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SDHD protein, human

SDHD protein is a subunit of the succinate dehydrogenase (SDH) complex, a key enzyme in the mitochondrial electron transport chain and tricarboxylic acid cycle.
It plays a crucial role in cellular energy production and is implicated in various diseases, including cancer and neurological disorders.
The SDHD protein is essential for the proper assembly and function of the SDH complex, and its dysregulation has been linked to the development of hereditary paraganglioma and pheochromocytoma.
Understanding the structure, function, and regulation of the SDHD protein is crucial for advancing research in these areas and developing potential therapeutic interventions.
The PubCompare.ai platform can help researchers optimize their SDHD protein research protocols and enhance reproducibility by providing intelligent comparisons across the scientific literature, preprints, and patents.

Most cited protocols related to «SDHD protein, human»

1
Optimizing MHC Epitope Clustering
Cited 24 times
For MHC class I epitopes, it is generally observed that a length of about 8–11 residues is optimal for T cell recognition and use in assays. Because of the structure of the class I binding groove, distinct class I sequences typically represent unique epitopes, even if they are nested within a longer sequence that is also recognized by T cells. Accordingly, for the present study, we have not subjected class I epitopes of nested or overlapping character to further processing.
For MHC class II epitopes, however, optimal epitopes are usually longer than the minimal T cell recognized 9-mer core. In general, class II epitopes are optimally of 13–20 residues in length [1 (link)]. Peptides of varying length but that carry the same core may all be similarly active and/or recognized by the same T cell specificity. Thus, many of the epitope structures contained in the IEDB for class II epitopes are redundant, nested or largely overlapping. For this reason, it is desirable to devise strategies to reduce the complexity of class II epitope sets. Here, we developed a clustering algorithm to generate consensus sequences or cluster of epitopes, an illustration of such a process can be found in Table 1. In order to solve this problem, our approach first sorts the peptides based on their RF scores. Then, taking the highest ranked peptide as starting sequence, we move down the ranked list aligning the sequences to find nested or overlapping epitopes by at least 9 residues. For this approach, we only consider identical matches over the region of overlap and identical nested peptides; given this definition, mismatches will be treated as separate epitopes. When a nested peptide is found, we will keep only the larger peptide and calculate a new RF score using the sum of all responded and tested subjects per epitope in the cluster. For overlapping epitopes, a consensus epitope or cluster will be generated combining the sequences, if the cluster length is up to 20 residues. In these cases, the RF score will be calculated as a new RF score as in the nested case. For the assay type scoring system, the highest ranked assay and application of all the assays associated with the set of nested epitopes will be considered.
Carrasco Pro S., Sidney J., Paul S., Lindestam Arlehamn C., Weiskopf D., Peters B, & Sette A. (2015). Automatic Generation of Validated Specific Epitope Sets. Journal of Immunology Research, 2015, 763461.
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Publication 2015
Biological Assay Character Consensus Sequence Epitopes Genes, MHC Class I Genes, MHC Class II Peptides SDHD protein, human T-Cell Specificity T-Lymphocyte
2
Population-Level HIV Incidence Measurement
Cited 23 times
The overall design of SHIMS was based on the direct measurement of HIV incidence at the population level before and after the scale-up of the national combination HIV prevention strategy. To identify eligible participants for the first incidence cohort, a nationally representative, household-based cross-sectional survey was conducted from December 2010 to June 2011, with key epidemiologic and bio-demographic information collected from Swaziland adults, 18 to 49 years of age. At ages 50+ years, recent (incident) HIV infections are very infrequent.
The household sample size was calculated at 14,927 to permit 80% power to detect a 45% reduction in HIV incidence in men from pre- to post- national scale up of the national combination HIV prevention strategy, assuming a baseline HIV incidence of 2.0% among men. We assumed a design effect of 1.25 (based on previous similar DHS surveys), a retention rate of 90%, a household vacancy rate of 13% and a household refusal rate of 5%; and that 10% of men would not be contactable, 23% would be HIV infected and 5% would refuse to participate in the survey. The households were selected using a two-stage cluster sampling procedure, similar in design to that used by the SDHS. In the first stage, a systematic random sample of 575 of the country’s 2076 enumeration areas (EAs) was drawn. In the second stage, a full listing of all households was conducted within each of the 575 EAs. This household listing provided the sampling frame from which a random sample of 26 households was drawn from each EA. Field teams contacted the selected households, and conducted a census of household residents with the head of household (or other available responsible adult household member).
Survey eligibility criteria included residing in or sleeping in the household the night before, reporting an age between 18-49 years inclusive, and the ability to provide informed consent in either SiSwati or English. Further information contributing to the SHIMS sampling methodology and weighting are provided elsewhere [6 ].
Bicego G.T., Nkambule R., Peterson I., Reed J., Donnell D., Ginindza H., Duong Y.T., Patel H., Bock N., Philip N., Mao C, & Justman J. (2013). Recent Patterns in Population-Based HIV Prevalence in Swaziland. PLoS ONE, 8(10), e77101.
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Publication 2013
Adult Eligibility Determination Head of Household HIV-2 HIV Infections Households Inclusion Bodies Reading Frames Retention (Psychology) SDHD protein, human SHIMS
3
Comparative Analysis of Real-Space Density Scores
Cited 14 times
The real-space R versions of Kleywegt and Dodson are defined as for the Jones version, except that ρcalc obtained by a Fourier transform of the calculated structure factors is used instead of Gaussian atomic peak profiles and hence all factors that affect the atomic density profiles are automatically taken into account. The values of the limiting radii used are chosen arbitrarily and vary between implementations (Fig. 3 ▶a); this causes RSR to vary wildly according to the software used (Fig. 3 ▶b). The values may be fixed (e.g. rmax = 1.5 Å in MAPMAN) or may depend only on B factor [e.g. rmax = 2.5(B + 25)1/2/2π Å in SFALL].
Fig. 4 ▶ shows plots of the main-chain mean B factor and RSR versus residue sequence number for PDB entries 1f83 and 3g94 (both for botulinum neurotoxin type B catalytic domain in complex with synaptobrevin II; Hanson & Stevens, 2000 ▶ ) and 2w96 (cyclin-dependent kinase 4 complex with cyclin D1; Day et al., 2009 ▶ ). Entry 1f83 was found to contain gross in­accuracies: the errors were subsequently corrected and 1f83 was obsoleted (2007) and replaced by 3g94; the latter was then also retracted (Hanson & Stevens, 2009 ▶ ) because the im­precise density observed for the ligand did not support the conclusions drawn. The CDK4–cyclin D1 complex was determined concurrently and independently to that of Day et al. (2009 ▶ ) by Takaki et al. (2009 ▶ ) and proved to be identical within the expected limits of precision. These three structures thus provide a nice comparative test of the various real-space density scores: we can take 1f83 and 3g94 as representatives of an inaccurate and an imprecise structure, respectively.
, & Tickle I.J. (2012). Statistical quality indicators for electron-density maps. Acta Crystallographica Section D: Biological Crystallography, 68(Pt 4), 454-467.
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Publication 2012
botulinum toxin type B Catalytic Domain Complement Factor B Cyclin-Dependent Kinase 4 Cyclin D1 factor A Ligands Radius SDHD protein, human Vesicle-Associated Membrane Proteins
4
Genetic Manipulation of Ustilago maydis
Cited 12 times
The U. maydis strains AB33nRFP, AB33paGRab5a, AB33GT_Peb1R, AB33G3Dyn2, and AB33G3Dyn2_ChRab5a were described previously (Schuchardt et al., 2005 (link); Lenz et al., 2006 (link); Schuster et al., 2011a (link), 2011b (link)). The orientation of MT was investigated in strain AB33EB1Y and in strain AB5Dyn2ts_ Peb1Y, which was generated by homologous integration of plasmid pPeb1Y_N (Lenz et al., 2006 (link)) into the strains AB33 and AB5Dyn2ts.
To visualize the MT minus ends, a 1013–base pair fragment near the 3′ end of the grc1 gene (γ-tubulin ring complex 1; RefSeq accession number: XP_757621.1), followed by egfp and the nos terminator, the hygromycin resistance cassette, and 1061 base pairs of the downstream sequence were cloned into a cloning vector resulting in plasmid pGrc1G. The plasmid pGrc1G was digested with BsrGI and two additional copies of gfp were introduced as BsrGI fragments, resulting in the plasmid pGrc1-3G. The plasmid pGrc1-3G was digested with DraI and integrated homologously into the grc1 locus of strain AB33, resulting in AB33Grc1-3G. The plasmid potefGFPTub1 (Steinberg et al., 2001 (link)) was digested with NcoI and NdeI to remove the gfp gene and replace it with mCherry gene, resulting in plasmid pomChTub1. The plasmid popGRab5a (Schuster et al., 2011b) was digested with BamHI and BsrGI to remove the pagfp gene and replace it with pamCherry gene, resulting in the plasmid popamChRab5a.The plasmids pomChTub1 and popamChRab5a were digested with SspI and integrated at the succinate dehydrogenase locus of strain AB33Grc1-3G, resulting in AB33Grc1-3G_mChTub1 and AB33Grc1-3G_pamChRab5a, respectively.
To analyze MT bundles, plasmid potefGFPTub1 (Steinberg et al., 2001 (link)) was ectopically introduced into strain AB33, resulting in AB33GT. The strain AB33GT_Peb1R was obtained by homologous integration of plasmid pPeb1R_N (Lenz et al., 2006 (link)) into AB33GT. The strain AB5Dyn2ts_GT was generated by ectopic integration of plasmid potefGFPTub1 in the strain AB5Dyn2ts. For colocalization studies of dynein and MT, plasmid potefGFPTub1 was ectopically integrated into strain AB33G3Dyn2, resulting in AB33G3Dyn2_GT. For strain AB33_ΔKin3_r Dyn1_GRab5a, the phleomycin resistance cassette of plasmid pcrgDyn1 (Lenz et al., 2006 (link)) was replaced by the hygromycin resistance cassette, resulting in plasmid pcrgDyn1-H. This plasmid was transformed in strain AB33_ΔKin3_GRab5a. potagRRab5a was generated by replacing the paGFP in plasmid popaGRab5a (Schuster et al., 2011b (link)) with TagRFP (Evrogen, Moscow, Russia). The resulting plasmid potagRRab5a was linearized with AgeI for homologous integration at the succinate dehydrogenase locus of strain AB33ΔKin3_Kin3tsG, resulting in AB33ΔKin3_ Kin3tsG_tagRRab5a.
To visualize Kin3-GFP, a 1036–base pair fragment near the 3′ end of the gene, followed by egfp and the nos terminator, the hygromycin resistance cassette, and 1032 base pairs of the downstream sequence were cloned into a cloning vector, resulting in plasmid pKin3G_H. The plasmid was integrated into the native kin3 locus, resulting in strain AB33Kin3G. All strains and plasmids used in this study are summarized in Table 1.
Schuster M., Kilaru S., Fink G., Collemare J., Roger Y, & Steinberg G. (2011). Kinesin-3 and dynein cooperate in long-range retrograde endosome motility along a nonuniform microtubule array. Molecular Biology of the Cell, 22(19), 3645-3657.
Publication 2011
Cloning Vectors Dynamin I Dynein ATPase Genes Genes, vif hygromycin A Phleomycins Plasmids SDHD protein, human Strains Tubulin
5
RIP3 Kinase Immunoprecipitation and Assay
Cited 12 times

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Publication 2009
Antibodies Antibodies, Anti-Idiotypic beta-glycerol phosphate Biological Assay Buffers Cells Complex, Immune Densitometry Edetic Acid Gels Glycerin HEPES Homo sapiens Immunoprecipitation Jurkat Cells Magnesium Chloride manganese chloride myosin phosphatase-Rho interacting protein, human NADH Dehydrogenase Complex 1 Nonidet P-40 Orthovanadate Phosphotransferases Rabbits SDHD protein, human Sepharose Sodium Sodium Chloride Tromethamine

Most recents protocols related to «SDHD protein, human»

1
Mitochondrial Enzyme Activity Assay
Succinate Dehydrogenase Activity—Krebs Cycle: The activity of the enzyme succinate dehydrogenase was determined according to the method described by Fischer et al. (1985) (link).
The activity of mitochondrial respiratory chain enzymes: Complex I activity was evaluated by the method described by Cassina and Radi (1996) (link). Complex II activity was measured by the method described by Fischer et al. (1985) (link).
da Silva L.A., Thirupathi A., Colares M.C., Haupenthal D.P., Venturini L.M., Corrêa M.E., Silveira G.D., Haupenthal A., do Bomfim F.R., de Andrade T.A., Gu Y, & Silveira P.C. (2023). The effectiveness of treadmill and swimming exercise in an animal model of osteoarthritis. Frontiers in Physiology, 14, 1101159.
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Publication 2023
enzyme activity Mitochondria NADH Dehydrogenase Complex 1 Respiratory Chain SDHD protein, human
2
Mitochondrial Respiration Assay in Rat Brain

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Publication 2023
Age Groups Alamethicin Antimycin A Ascorbic Acid Brain Buffers Cell Culture Techniques Cold Temperature Cytochromes c Egtazic Acid Freezing HEPES Ice inhibitors Kidney Cortex Magnesium Chloride Mannitol Mitochondria Mitochondrial Proteins Proteins Rattus Respiratory Rate Rotenone SDHD protein, human Seahorses Sodium Azide Succinate Sucrose Tissues
3
Bioinformatic analysis of Mayo PDX RNAseq data
We derived RNAseq RPKM expressions of Mayo PDX cells from Vaubel et al., 2020 [34 (link)] (19,552 genes in 20 MES patients, 16 PN patients, and 30 CL patients, www.cbioportal.org). We filtered out genes with geometric means small than 1 and with counts in less than 80% of patients, and added a pseudo count of 0.1, to achieve a normal gene expression distribution compared to original distribution (Figure S6a,S6b, 11752 genes left). We applied the two-sample t-test to the RNAseq-derived mRNA expression levels of Mayo MES and PN lines, and derived 1,177 differential genes with p<0.05 and FC>2 in the volcano plot (Figure S6c). We applied enrichment analysis in Gene Ontology (http://geneontology.org) [38 (link)] and derived 216 migration genes in “cell adhesion” and “cell motility” biological processes. We further applied the enrichment analysis and derived 23 actin genes (Figure 5a), 9 motor genes (Figure 5b), and 47 clutch (Figure 5c) genes in “actin cytoskeleton,” “actomyosin” coupled with “myosin II complex,” and “focal adhesion” cellular components, respectively.
We applied the correlation analysis between the mRNA expression ratios of the actin (Figure 5a), motor (Figure 5b), clutch (Figure 5c) genes in the 10 Mayo lines used in the present study (no mRNA data available for Mayo 16 line) and their CMS parameter values (vpoly, nm, nc), respectively. The correlation coefficients (R) of all the genes were sorted and plotted in Figure 5, with the significant correlation coefficients in red.
We applied Cox regression analysis between the mRNA expression ratios of the actin (Figure S7a), motor (Figure S7b), and clutch (Figure S7c) genes in a cohort of 66 Mayo patients and their overall survival, and their hazard ratios with 95% Confidence Interval were sorted and plotted in Figure S7, with the significant hazard ratios in red.
Hou J., McMahon M., Sarkaria J.N., Chen C.C, & Odde D.J. (2023). Main Manuscript for Cell migration simulator-based biomarkers for glioblastoma. bioRxiv.
Publication Preprint 2023
Actins Actomyosin Biological Processes Birth Cohort Cell Adhesion Cells Cellular Structures Focal Adhesions Gene Expression Genes Microfilaments Motility, Cell Myosin ATPase Patients RNA, Messenger SDHD protein, human
4
Murine Dendritic Cell Culture and Activation
The murine bone marrow-derived dendritic cell line, DC2.4, was cultured in RPMI 1640 medium (pH 7.4) (Gibco) supplemented with 10% fetal calf serum (FCS, Thermo Fisher Scientific, Australia), 1% pen-strep (Gibco), 1% l-glutamine (Gibco), and 0.1% 2-mercaptoethanol (Gibco) at 37°C + 5% CO2. Cells were passaged once adherent cells were 90% confluent, approximately every 3 days.
For DC activation and maturation studies, dendritic cells were harvested from culture and incubated with Strep A at an MOI of 2:1 or 10:1 (Strep A:DC). Lipopolysaccharide (2 μg/mL, Sigma-Aldrich, Australia) was used as a positive control, with DCs in medium alone used as the negative control. DC/Strep A cultures were incubated without antibiotics for 12 h at 37°C + 5% CO2. Cells were collected via centrifugation and supernatants were stored at −80°C for cytokine analyses. Cells were resuspended in Fc block (CD16/CD32; BD Pharminogen, Australia) and incubated on ice for 10 min to prevent nonspecific binding of antibodies. The LIVE/DEAD Fixable Cell Stain (Life Technologies, Australia) was used according to manufacturer’s instructions. For DC maturation assessment, fluorochrome-conjugated antibodies were added in a 1:100 dilution in PBS + 1% bovine serum albumin and incubated on ice for 40 min protected from light. The antibody cocktail used included anti-mouse/rat major histocompatibility complex (MHC) II (I-Ek) fluorescein isothiocyanate (Affymetrix eBioscience), rat anti-mouse CD86 (GL-1) PE (BD Pharminogen, Australia), and hamster anti-mouse CD80 APC (16-10A1; BD Pharminogen, Australia) with the appropriate isotype controls. Samples were analyzed using a CyAn ADP flow cytometer (Beckman Coulter) employing Summit software v4.3 (Beckman Coulter).
Langshaw E.L., Reynolds S., Ozberk V., Dooley J., Calcutt A., Zaman M., Walker M.J., Batzloff M.R., Davies M.R., Good M.F, & Pandey M. (2023). Streptolysin O Deficiency in Streptococcus pyogenes M1T1 covR/S Mutant Strain Attenuates Virulence in In Vitro and In Vivo Infection Models. mBio, 14(1), e03488-22.
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Publication 2023
2-Mercaptoethanol Antibiotics Antibodies Bone Marrow Bos taurus Cell Lines Cells Centrifugation Combined Antibody Therapeutics Cytokine Dendrites Dendritic Cells Fluorescein Fluorescent Dyes galiximab Glutamine Hamsters Immunoglobulin Isotypes isothiocyanate Light Lipopolysaccharides Mus SDHD protein, human Serum Albumin Stains Streptococcal Infections Technique, Dilution
5
Cell Viability Assay with CCK-8
HEI-OC1 cells were collected, washed after the treatment, and plated on a 96-well plate at a density of 10,000 cells/well. The CCK-8 reagent (40203ES76; YEASEN, China; 10 μL), which can undergo a reduction reaction with succinate dehydrogenase in the mitochondria of living cells, was added to HEI-OC1 cells for 4 h of incubation (conventional culture conditions). The 96-well plate was placed in a microplate reader to analyze the absorbance at 450 nm.
Zhang X., Zheng J., Xu H, & Ma Z. (2023). UHRF1-induced connexin26 methylation is involved in hearing damage triggered by intermittent hypoxia in neonatal rats. Open Medicine, 18(1), 20230650.
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Publication 2023
Cells Mitochondria SDHD protein, human Sincalide

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MTT is a colorimetric assay used to measure cell metabolic activity. It is a lab equipment product developed by Merck Group. MTT is a tetrazolium dye that is reduced by metabolically active cells, producing a colored formazan product that can be quantified spectrophotometrically.
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Complex 2 enzyme activity microplate assay kit by Abcam
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The Complex II Enzyme Activity Microplate Assay Kit is a laboratory tool used to measure the activity of Complex II, also known as succinate dehydrogenase, in biological samples. The kit provides a straightforward and quantitative method to assess the enzymatic function of this crucial component of the electron transport chain in the mitochondria.
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The Complex I Enzyme Activity Microplate Assay Kit is a laboratory equipment product that provides a method to measure the activity of the mitochondrial respiratory complex I. The kit includes a microplate, reagents, and necessary components to perform the assay.

More about "SDHD protein, human"

The SDHD protein, also known as the Succinate Dehydrogenase Complex, Subunit D, plays a crucial role in cellular energy production and is implicated in various diseases, including cancer and neurological disorders.
This mitochondrial enzyme complex is essential for the proper functioning of the electron transport chain and the tricarboxylic acid cycle, making it a key player in cellular respiration and metabolism.
Researchers can leverage the PubCompare.ai platform to optimize their SDHD protein research protocols and enhance reproducibility.
By providing intelligent comparisons across the scientific literature, preprints, and patents, the platform can help researchers identify the best experimental procedures, reagents, and products for their studies.
For example, researchers may use Oxygraph-2k, a high-resolution respirometry system, to measure the oxygen consumption rate and mitochondrial function in cells expressing SDHD.
The MTT assay can be employed to assess cell viability and proliferation, while the Complex II Enzyme Activity Microplate Assay Kit can be used to directly measure the activity of the SDH complex.
Additionally, the RNeasy Mini Kit can be used to extract high-quality RNA from cells or tissues, enabling the analysis of SDHD gene expression using techniques like qRT-PCR or RNA-sequencing.
The DatLab software can be utilized to analyze and visualize the data obtained from these experiments.
Researchers may also need to manipulate the SDHD protein or its associated pathways, for which compounds like Rotenone (a Complex I inhibitor) or Antimycin A (a Complex III inhibitor) can be employed.
The High-Capacity cDNA Reverse Transcription Kit can be used to generate cDNA from the extracted RNA, allowing for the modulation of SDHD expression through techniques like overexpression or silencing.
Furthermore, the metabolic substrate Succinate, which is a key intermediate in the tricarboxylic acid cycle, may be of interest in SDHD-related studies, as its accumulation has been linked to various pathological conditions.
By leveraging the insights and tools available through PubCompare.ai and the related techniques and reagents, researchers can optimize their SDHD protein research, enhance reproducibility, and unlock new discoveries in the fields of cellular metabolism, cancer biology, and neurodegeneration.