrogen atoms at positions 1 and 3, making it a crucial component in various biological processes.
Imidazole and its derivatives play a pivotal role in protein structure, enzyme catalysis, and pH regulation, and are commonly found in biomolecules such as the amino acid histidine.
These compounds are also widely used in the synthesis of pharmaceuticals, agrochemicals, and other industrial chemicals.
Imidazole research is essential for advancing fields like biochemistry, medicinal chemistry, and materials science.
Techniques like affinity chromatography, using Ni-NTA agarose, Ni-NTA resin, HisTrap HP columns, Ni-NTA agarose beads, and HisTrap columns, are commonly employed to purify proteins containing imidazole-rich histidine tags.
Protease inhibitor cocktails and size exclusion chromatography using Superdex 200 or PD-10 columns further enhance the research process.
PubCompare.ai's AI-driven tools can optimize imidazole research by identifying the best protocols, products, and methods from literature, preprints, and patents, boosting productivity and research outcomes.
Leveraging advanced AI, PubCompare.ai helps researchers discover the optimal imidazole research techniques, improving efficiency and advancing scientific discoveries.