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Hydrolase

Hydrolases are a diverse class of enzymes that catalyze the hydrolytic cleavage of various chemical bonds, including ester, ether, peptide, and glycosidic linkages.
These enzymes play crucial roles in a wide range of biological processes, such as digestion, cellular signaling, and metabolic pathways.
Hydrolases can be further subdivided into numerous subclasses based on the specificity of their substrates and the type of reaction they catalyze.
Understanding the characteristics and functions of different hydrolases is essential for researchers studying topics like enzyme kinetics, drug development, and industrial biotechnology.
Optimizing hydrolase research through tools like PubCompare.ai can enhance reproducibility, accuracy, and the discovery of effective experimental methods.

Most cited protocols related to «Hydrolase»

Data from 47 structures in the PHENIX library of MAD, SAD and MIR data sets were used along with 246 MAD and SAD structures from the Joint Center for Structural Genomics (JCSG; http://www.jcs.org). The structures from the PHENIX library included 1029B (PDB code 1n0e; Chen et al., 2004 ▶ ), 1038B (1lql; Choi et al., 2003 ▶ ), 1063B (1lfp; Shin et al., 2002 ▶ ), 1071B (1nf2; Shin, Roberts et al., 2003 ▶ ), 1102B (1l2f; Shin, Nguyen et al., 2003 ▶ ), 1167B (1s12; Shin et al., 2005 ▶ ), aep-transaminase (1m32; Chen et al., 2002 ▶ ), armadillo (3bct; Huber et al., 1997 ▶ ), calmodulin (1exr; Wilson & Brunger, 2000 ▶ ), cobd (1kus; Cheong et al., 2002 ▶ ), cp-synthase (1l1e; Huang et al., 2002 ▶ ), cyanase (1dw9; Walsh et al., 2000 ▶ ), epsin (1edu; Hyman et al., 2000 ▶ ), flr (1bkj; Tanner et al., 1996 ▶ ), fusion-complex (1sfc; Sutton et al., 1998 ▶ ), gene-5 (1vqb; Skinner et al., 1994 ▶ ), gere (1fse; Ducros et al., 2001 ▶ ), gpatase (1ecf; Muchmore et al., 1998 ▶ ), granulocyte (2gmf; Rozwarski et al., 1996 ▶ ), groEL (1oel; Braig et al., 1995 ▶ ), group2-intron (1kxk; Zhang & Doudna, 2002 ▶ ), hn-rnp (1ha1; Shamoo et al., 1997 ▶ ), ic-lyase (1f61; Sharma et al., 2000 ▶ ), insulin (2bn3; Nanao et al., 2005 ▶ ), lysozyme (unpublished results; CSHL Macromolecular Crystallo­graphy Course), mbp (1ytt; Burling et al., 1996 ▶ ), mev-kinase (1kkh; Yang et al., 2002 ▶ ), myoglobin (A. Gonzales, personal communication), nsf-d2 (1nsf; Yu et al., 1998 ▶ ), nsf-n (1qcs; Yu et al., 1999 ▶ ), p32 (1p32; Jiang et al., 1999 ▶ ), p9 (1bkb; Peat et al., 1998 ▶ ), pdz (1kwa; Daniels et al., 1998 ▶ ), penicillopepsin (3app; James & Sielecki, 1983 ▶ ), psd-95 (1jxm; Tavares et al., 2001 ▶ ), qaprtase (1qpo; Sharma et al., 1998 ▶ ), rab3a (1zbd; Ostermeier & Brunger, 1999 ▶ ), rh-dehalogenase (1bn7; Newman et al., 1999 ▶ ), rnase-p (1nz0; Kazantsev et al., 2003 ▶ ), rnase-s (1rge; Sevcik et al., 1996 ▶ ), rop (1f4n; Willis et al., 2000 ▶ ), s-hydrolase (1a7a; Turner et al., 1998 ▶ ), sec17 (1qqe; Rice & Brunger, 1999 ▶ ), synapsin (1auv; Esser et al., 1998 ▶ ), synaptotagmin (1dqv; Sutton et al., 1999 ▶ ), tryparedoxin (1qk8; Alphey et al., 1999 ▶ ), ut-synthase (1e8c; Gordon et al., 2001 ▶ ) and vmp ( l8w; Eicken et al., 2002 ▶ ).
The structures from the JCSG included PDB (Bernstein et al., 1977 ▶ ; Berman et al., 2000 ▶ ) entries 1o1x (Xu et al., 2004 ▶ ), 1vjf, 1vjr, 1vk4, 1vk8, 1vk9, 1vkd, 1vkn, 1vl0, 1vl5, 1vli, 1vlo, 1vly, 1vm8, 1vmg, 1vmi, 1vp8, 1vpm, 1vpz (Rife et al., 2005 ▶ ), 1vqr (Xu, Schwarzenbacher, McMullan et al., 2006 ▶ ), 1vqs, 1vqy, 1vqz, 1vr0 (DiDonato et al., 2006 ▶ ), 1vr3 (Xu, Schwarzenbacher, Krishna et al., 2006 ▶ ), 1vr5, 1vr8 (Xu, Krishna et al., 2006 ▶ ), 1vrm (Han et al., 2006 ▶ ), 1z82, 1z85, 1zbt, 1zej, 1zh8, 1zko, 1ztc, 1zx8 (Jin et al., 2006 ▶ ), 1zy9, 1zyb, 2a3n, 2aam, 2aml, 2ax3, 2b8n (Schwarzenbacher et al., 2006 ▶ ), 2etd, 2ets, 2evr, 2f4i, 2f4l, 2fg0, 2fg9, 2fna, 2ftr, 2fup, 2fur, 2g0w, 2gb5, 2gc9, 2gf6, 2gfg, 2ghr (Zubieta et al., 2007 ▶ ), 2gno, 2go7, 2gpi, 2gpj, 2grj, 2gvh, 2h1q, 2h1t, 2h9f, 2hcf, 2hh6, 2hhz, 2hi0, 2hq7, 2hq9, 2hr2, 2hsz, 2huh, 2hx1, 2hx5, 2hxv, 2i02, 2i8d, 2i9w, 2ig6, 2ii1, 2ilb, 2isb, 2it9, 2itb, 2nuj, 2o08, 2o2g, 2o2x, 2o2z, 2o3l, 2o62, 2oa2, 2oaf, 2oc6, 2od5, 2ogi, 2oh1, 2oh3, 2oik, 2ooj, 2ook, 2op5, 2opl, 2oqm, 2ord, 2osd, 2otm, 2ou3, 2ou5, 2ou6, 2own, 2oyo, 2ozg, 2ozj, 2p10, 2p1a, 2p7i, 2p8j, 2pbl, 2peb, 2pfw, 2pg4, 2pgc, 2pke, 2pn1, 2pq7, 2pr7, 2prr, 2prv, 2pv4, 2pv7, 2pwn, 2py6, 2pyq, 2pyx, 2q02, 2q04, 2q0t, 2q14, 2q3l, 2q78, 2q7x, 2q9k, 2q9r, 2qe6, 2qe9, 2qez, 2qg3, 2qhp, 2qj8, 2ql8, 2qml, 2qpx, 2qr6, 2qtp, 2qtq, 2qw5, 2qww, 2qwz, 2qyv, 2r01, 2r0x, 2r1i, 2r3b, 2r44, 2r4i, 2r9v, 2ra9, 2ras, 2rcc, 2rcd, 2rd9, 2rdc, 2re3, 2re7, 2rfp, 2rgq, 2rha, 2rhm, 2rij, 2ril, 2rkh, 3b5e, 3b5o, 3b77, 3b7f, 3b81, 3b8l, 3bb5, 3bb9, 3bcw, 3bdd and 3bde.
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Publication 2009
Armadillos Calmodulin cyanase DNA Library epsin Genes Granulocyte Hydrolase Insulin Introns Joints Lyase Muramidase Myoglobin Nicotinate-nucleotide pyrophosphorylase (carboxylating) Nitric Oxide Synthase Oryza sativa Phosphotransferases Ribonucleases RNase P Synapsins Synaptotagmins Transaminases tryparedoxin
Transposable elements were identified using Repeat-Masker [6 ] and MIPS Repeat Element Database (mips-REdat) and Catalog (mips-REcat) [27 ,28 (link)]. This database provides a hierarchical classification of plant transposable elements and other repeat types. Before use, the database was screened for non-TE related sequences and the following identifiers were removed: 'bsr1' (containing cytochrome P450 and hydrolase sequences), 'k_1' (containing proton-ATPase sequence), and 'magellan_cone' (containing myb transcription factor sequence).
Receiver operating characteristic (ROC) curves were compared by the method of [29 (link)], as implemented in the MedCalc® statistical software package.
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Publication 2008
Adenosine Triphosphatases Cytochrome P450 DNA Transposable Elements Hydrolase Macrophage Inflammatory Protein-1 Plant Cone Plants Protons Transcription Factor

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Publication 2015
Caspase Cathepsins Cell Extracts Cells Cholesterol Cysteine Cytosol Detergents Digitonin Glucosaminidases Hydrolase Lysosomes Plasma Membrane Tissue, Membrane Titrimetry

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Publication 2009
10-(fluoroethoxyphosphinyl)-N-(biotinamidopentyl)decanamide Biological Assay bropirimine Cells Hydrolase Hydrolysis Malignant Neoplasms Proteome Rhodamine Serine
In order to study the effects of Vssc mutations S989P + V1016G (kdr) without the influence of other resistance mechanisms or strain variations, we needed a strain of A. aegypti that was closely related to a susceptible strain but containing kdr. To accomplish this, we used the following parental strains: Rockefeller (ROCK), an insecticide‐susceptible strain that has been reared in laboratories without exposure to insecticides for decades, which originated from the Caribbean,17 and Singapore (SP), a pyrethroid‐resistant strain in which the mechanisms of resistance have been well studied.14 Adult SP are 579‐fold resistant to permethrin (relative to ROCK) due to kdr and CYP‐mediated detoxification, whereas hydrolases and decreased penetration are not involved.14Mosquitoes were reared at 27 ± 1 °C and 70–80% relative humidity (RH). Females were blood‐fed using membrane‐covered water‐jacketed glass feeders with cow blood obtained locally. Adults were maintained on 10% sugar water in cages ∼ 35 × 25 × 25 cm holding ≤1000 mosquitoes. Larvae were reared in 27.5 × 21.5 × 7.5 cm containers with ∼ 2 L deionized water and fed Cichlid Gold fish food pellets (Hikari, Hayward, CA, USA) (ground pellets for first instar and medium size pellets for second to fourth instars). Food pellets were given daily, as needed depending on larval density (∼ 400–600) and instar.
The strain KDR:ROCK was isolated from crossing ROCK with SP followed by four backcrosses and genotype selections (see Section 2.2). KDR:ROCK is congenic to ROCK, but resistant to pyrethroids due to the Vssc mutations S989P + V1016G while containing no CYP‐mediated resistance. The procedure for isolating KDR:ROCK is illustrated in Fig. 1. In short, unmated SP females were crossed en masse with ROCK males. Unmated F1 females were backcrossed with ROCK and unmated BC1 females were genotyped for the presence of Vssc mutations S989P + V1016G (see Section 2.2). BC1 females that were heterozygous for P989 + G1016 (kdr) were backcrossed to ROCK males. This process was repeated for the BC2 and BC3 generations. At BC4, both males and unmated females were genotyped and individuals that were heterozygous for P989 + G1016 were reared en masse. Males and unmated females from the next generation were genotyped and individuals that were homozygous for P989 + G1016 were reared en masse. The resultant strain was named KDR:ROCK (Fig. 1).
Publication 2017
Adult Blood Carbohydrates Caribbean People Cichlids Culicidae Females Food Gold Heterozygote Homozygote Humidity Hydrolase Insecticides Larva Males Metabolic Detoxication, Drug Mutation Parent Pellets, Drug Permethrin Pyrethroids Strains Tissue, Membrane

Most recents protocols related to «Hydrolase»

Example 5

Three tobacco lines, FC401 wild type (Wt); FC40-M207 mutant line fourth generation (M4) and FC401-M544 mutant line fourth generation (M4) were used for candidate gene screening. Low anatabine traits were confirmed for the two tobacco mutant lines (M207 and M544) in root and leaf before screening (see FIG. 3).

RNA was extracted from root tissues of wild type (Wt) FC401, M207 and M544 with RNeasy Plus Mini kit from Quiagen Inc. following the manufacturer's protocol. cDNA libraries were prepared from the RNAs using In-Fusion® SMARTer® Directional cDNA Library Construction Kit from Clontech Inc. cDNA libraries were diluted to 100 ng/μl and used as the template for candidate gene PCR screening.

PCR amplifications were performed in 50 μl final volumes that contained 50-100 ng of template DNA (i.e., the cDNA library) and 0.2 μM of primers (Fisher Scientific) using the Platinum® Taq DNA Polymerase High Fidelity kit (Life Technology Inc.). Thermocycling conditions included a 5 min incubation at 94° C.; followed by 34 cycles of 30 seconds at 94° C., 30 seconds at 58° C., 1 min 30 seconds at 68° C.; with a final reaction step of 68° C. for 7 mins. The PCR products were evaluated by agarose gel electrophoresis, and desired bands were gel purified and sequenced using an ABI 3730 DNA Analyzer (ABI).

51 candidate genes (listed in Table 4) were cloned from F401, Wt, M207 and M544 lines, and sequenced for single nucleotide polymorphism (SNP) detection.

TABLE 4
Listing of Candidate Genes for Screening
Quinolinate Synthase A-1Pathogenesis related protein 1
Allene oxide synthaseAllene oxide cyclase
ET861088.1 Methyl esteraseFH733463.1 TGACG-sequence specific transcription factor
FH129193.1 Aquaporin-TransportFH297656.1 Universal stress protein
Universal stress protein Tabacum sequenceFH077657.1 Scarecrow-like protein
FH864888.1 EIN3-binding F-box proteinFH029529.1 4,5 DOPA dioxygenase
FI010668.1 Ethylene-responsive transcription EB430189 Carboxylesterase
factor
DW001704 Glutathione S transferaseEB683763 Bifunctional inhibitor/lipid transfer protein/seed
storage 2S albumin
DW002318 Serine/threonine protein kinaseDW004086 Superoxide dismutase
DW001733 Lipid transfer protein DIRIDW001944 Protein phosphatase 2C
DW002033EB683763 Bifunctional inhibitor/lipid transfer protein/seed
storage 2S albumin
DW002318 Serine/threonine protein kinaseDW002576 Glycosyl hydrolase of unknown function DUF1680
EB683279EB683763
EB683951FG141784 (FAD Oxidoreductase)
BBLa-Tabacum sequencesBBLb
BBLeBBLd
PdrlPdr2
Pdr3Pdr5a
Pdr5bNtMATEl
NtMATE2NtMATE3
WRKY8EIG-I24
WRKY3WRKY9
EIG-E17AJ748263.1 QPT2 quinolinate phosphoribosyltransferase
AJ748262.1 QPT1

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Patent 2024
Albumins allene oxide cyclase allene oxide synthase Amino Acid Sequence anatabine Carboxylesterase cDNA Library Dioxygenases Dopa Electrophoresis, Agar Gel Esterases Ethylenes Genes Glutathione S-Transferase Heat Shock Proteins Histocompatibility Testing Hydrolase lipid transfer protein Neoplasm Metastasis Nicotiana Nicotinate-nucleotide pyrophosphorylase (carboxylating) NOS1 protein, human Oligonucleotide Primers Oxidoreductase pathogenesis Plant Leaves Plant Roots Platinum Protein-Serine-Threonine Kinases Protein-Threonine Phosphatase Protein Kinases protein methylesterase Protein Phosphatase Protein Phosphatase 2C Proteins Quinolinate RNA Single Nucleotide Polymorphism Superoxide Dismutase Synapsin I Taq Polymerase Transcription, Genetic Transcription Factor Transfer Factor Water Channel

Example 39

Generally, pharmacophores for FAAH inhibitors, urea and non-urea based, interact by either carbamoylating or forming transition-state mimics with the catalytic serine residue. However, since a large number of hydrolases utilize a similar catalytic serine residue, many FAAH inhibitors have suffered from poor selectivity. Therefore, the potency of t-TUCB, A-14 and A-21 on several other serine hydrolases was tested. Included in this panel were carboxylesterases, hydrolases involved in xenobiotic detoxification, and paraoxonases and esterases involved in the regulation of arterosclerosis. As is shown in Table 5 below, none of these serine hydrolases were inhibited by t-TUCB, A-14, or A-21.

TABLE 5
Selectivity of A-14 and A-15 against other serine hydrolases.
IC50 (nM)
Enzyme1728A-14A-21
FAAH14024120
sEH0.832
MAGL>10,000>10,000>10,000
hCE1>10,000>10,000>10,000
hCE2>10,000>10,000>10,000
PON1>10,000>10,000>10,000
PON2>10,000>10,000>10,000
PON3>10,000>10,000>10,000
AADAC>10,000>10,0005,400

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Patent 2024
Aryldialkylphosphatase Carboxylic Ester Hydrolases Catalysis Enzymes Esterases Genetic Selection Hydrolase inhibitors Metabolic Detoxication, Drug PON1 protein, human PON2 protein, human Serine Urea Xenobiotics
The tissue was ground in liquid nitrogen, resuspended in cold lysis buffer (20 mM HEPES pH 7.2, 2 mM DTT, 250 mM sucrose, 1 mM MgCl2, 2.5 U/mL benzonase), and incubated on ice (15–30 min). Protein concentrations were determined by a Quick StartTM Bradford Protein Assay and diluted samples were flash-frozen in liquid nitrogen and stored at −80 °C until further use.
The sample was diluted to 2 mg/mL, and 50 μL was absorbed. The probe was balanced in desiccant to room temperature, and 100 μL DMSO was added to prepare a 0.1 mm storage solution. 1 μL of ActivX® Serine Hydrolase Probes (Thermo, 88318) was added to each sample at a final concentration of 2 μm/μL. After mixing, the samples were incubated for 1 h at room temperature under the light. The reaction was terminated by boiling 10 μL 6X SDS–PAGE protein loading buffer for 5 min. The reaction was electrophoresed with 12% SDS–PAGE. Gels were scanned using Cy3 and Cy5 multichannel settings (605/50 and 695/55, filters respectively) and stained with Coomassie after scanning. Fluorescence intensity was analyzed by Image J. The SDS–PAGE with fluorescence coloring was placed in Coomassie brilliant blue glue dye solution and stained on a shaker for 2 h. Then, the molecules with fluorescence coloring and Coomassie brilliant blue staining were decolorized and scanned, and the different bands were cut out for identification.
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Publication 2023
Benzonase Biological Assay brilliant blue G Buffers Cold Temperature Desiccants Fluorescence Freezing Gels HEPES Hydrolase Magnesium Chloride Nitrogen Proteins SDS-PAGE Serine Staphylococcal Protein A Sucrose Sulfoxide, Dimethyl Tissues TNFSF14 protein, human

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Publication 2023
Alginate Bacteriophages Dextranase enzyme activity Enzymes Genome Helix (Snails) Hyaluronidase Hydrolase Hypertelorism, Severe, With Midface Prominence, Myopia, Mental Retardation, And Bone Fragility Klebsiella levanase Lipase Lyase Neuraminidase pectate Pectins Proteins Tropism

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Publication 2023
ACE2 protein, human cepharanthine COVID 19 Hydrolase M protein, multiple myeloma NSP12 protein, SARS-CoV-2 Protein Targeting, Cellular Rumex SARS-CoV-2

Top products related to «Hydrolase»

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The ActivX TAMRA-FP Serine Hydrolase Probe is a fluorescent dye-labeled chemical probe designed for the selective and covalent labeling of serine hydrolases. It enables the detection and identification of active serine hydrolases in complex biological samples.
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LDS sample buffer is a laboratory reagent used in the preparation of samples for protein analysis. It functions as a denaturing agent that helps unfold and solubilize proteins prior to electrophoresis or other analytical techniques. The buffer contains lithium dodecyl sulfate (LDS), a mild detergent, which disrupts non-covalent protein interactions and maintains the solubility of the denatured proteins.
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Anti-tyrosine hydrolase (Polyclonal rabbit) antibody is a laboratory reagent used to detect and study the tyrosine hydrolase enzyme. It is a polyclonal antibody produced in rabbits. The antibody binds to and identifies the tyrosine hydrolase protein, allowing researchers to investigate its presence and function in various biological samples.
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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.
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The Anti-Iba1 antibody is a laboratory reagent used to detect the Iba1 protein in biological samples. Iba1 is a calcium-binding protein that is expressed in microglia, the resident immune cells of the central nervous system. The Anti-Iba1 antibody can be used in various immunochemical techniques, such as immunohistochemistry and Western blotting, to study the distribution and expression of Iba1 in tissues and cells.
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Potassium dihydrogen phosphate is a chemical compound with the formula KH2PO4. It is a white, crystalline solid that is soluble in water. The primary function of potassium dihydrogen phosphate is to serve as a buffer solution, maintaining a stable pH in various applications.
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More about "Hydrolase"

Hydrolases are a diverse class of enzymes that play crucial roles in a wide range of biological processes, from digestion and cellular signaling to metabolic pathways.
These remarkable enzymes catalyze the hydrolytic cleavage of various chemical bonds, including ester, ether, peptide, and glycosidic linkages.
Hydrolases can be further subdivided into numerous subclasses, each with its own unique substrate specificity and catalytic mechanism.
Understanding the characteristics and functions of different hydrolases, such as serine hydrolases, is essential for researchers studying enzyme kinetics, drug development, and industrial biotechnology.
Tools like the ActivX TAMRA-FP Serine Hydrolase Probe can help identify and quantify active serine hydrolases in complex biological samples, while LDS sample buffer and Ni-NTA agarose can be used to prepare and purify hydrolase enzymes for further analysis.
The Anti-tyrosine hydrolase (Polyclonal rabbit) antibody can be employed to study the expression and localization of tyrosine hydrolases, which play a key role in neurotransmitter metabolism.
DMSO, a versatile solvent, is commonly used to solubilize hydrolase enzymes and other biomolecules for various experiments.
AutoDock Tools 1.5.6, a popular molecular docking software, can be utilized to study the interactions between hydrolases and potential inhibitors or substrates, aiding in drug discovery and enzyme engineering.
The Anti-Iba1 antibody is a useful tool for investigating the role of hydrolases in microglial activation and neuroinflammation, while COX-2 inhibitors can modulate the activity of hydrolases involved in prostaglandin synthesis.
Ultimately, optimizing hydrolase research through innovative tools like PubCompare.ai can enhance reproducibility, accuracy, and the discovery of effective experimental methods, allowing researchers to push the boundaries of our understanding of these essential enzymes.