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Spectrin

Spectrins are a family of structural proteins found in the cytoskeleton of many cell types, including erythrocytes, neurons, and other tissues.
They play a critical role in maintaining cell shape, membrane stability, and signal transduction.
Spectirn research is vital for understanding a range of conditions, from hereditary spherocytosis to neurodegenerative disorders.
PubCompare.ai's AI-driven platform can help optimize Spectrin research by easily locating relevant literature, preprints, and patents through intelligent comparisons, enhancing reproducibility and efficiency in this important field of study.

Most cited protocols related to «Spectrin»

Eukaryotic Orthologous Groups Construction

Cited 655 times

The construction of KOGs followed the previously outlined strategy based on sets of consistent BeTs [9 (link),15 (link)], but included additional steps that reflected specific features of eukaryotic proteins. Briefly, the procedure was as follows. 1. Detection and masking of widespread, typically repetitive domains, which was performed by using the RPS-BLAST program and the PSSMs for the respective domains from the CDD collection [40 (link)]. These domains, namely, PPR (pfam01535), WD40 (pfam00400), IG (pfam00047), IGc1, Igv, IG_like, RRM (pfam00076), ANK (pfam00023), myosin tail (pfam01576), Fn3 (pfam00041), CA, (IG), ANK, kelch (pfam01344), OAD_kelch, SH3 (pfam00018), intermediate filaments (pfam00038), C2H2 finger (pfam00096), PDZ (pfam00595), POZ (pfam00651), PH (pfam00169), ZnF-C4 (pfam00105), spectrin (pfam00435), Sushi (pfam00084), TPR (pfam00017), BTB, LRR_CC, LY, ARM, SH2, and CH, were detected and masked prior to applying the COG construction procedure. Masking these domains was required to ensure the robust classification of the eukaryotic orthologous clusters with the KOG detection procedure because hits between these common, "promiscuous" domains resulted in spurious lumping of numerous non-orthologous proteins. 2. All-against-all comparison of protein sequences from the analyzed genomes by using the gapped BLAST program [58 (link)], with filtering for low sequence complexity regions performed using the SEG program [59 (link)]. 3. Detection of triangles of mutually consistent, genome-specific best hits (BeTs). 4. Merging triangles with a common side to form crude, preliminary KOGs. 5. Case by case analysis of each candidate KOG. This analysis serves to eliminate the false-positives that are incorporated in the KOGs during the automatic steps and included, primarily, examination of the domain composition of KOG members, which was determined using the RPS-BLAST program and the CDD collection of position-specific scoring matrices (PSSMs) for individual domains [40 (link)]. Generally, proteins were kept in the same KOG when they shared a conserved core domain architecture. However, in cases when KOGs were artificially bridged by multidomain proteins, the latter were split into individual domains (or arrays of domains) and steps (1)-(4) were repeated with these sequences; this results in the assignment of individual domains to KOGs in accordance with their distinct evolutionary affinities. 6. Assignment of proteins containing promiscuous domains. In cases when a sequence assigned to a KOG contained one or more masked promiscuous domains, these domains were restored and became part of the respective KOG. Proteins containing promiscuous domains but not assigned to any KOG were classified in Fuzzy Orthologous Groups (FOGs) named after the respective domains. 7. Examination of large KOGs, which included multiple members from all or several of the compared genomes by using phylogenetic trees, cluster analysis with the BLASTCLUST program , comparison of domain architectures, and visual inspection of alignments; as a result, some of these protein sets were split into two or more smaller ones that were included in the final set of KOGs.
The KOGs were annotated on the basis of the annotations available through GenBank and other public databases, which were critically assessed against the primary literature. For proteins that are currently annotated as "hypothetical" or "unknown", iterative sequence similarity searches with the PSI-BLAST program [58 (link)], the results of the RPS-BLAST searches, additional domain architecture analysis performed by using the SMART system [60 (link)], and comparison to the COG database by using the COGNITOR program (RLT, unpublished results) were employed to identify distant homologs with experimentally characterized functions and/or structures. The known and predicted functions of KOGs were classified into 23 categories (see legend to Fig. 4); these were modified from the functional classification previously employed for prokaryotic COGs [15 (link)] by including several specific eukaryotic categories.

Tatusov R.L., Fedorova N.D., Jackson J.D., Jacobs A.R., Kiryutin B., Koonin E.V., Krylov D.M., Mazumder R., Mekhedov S.L., Nikolskaya A.N., Rao B.S., Smirnov S., Sverdlov A.V., Vasudevan S., Wolf Y.I., Yin J.J, & Natale D.A. (2003). The COG database: an updated version includes eukaryotes. BMC Bioinformatics, 4, 41.

Publication 2003

Amino Acid Sequence Biological Evolution Eukaryota Fingers Genome Intermediate Filaments Myosin ATPase Prokaryotic Cells Protein Domain Proteins Repetitive Region SET protein, human Spectrin Tail

Benchmark Dataset for Protein Stability

Cited 34 times

Except for comparison to the results of Potapov et al. mentioned in the discussion, all tests reported in this article utilized a benchmark set comprised of 1210 single mutations obtained from Protherm.^{8 (link)} Duplicate entries were resolved by taking the highest resolution structure, and if multiple experimental measurements were recorded, the mean of all reported measurements was used. Structures greater than 350 residues were eliminated due to the computational intensiveness of some of the protocols tested. A representative set of 771 mutations was used to assess the most computationally intensive protocols, including the proteins barnase (1a2p), apomyoglobin (1bvc), FK506 binding protein (1fkj), staphylococcal nuclease (1stn), a-spectrin (1u5p), chymotrypsin inhibitor II (2ci2), and T4-lysozyme (2lzm).

Kellogg E.H., Leaver-Fay A, & Baker D. (2010). Role of conformational sampling in computing mutation-induced changes in protein structure and stability. Proteins, 79(3), 830-838.

Publication 2010

apomyoglobin Bacillus amyloliquefaciens ribonuclease chymotrypsin inhibitor 2 hen egg lysozyme Micrococcal Nuclease Mutation Proteins Spectrin Tacrolimus Binding Proteins

Quantitative Proteomic Data Analysis

Cited 25 times

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Publication 2016

Acetylation Amino Acid Sequence Asparagine Brain Cysteine Cytokeratin Glutamine Homo sapiens Immune Tolerance Isotopes Methionine NR4A2 protein, human nucleoprotein, Measles virus Peptides Proteins Proteome Radionuclide Imaging Retention (Psychology) Spectrin Tandem Mass Spectrometry Trypsin

Gut Dissection and Immunostaining in Drosophila

Cited 15 times

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Publication 2009

alexa 568 anti-IgG Antibodies Cloning Vectors DAPI Diptera Dissection Females Formaldehyde Gastrointestinal Tract Goat Histone H3 Hybridomas Males Mice, House Microscopy, Confocal Molecular Probes Phenotype Promega Rabbits Serum Spectrin Technique, Dilution

Drosophila Embryo Fixation and Immunostaining

Cited 13 times

Oregon-R embryos were dechorionated as in Rothwell et al. 1999, quickly rinsed in 0.1% Triton X-100, and incubated in heptane for 45 s before adding an equal volume of 19.5% formaldehyde + 2.2–3.3% methanol. The embryos were fixed for 15–30 min at 25°C. Four different preparative conditions were also used: formalin for 5 min, 37.5% EM-grade paraformaldehyde (EM Sciences) for 5 min, heptane presaturated against 0.25% glutaraldehyde + methanol (1:1) for 30 min according to Thomas and Kiehart 1994, and our initial fixation method in the absence of Triton X-100 before or after the fix; otherwise, the post-fix treatment was according to Rothwell et al. 1999. Detection of plasma membrane (PM)-Spectrin requires post-fixation treatments with >0.5% Triton X-100, while Golgi-Spectrin requires 0.05% Triton X-100. Affinity-purified, goat anti–rabbit IgG-Cy5 and goat anti–mouse IgG-fluorescein antibodies (Chemicon) were used to detect primary antibodies. Embryos were imaged according to Rothwell et al. 1999.

Sisson J.C., Field C., Ventura R., Royou A, & Sullivan W. (2000). Lava Lamp, a Novel Peripheral Golgi Protein, Is Required for Drosophila melanogaster Cellularization. The Journal of Cell Biology, 151(4), 905-918.

Publication 2000

anti-IgG Antibodies Embryo Fluorescein Formaldehyde Formalin Glutaral Goat Golgi Apparatus Heptane Methanol Mice, House paraform Plasma Membrane Rabbits Spectrin Triton X-100

Most recents protocols related to «Spectrin»

Hippocampal Protein Expression Analysis

Western blotting was performed to determine the expression of occludin, alpha-2
spectrin, ERK1/2, phosphorylated ERK1/2 (pERK1/2), AKT, pAKT, and β-actin
(loading control) in the ipsilateral hippocampus of animals in different
experimental groups. The ipsilateral hippocampi were manually homogenized in
ice-cold lysis buffer, and respective supernatants were processed for
electrophoresis as we previously described.^{34 (link)–36 (link, link),39 (link)} Total proteins (25 μg)
from each supernatant were separated by electrophoresis on 4-12%
SDS-polyacrylamide gels (Invitrogen, CA), then transferred to a nitrocellulose
membrane (Sigma, MO). Membranes were blocked with 5% non-fat milk in
Tris-buffered saline with .1% Tween-20 (TBST) and incubated overnight at 4°C in
rabbit polyclonal antibodies against occludin (1:2000; Abcam, MA), α-ii spectrin
(1:3000; Invitrogen/ThermoFisher Scientific, NY) ERK, 1/2, pERK1/2, AKT, pAKT
(1:1000; Cell Signaling Technology, MA) or a mouse anti-β-actin (1:4000; Sigma,
MO). Blots were washed in Tris-buffered saline with .1% Tween-20 and incubated
for 1 h at room temperature with corresponding HRP-conjugated secondary
antibodies (1:5000; Millipore, MA). Horseradish peroxidase-labeled proteins were
detected by enhanced chemiluminescence (ECL, Thermo Scientific, IL), and protein
bands were visualized using a digital blot scanner (LI-COR, NE).

Tchantchou F., Hsia R.C., Puche A, & Fiskum G. (2023). Hippocampal vulnerability to hyperhomocysteinemia worsens pathological outcomes of mild traumatic brain injury in rats. Journal of Central Nervous System Disease, 15, 11795735231160025.

Publication 2023

Actins Animals Antibodies Chemiluminescence Cold Temperature Electrophoresis Fingers Horseradish Peroxidase Milk, Cow's Mitogen-Activated Protein Kinase 3 Mus Occludin polyacrylamide gels Proteins Saline Solution Seahorses Spectrin Tissue, Membrane Tween 20

Immunofluorescence Staining of Testicular Cells

Testes from 1-day-old males were dissected in phosphate-buffered saline (PBS, pH 7.4), then transferred to 4% polyformaldehyde (PFA) to fix for 30 min at room temperature. The fixed testes were washed with PBST (PBS containing 0.1% Triton X-100) for 30 min and then incubated with primary antibodies, which were diluted in PBST with 0.2% BSA, at 4 °C overnight. After washing for 30 min in PBST, the samples were incubated with the secondary antibody in PBST with 0.2% BSA for 1 h at room temperature followed by washing as above, and mounted in VECTASHIELD^® Mounting Medium with DAPI (VectorLabs, Newark, CA, USA). Images were obtained from a Leica SP8 405 Laser confocal microscope (Leica, Wetzlar, Germany) and processed using Adobe Photoshop and ImageJ software (v2.0.0, Wayne Rasband, NIH, USA).
For MitoTracker Red CMXRos (Life Technologies, Shanghai, China) staining, the testes were dissected in PBS and then incubated in the dye solution at a 50 μM concentration for 10 min. The samples were washed three times with PBS and then fixed in 4% formaldehyde for 30 min. The following steps are the same as above. For the phalloidin staining, the TRITC-phalloidin (Solarbio, 1:200) was added together with secondary antibodies to stain the testes.
The primary antibodies used in this study were as follows: rat anti-vasa (Developmental Studies Hybridoma Bank [DSHB, Iowa City, IA, USA], 1:200); mouse anti-α-spectrin (DSHB, 1:400); mouse anti-AXO-49 (Merck, Darmstadt, Germany, 1:5000). The secondary antibodies Alexa Fluor 488/594 conjugated anti-mouse/rat IgG (1:200) were purchased from Life Technologies.

Fang Y., Zhang F., Zhan Y., Lu M., Xu D., Wang J., Li Q., Zhao L, & Su Y. (2023). RpS3 Is Required for Spermatogenesis of Drosophila melanogaster. Cells, 12(4), 573.

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Publication 2023

alexa fluor 488 anti-IgG Antibodies DAPI Formaldehyde Hybridomas Immunoglobulins Laser Microscopy Males Mice, House MitoTracker red CMXRos Phalloidine Phosphates Saline Solution Spectrin Stains Testis tetramethylrhodaminylphalloidine Triton X-100

Genotype-Phenotype Correlation in Probands

The data considered for the genotype-phenotype correlation in the probands were: red blood cell count (RBC), Hb, MCV, MCH, MCHC, red cell distribution width (RDW-SD), red cell distribution width—coefficient of variation (RDW-CV), hematocrit (HCT), Ret%, T-Bil, and D-Bil. Genotypes were subdivided by different types of mutations (non-sense, frameshift, splicing, and missense) and the location of the mutations (membrane binding domain, spectrin binding domain, and regulatory domain).

Kang M., Li H., Zhu J., Zhu L., Hong Y, & Fang Y. (2023). Clinical manifestations of 17 Chinese children with hereditary spherocytosis caused by novel mutations of the ANK1 gene and phenotypic analysis. Frontiers in Genetics, 14, 1088985.

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Publication 2023

Erythrocyte Count Frameshift Mutation Genotype Mutation Red Cell Distribution Width Spectrin Tissue, Membrane

Purification and Characterization of Spectrin Tetramers

Antibodies to canine 4.1R, spectrin, and band 3 have been described previously (18 (link), 34 (link), 54 (link)). Rabbit antibody to the exon 14–derived sequence (anti-e14) was generated by the injection of a synthetic peptide with the amino acid sequence of NH2-⁴¹⁹VEKTHIEVTVPTSDGDQTQ⁴³⁷-COOH. The amino acid sequence encoded by alternative exon 14 is identical in various species, including alpacas, dogs, and humans (Fig. S3). The Asn⁴³² residue deduced from the cDNA sequence was converted to Asp (underlined) because Asp was present in the peptides detected by MS/MS analysis (Table S1), presumably due to a rapid posttranslational deamidation at the Asn-Gly sequence (19 (link)). In some experiments, the anti-e14 antibody was incubated with an excess amount of alpaca RBC membrane ghosts (200 μg membrane protein/μg antibody) in 10 mM Tris–Cl (pH 7.5), 500 mM NaCl on ice for 2 h followed by sedimentation of the ghosts by centrifugation. The antibody was subjected to mock treatment by adding it to the ghosts just before centrifugation.
Spectrin tetramers were prepared as described (55 (link), 56 (link)). Briefly, spectrin was extracted from dog RBC membranes and subjected to gel permeation chromatography on a Sepharose 4B column to separate dimers and tetramers. Fractions containing dimers were collected, concentrated by ultrafiltration, and incubated at 30 °C for 2 h to promote conversion of dimers to tetramers. The samples were again subjected to gel permeation chromatography, and the tetramers were pooled and concentrated. Rabbit muscle actin was purchased from Cytoskeleton Inc.

Chen Y., Miyazono K., Otsuka Y., Kanamori M., Yamashita A., Arashiki N., Matsumoto T., Takada K., Sato K., Mohandas N, & Inaba M. (2023). Membrane skeleton hyperstability due to a novel alternatively spliced 4.1R can account for ellipsoidal camelid red cells with decreased deformability. The Journal of Biological Chemistry, 299(2), 102877.

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Publication 2023

Actins Amino Acid Sequence Antibodies Antibodies, Anti-Idiotypic Centrifugation Cytoskeleton DNA, Complementary Exons Gel Chromatography Homo sapiens Immunoglobulins Membrane Proteins Muscle Tissue Peptides Rabbits Red Cell Ghost Sepharose 4B Sodium Chloride Spectrin Tandem Mass Spectrometry Tetrameres Tissue, Membrane Tromethamine Ultrafiltration Vicugna pacos

Spectrin-Actin-4.1R Ternary Complex Formation

Spectrin–actin–4.1R ternary complex formation was measured by the falling ball viscometry assay, as described (59 (link), 60 (link)). In brief, spectrin, F-actin, and GST-h4.1R mutants at appropriate concentrations were mixed in 10 mM Tris–Cl (pH 7.6), 20 mM KCl, 2 mM MgCl2, and 1 mM ATP. A 100 μl microcapillary tube (Drummond Scientific) was filled with this solution, sealed at one end, and incubated at the indicated temperature. After incubation, the tube was placed at a 70° angle from the horizontal; a steel ball (diameter 0.6 mm, Tsubaki-Nakashima Co) was placed under the meniscus of the solution using a magnet; and the time required by the ball to fall a specific distance (6 cm) at 25 °C was measured. Sedimentation velocity was calculated from the falling time (F_t, s/cm) and converted to apparent viscosity (mPa·s) using glycerol standards of known viscosity. The apparent viscosity of reactions containing only spectrin and F-actin was used as the control. If the ball did not move from its initial position for 120 s, the protein mixture was thought to form a gel. In most measurements, spectrin and F-actin concentrations were 10 and 250 μg/ml, respectively; to this, GST-h4.1R recombinants were added at the concentrations of 0 to 20 μg/ml, yielding a spectrin:actin:4.1R M ratio of 1:125:0–5.

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Publication 2023

Actins Biological Assay F-Actin Glycerin Magnesium Chloride Meniscus Proteins Spectrin Steel Tromethamine Viscosity

Top products related to «Spectrin»

Rabbit anti gfp by Thermo Fisher Scientific

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Rabbit anti-GFP is a polyclonal antibody raised against green fluorescent protein (GFP) in rabbits. This antibody can be used to detect and visualize GFP-tagged proteins in various experimental applications.

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Lipofectamine 2000 is a cationic lipid-based transfection reagent designed for efficient and reliable delivery of nucleic acids, such as plasmid DNA and small interfering RNA (siRNA), into a wide range of eukaryotic cell types. It facilitates the formation of complexes between the nucleic acid and the lipid components, which can then be introduced into cells to enable gene expression or gene silencing studies.

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Anti spectrin by Merck Group

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Anti-spectrin is a laboratory reagent used to detect and quantify the presence of spectrin, a cytoskeletal protein found in various cell types. It serves as a tool for researchers and clinicians to analyze and study the structure and function of cells.

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More about "Spectrin"

Spectrins are a family of cytoskeletal proteins found in a variety of cell types, including erythrocytes, neurons, and other tissues.
These structural proteins play a crucial role in maintaining cell shape, membrane stability, and signal transduction.
Spectrin research is vital for understanding a range of conditions, from hereditary spherocytosis to neurodegenerative disorders.
PubCompare.ai's AI-driven platform can help optimize Spectrin research by easily locating relevant literature, preprints, and patents through intelligent comparisons, enhancing reproducibility and efficiency in this important field of study.
The platform can also help researchers find and compare antibodies like Rabbit anti-GFP, Alexa Fluor 488, and MAB1622, as well as other useful tools like Lipofectamine 2000, β-actin, Cleaved caspase-3, and PVDF membranes.
Advancements in Spectrin research, facilitated by tools like PubCompare.ai, can provide valuable insights into the mechanisms underlying various diseases, such as hereditary spherocytosis, a red blood cell disorder, and neurodegenerative conditions.
By optimizing the research process, researchers can more efficiently explore the role of Spectrin in cell function and develop potential therapies targeting the Spectrin protein, such as the use of Anti-spectrin or the compound BML-FG6090.
Utilizing PubCompare.ai's AI-powered platform can help researchers in the Spectrin field enhance their work, leading to breakthroughs that improve our understanding of this crucial cytoskeletal protein and its impact on human health.