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Mitochondrial Proteins

Mitochondrial Proteins are a diverse group of proteins found within the mitochondria, the powerhouses of eukaryotic cells.
These proteins play crucial roles in energy production, metabolism, and cellular signaling.
Mitochondrial Proteins include enzymes, structural components, and regulatory factors essential for the proper functioning of the mitochondria.
Understanding the complexities of Mitochondrial Proteins is crucial for unraveling the underlying mechanisms of mitochondrial dysfunction, which has been implicated in a wide range of diseases, including neurodegeneration, cardiomyopathy, and metabolic disorders.
Researchers can leverage cutting-edge AI-driven platforms like PubCompare.ai to access the most accurate and reproducible protocols from literature, pre-prints, and patents, enabling them to identify the best methods and products for their Mitochondrial Protein studies and elevate the accuracy and reproducibility of their research.

Most cited protocols related to «Mitochondrial Proteins»

1
Comparative Mitochondrial Respiration Assays
Cited 70 times
Clark electrode assays performed for comparative purposes utilized a Hansatech Oxytherm apparatus (PP Systems, Amesbury, MA) for rat heart mitochondria or a Rank system (Rank Brothers, Bottisham, Cambridge, England) for mouse liver mitochondria. For rat heart mitochondria, assays were performed in parallel with the same mitochondrial preparation, MAS, substrates and compounds as for the XF24 assays. Typically 62.5–125 µg of mitochondria were used in a volume of 500 µl MAS plus the appropriate substrate. Respiration was initiated by adding mitochondria, and followed by sequential addition of ADP, oligomycin and FCCP. Concentrations of substrate, ADP, oligomycin, and FCCP were identical to those used in the XF24 experiments. For mouse liver mitochondria, assays were performed in parallel the same mitochondrial preparation, MAS, substrates and compounds as for the XF24 assays with the following modifications: substrate was 5 mM succinate, 2 µM rotenone and 300 µM ADP was used. Typically, 0.3 mg/ml of mitochondria were used in a volume of 2.0–3.5 ml MAS plus the appropriate substrate. Respiration was initiated by adding mitochondria, followed by sequential addition of ADP, oligomycin and FCCP. Concentrations of oligomycin and FCCP were identical to those used in the XF24 experiments. Oxygen consumption rates were converted from nmol O/min/ml to pmol O2/min/µg mitochondrial protein.
Rogers G.W., Brand M.D., Petrosyan S., Ashok D., Elorza A.A., Ferrick D.A, & Murphy A.N. (2011). High Throughput Microplate Respiratory Measurements Using Minimal Quantities Of Isolated Mitochondria. PLoS ONE, 6(7), e21746.
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Publication 2011
Biological Assay Brothers Carbonyl Cyanide p-Trifluoromethoxyphenylhydrazone Cell Respiration Mice, House Mitochondria Mitochondria, Heart Mitochondria, Liver Mitochondrial Proteins Oligomycins Oxygen Consumption Rotenone Succinate
2
Comparative Analysis of Mammalian Mitochondrial Proteins
Cited 53 times
Mitochondrial protein (mtProtein) sequences of 17 different
mammalian members were retrieved in FASTA format from
National Centre of Biotechnology Information on a single
notepad file with “.txt” extension was created. The FASTA
format of protein chosen must start with >lcl| then followed by
accession number or description. In the end there should be at
least one bracket “[ ]” and in this bracket there may be species
name or other details, sequence length should start after
bracket. The input FASTA file of different mammalian protein
has been illustrated in Figure 1.
Garg V.K., Avashthi H., Tiwari A., Jain P.A., Ramkete P.W., Kayastha A.M, & Singh V.K. (2016). MFPPI – Multi FASTA ProtParam Interface. Bioinformation, 12(2), 74-77.
Publication 2016
Mammals Mitochondrial Proteins Proteins
3
Isolation of Mouse Liver Mitochondria
Cited 51 times
Ethics Statement: Animal housing, euthanasia, and tissue harvest procedures were conducted in accordance with and approved by the UCSD Institutional Animal Care and Use Committee (protocol #S09186) and the Buck Institute Animal Care Committee (protocol #10180). Mitochondria from C57bl/6 (male and female) mice aged 4–6 weeks were isolated by two similar differential centrifugation methods, based upon Schnaitman and Greenawalt [14] (link) or Chappell and Hansford [15] . Specifically, the liver was extracted and minced in ∼10 volumes of MSHE+BSA (4°C), and all subsequent steps of the preparation were performed on ice. The material was rinsed several times to remove blood. The tissue was disrupted using a drill-driven Teflon glass homogenizer with 2–3 strokes. Homogenate was centrifuged at 800 g for 10 min at 4°C. Following centrifugation, fat/lipid was carefully aspirated, and the remaining supernatant was decanted through 2 layers of cheesecloth to a separate tube and centrifuged at 8000 g for 10 min at 4°C. After removal of the light mitochondrial layer, the pellet was resuspended in MSHE+BSA, and the centrifugation was repeated. The final pellet was resuspended in a minimal volume of MSHE+BSA. Total protein (mg/ml) was determined using Bradford Assay reagent (Bio-Rad). Typically, ∼7.5 mg of mitochondria (100 µl volume) was obtained from a single mouse liver. In separate studies in which respiratory rates in the Seahorse and the Rank Clark electrode system were compared, mouse liver mitochondria were isolated according to Chappell and Hansford [15] in 250 mM Sucrose, 5 mM Tris and 2 mM EGTA (STE) on ice. Tissue was homogenized 10 times with a Teflon-glass homogenizer, and the homogenate was centrifuged at 1000 g for 3 minutes (4°C). The supernatant was collected and centrifuged at 11,600 g for 10 minutes. The pellet was resuspended in STE after discarding the whitish layer. The above step was repeated two times to get the final mitochondrial pellet. 8–10 mg of mitochondrial protein was obtained from each mouse liver and resuspended in 400–500 µl of STE.
Rogers G.W., Brand M.D., Petrosyan S., Ashok D., Elorza A.A., Ferrick D.A, & Murphy A.N. (2011). High Throughput Microplate Respiratory Measurements Using Minimal Quantities Of Isolated Mitochondria. PLoS ONE, 6(7), e21746.
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Publication 2011
Animal Care Committees Biological Assay BLOOD Centrifugation Cerebrovascular Accident Drill Egtazic Acid Euthanasia Females G-800 Institutional Animal Care and Use Committees Light Lipids Liver Males Mice, House Mitochondria Mitochondria, Liver Mitochondrial Proteins Proteins Respiratory Rate Seahorses Sucrose Teflon Tissue Harvesting Tissues Tromethamine
4
Constructing Robust Mitochondrial Presequence Predictor
Cited 25 times
We prepared a data set of 759 presequence containing mitochondrial proteins by combining the data sets of TargetP and Predotar (containing proteins from various eukaryotes) with presequences identified via recent mitochondrial N-terminal proteome measurements on S. cerevisiae (7 (link)), and on A.thaliana and O.sativa (22 (link)). Based on an initial inspection of the data, when developing MitoFates we decided to discard any putative mature N-termini from these studies that cannot be explained as the product of cleavage by MPP with an arginine at the −2 position (possibly followed by secondary cleavage by Icp55 or Oct1). We made this decision because for the rest of the data we failed to discern any overall pattern in either the local sequence surrounding the putative cleavage sites or the distance from the original N-termini. Presumably, this non-R-2 site data includes proteins processed by proteases such as IMP and m-AAA, possibly some noncanonical MPP cleavage and probably some nonspecific degradation products. Although we did not include these sites when developing MitoFates itself, we did include them in an exploratory clustering experiment described below. Note that we did include plant mature N-termini with an arginine at the −3 position as they could plausibly be explained as the product of canonical MPP cleavage followed by an additional cleavage of one N-terminal residue by a plant counterpart to yeast Icp55. For negative examples, we used 6310 nonmitochondrial proteins with clear UniProt annotation of subcellular localization and 108 noncleaved yeast mitochondrial proteins (7 (link)). These sequences (taken from UniProt (23 (link)) ver. 2012 10) were selected such that no pair shared more than 80% mutual sequence identity within the positive or negative data sets. To compare the prediction performance of MitoFates with previous methods, we prepared an independent test data set consisting of 78 mitochondrial proteins possessing a presequence and 8934 nonmitochondrial proteins; in such a way that the sequence identity between training and test data sets and within the positive and negative data sets is less than 25%.
Fukasawa Y., Tsuji J., Fu S.C., Tomii K., Horton P, & Imai K. (2015). MitoFates: Improved Prediction of Mitochondrial Targeting Sequences and Their Cleavage Sites. Molecular & Cellular Proteomics : MCP, 14(4), 1113-1126.
Publication 2015
Arginine Cytokinesis Eukaryota Mitochondria Mitochondrial Proteins Peptide Hydrolases Plants POU2F1 protein, human Protein Annotation Proteins Proteome Saccharomyces cerevisiae Yeast Proteins
5
Large-Scale Proteomic Analysis Using 2D-LE
Cited 25 times
For large scale global analysis, HeLa S3 cells were prefractionated using custom 2D-LE platform, comprised of sIEF coupled to multiplexed GELFrEE12 (link),13 (link). HeLa S3, H1299, B16F10 cells, and mitochondrial membrane proteins were also fractionated using the custom GELFrEE13 (link) device alone (no sIEF). After separation, detergent and salt were removed, and the fractions were injected into nanocapillary RPLC columns for elution into a 12 Tesla LTQ FTMS for online detection and fragmentation14 (link),15 (link). The MS RAW files were processed with in-house software called crawler to assign masses. Using this program, determination of both the intact masses and the corresponding fragment masses were performed and these data were searched against a human proteome database. Extensive statistical workups were also performed using several FDR estimation approaches (with decoy databases both concatenated and not). A final q-value procedure is described in detail (Methods), with the data above reported using a 5% instantaneous FDR (i.e., q-value) cutoff at the protein level (Supplementary Fig. 14).
Tran J.C., Zamdborg L., Ahlf D.R., Lee J.E., Catherman A.D., Durbin K.R., Tipton J.D., Vellaichamy A., Kellie J.F., Li M., Wu C., Sweet S.M., Early B.P., Siuti N., LeDuc R.D., Compton P.D., Thomas P.M, & Kelleher N.L. (2011). Mapping Intact Protein Isoforms in Discovery Mode Using Top Down Proteomics. Nature, 480(7376), 254-258.
Publication 2011
Cells Detergents HeLa Cells Homo sapiens Medical Devices Membrane Proteins Mitochondria Mitochondrial Membranes Mitochondrial Proteins Proteins Proteome Sodium Chloride Tissue, Membrane

Most recents protocols related to «Mitochondrial Proteins»

1
Restoring Mitochondrial Function in Friedreich's Ataxia Neurons
Not available on PMC !

Example 2

The next experiments asked whether inhibition of the same set of FXN-RFs would also upregulate transcription of the TRE-FXN gene in post-mitotic neurons, which is the cell type most relevant to FA. To derive post-mitotic FA neurons, FA(GM23404) iPSCs were stably transduced with lentiviral vectors over-expressing Neurogenin-1 and Neurogenin-2 to drive neuronal differentiation, according to published methods (Busskamp et al. 2014, Mol Syst Biol 10:760); for convenience, these cells are referred to herein as FA neurons. Neuronal differentiation was assessed and confirmed by staining with the neuronal marker TUJ1 (FIG. 2A). As expected, the FA neurons were post-mitotic as evidenced by the lack of the mitotic marker phosphorylated histone H3 (FIG. 2B). Treatment of FA neurons with an shRNA targeting any one of the 10 FXN-RFs upregulated TRE-FXN transcription (FIG. 2C) and increased frataxin (FIG. 2D) to levels comparable to that of normal neurons. Likewise, treatment of FA neurons with small molecule FXN-RF inhibitors also upregulated TRE-FXN transcription (FIG. 2E) and increased frataxin (FIG. 2F) to levels comparable to that of normal neurons.

It was next determined whether shRNA-mediated inhibition of FXN-RFs could ameliorate two of the characteristic mitochondrial defects of FA neurons: (1) increased levels of reactive oxygen species (ROS), and (2) decreased oxygen consumption. To assay for mitochondrial dysfunction, FA neurons an FXN-RF shRNA or treated with a small molecule FXN-RF inhibitor were stained with MitoSOX, (an indicator of mitochondrial superoxide levels, or ROS-generating mitochondria) followed by FACS analysis. FIG. 3A shows that FA neurons expressing an NS shRNA accumulated increased mitochondrial ROS production compared to EZH2- or HDAC5-knockdown FA neurons. FIG. 3B shows that FA neurons had increased levels of mitochondrial ROS production compared to normal neurons (Codazzi et al., (2016) Hum Mol Genet 25(22): 4847-485). Notably, inhibition of FXN-RFs in FA neurons restored mitochondrial ROS production to levels comparable to that observed in normal neurons. In the second set of experiments, mitochondrial oxygen consumption, which is related to ATP production, was measured using an Agilent Seahorse XF Analyzer (Divakaruni et al., (2014) Methods Enzymol 547:309-54). FIG. 3C shows that oxygen consumption in FA neurons was ˜60% of the level observed in normal neurons. Notably, inhibition of FXN-RFs in FA neurons restored oxygen consumption to levels comparable to that observed in normal neurons. Collectively, these preliminary results provide important proof-of-concept that inhibition of FXN-RFs can ameliorate the mitochondrial defects of FA post-mitotic neurons.

Mitochondrial dysfunction results in reduced levels of several mitochondrial Fe-S proteins, such as aconitase 2 (ACO2), iron-sulfur cluster assembly enzyme (ISCU) and NADH:ubiquinone oxidoreductase core subunit S3 (NDUFS3), and lipoic acid-containing proteins, such as pyruvate dehydrogenase (PDH) and 2-oxoglutarate dehydrogenase (OGDH), as well as elevated levels of mitochondria superoxide dismutase (SOD2) (Urrutia et al., (2014) Front Pharmacol 5:38). Immunoblot analysis is performed using methods known in the art to determine whether treatment with an FXN-RF shRNA or a small molecule FXN-RF inhibitor restores the normal levels of these mitochondrial proteins in FA neurons.

US11873494B2. Genetic and pharmacological transcriptional upregulation of the repressed FXN gene as a therapeutic strategy for Friedreich ataxia (2024-01-16). University of Massachusetts [US]. Inventors: Michael R. Green [US], Minggang Fang [US].
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Patent 2024
Aconitate Hydratase Biological Assay Cells Cloning Vectors Enzymes EZH2 protein, human frataxin Genets HDAC5 protein, human Histone H3 Immunoblotting Induced Pluripotent Stem Cells inhibitors Iron Ketoglutarate Dehydrogenase Complex Mitochondria Mitochondrial Inheritance Mitochondrial Proteins MitoSOX NADH NADH Dehydrogenase Complex 1 NEUROG1 protein, human Neurons Oxidoreductase Oxygen Consumption Proteins Protein Subunits Psychological Inhibition Pyruvates Reactive Oxygen Species Repression, Psychology Seahorses Short Hairpin RNA Sulfur sulofenur Superoxide Dismutase Superoxides Thioctic Acid Transcription, Genetic
2
In Vitro Expression of Human OTC in HeLa Cells
Not available on PMC !

Example 14

To measure in vitro expression of human OTC in HeLa cells, those cells were seeded on 12-well plates (BD Biosciences, San Jose, USA) one day prior to transfection. mRNA formulations comprising human OTC or a GFP control was transfected using 800 ng mRNA and 2 μL Lipofectamin 2000 in 60 μL OPTI-MEM per well and incubated.

After 24 hours, the cells in each well were lysed using a consistent amount of lysis buffer. Appropriate controls were used, including citrate synthesase, a mitochondrial marker. Protein concentrations of each were determined using a BCA assay according to manufacturer's instructions. To analyze OTC expression, equal loads of each lysate (24 μg) were prepared in a loading buffer and subjected to standard Western blot analysis. For detection of OTC, a commercial anti-OTC antibody was used according to the manufacturer's instructions. The mRNA expressed OTC was compared to loaded recombinant human OTC protein (10, 5, and 2.5 ng).

FIG. 1A shows the expression level of human OTC (construct ahOTC; SEQ ID NO: 61) and the citrate synthesase mitochondrial protein control. FIG. 1B shows that the expressed human OTC (construct ahOTC; SEQ ID NO: 61) co-localizes with the mitotracker mitochondrial marker, and is therefore present in the mitochondria of cells.

US11859215B2. Polynucleotides encoding ornithine transcarbamylase for the treatment of urea cycle disorders (2024-01-02). ModernaTX, Inc. [US]. Inventors: Zhijian Zhuo [US], Andrea Lea Frassetto [US], Paolo G. V. Martini [US], Vladimir Presnyak [US], Patrick Finn [US].
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Patent 2024
Antibodies, Anti-Idiotypic Biological Assay Buffers Cells Citrates HeLa Cells Homo sapiens Mitochondria Mitochondrial Proteins OTC protein, human Proteins RNA, Messenger Transfection Western Blot
3
Identifying Mitochondrial Proteins in Protists
Several searching strategies were employed to identify putative mitochondrial proteins in P. canceri and M. mackini (Burki et al. 2013 (link)). The predicted proteomes of P. canceri and M. mackini were inspected for the presence of proteins encoding MRO-localized proteins using the functional annotation and subcellular localization determined in the previous section. The output of eggNOG-mapper and Interproscan were additionally searched for any components of the protein import machinery or mitochondrial carrier family proteins. Moreover, the predicted mitochondrial proteomes from Pygsuia biforma (Stairs et al. 2014 (link)), Blastocystis sp. (Abrahamian et al. 2017 ) and B. motovehiculus (Gawryluk et al. 2016 (link)) were used as query sequences against the predicted proteins from P. canceri and M. mackini using BLAST v.2.1.8 (Altschul et al. 1990 (link)). Any protein that was predicted to be mitochondrial related based on at least one software tool used above or had one mitochondrial subject sequence retrieved in the top 100 BLAST hits was further investigated for completeness, annotation and mitosomal provenance. First, the gene model's completeness was assessed by manually examining the query coverage to similar sequences via BLAST. Those P. canceri predicted proteins that did not match to any sequence with BLAST or only aligned with hypothetical proteins were not examined but can be found in supplementary Table S1A and C, Supplementary Material online. Those predicted protein sequences with a methionine that align with the starting methionine of subject sequences were annotated as “complete“. In case that some but not all components of a certain metabolic pathway were predicted to be present in P. canceri, the putative missing genes were further searched in the metagenomic and metatranscriptomic predicted proteomes. If these searches proved negative, the raw reads of each library were further investigated with Phylomagnet (Schön et al. 2020 (link)). This program employs a gene centric approach to retrieve and assemble genes of interest directly from a raw read library. None of the investigated genes could be recovered from the raw reads.
Onuț-Brännström I., Stairs C.W., Campos K.I., Thorén M.H., Ettema T.J., Keeling P.J., Bass D, & Burki F. (2023). A Mitosome With Distinct Metabolism in the Uncultured Protist Parasite Paramikrocytos canceri (Rhizaria, Ascetosporea). Genome Biology and Evolution, 15(3), evad022.
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Publication 2023
Amino Acid Sequence Blastocystis Carrier Proteins cDNA Library FCER2 protein, human Genes Metagenome Methionine Mitochondria Mitochondrial Proteins OCA2 protein, human Proteins Proteome
4
Phylogenetic Validation of Mitochondrial Proteins
To confirm the taxonomic identity of the putative mitochondrial-related protein identified in P. canceri and eliminate the possibility of residual contamination, maximum-likelihood phylogenetic trees were constructed (supplementary fig. S5, Supplementary Material online). Except for the mitochondrial ABC transporter gene (atm1), the phylogenetic analysis workflow was performed as follows. All mitochondrial-related proteins identified in P. canceri were queried against the NCBI nr database (August, 2020) with BLAST v.2.1.9 (Altschul et al. 1990 (link)) using the BLASTP algorithm. The top 5,000 hits with an e-value less than 1e-10 (or 1e-5 if few hits were identified) were retrieved and clustered at 90% identity with CD-HIT v.4.8.1 (Edgar 2010 (link)). The predicted proteomes of M. mackini and C. pagurus were searched with BLASTP to retrieve homologous proteins. Lastly, a reciprocal BLASTP in all P. canceri predicted proteoms was performed. The sequences were aligned (Mafft v.7.407 (Katoh and Standley 2013 (link)), mafft-auto). The alignments were trimmed of ambiguous sites with (trimAL v.1.4.1 (Capella-Gutierrez et al. 2009 (link)), -automated1). The amino acid substitution model was determined with IQ-TREE2.1.6.5 using the default settings (Kalyaanamoorthy et al. 2017 (link)). Phylogenies and 1,000 ultrafast bootstrap trees with 1,000 SH-aLRT replicates were constructed with IQ-TREE2 v.1.6.5 (Minh et al. 2013 (link)). These initial phylogenies were visualized in FigTree v.1.4.4 and manually pruned to reduce the number of taxa. The reduced data set was aligned (Mafft v.7.407 (Katoh and Standley 2013 (link)), mafft-linsi). Removal of ambiguous sites, evaluation of amino acid substitution models, and phylogenetic reconstruction proceeded as above. For the putative atm1 transporter, a Hidden Markov Model profile for orthologous group KOG0057 (retrieved from EggNOG 5.0.0 (Huerta-Cepas et al. 2019 (link)) database) was used to retrieve the protein models of P. canceri and M. mackini using the default settings of with hmmsearch. The resulting hits were used as queries against the NCBI nr database (August 2020) as described above. This dataset was supplemented with atm1 sequences reported previously (Freibert et al. 2017 (link)). The proteins were aligned with hmmalign from HMMER v.3.2.1 (http://hmmer.org/) and the Atm1 phylogeny was performed as described above.
Onuț-Brännström I., Stairs C.W., Campos K.I., Thorén M.H., Ettema T.J., Keeling P.J., Bass D, & Burki F. (2023). A Mitosome With Distinct Metabolism in the Uncultured Protist Parasite Paramikrocytos canceri (Rhizaria, Ascetosporea). Genome Biology and Evolution, 15(3), evad022.
Full text: Click here
Publication 2023
Amino Acid Substitution ATP-Binding Cassette Transporters FCER2 protein, human Genes, Mitochondrial Membrane Transport Proteins Mitochondrial Proteins Pagurus Proteins Proteome Trees
5
Multiprotein Extraction and Western Blot Analysis

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Publication 2023
Anti-Antibodies anti-c antibody Antibodies Antibodies, Anti-Idiotypic bcl-2 Gene Biological Assay Buffers Caspase 3 Caspase 9 Cells Chemiluminescence Cytochromes Cytoplasm GAPDH protein, human Gels Horseradish Peroxidase Intravenous Immunoglobulins Milk, Cow's Mitochondrial Proteins Mus Phenylmethylsulfonyl Fluoride polyvinylidene fluoride Proteins Rabbits Radioimmunoprecipitation Assay SDS-PAGE Tissue, Membrane WISP2 protein, human

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Oxygraph 2k by Oroboros
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More about "Mitochondrial Proteins"

Mitochondrial Proteins are a diverse group of biomolecules found within the mitochondria, the cellular powerhouses of eukaryotic organisms.
These proteins play pivotal roles in energy production, metabolic processes, and cellular signaling.
The Mitochondrial Proteome encompasses a wide range of enzymes, structural components, and regulatory factors essential for the proper functioning of the mitochondria.
Understanding the complexities of Mitochondrial Proteins is crucial for unraveling the underlying mechanisms of mitochondrial dysfunction, which has been implicated in a variety of diseases, including neurodegenerative disorders, cardiomyopathies, and metabolic disorders.
Researchers can leverage cutting-edge AI-driven platforms like PubCompare.ai to access the most accurate and reproducible protocols from literature, pre-prints, and patents, enabling them to identify the best methods and products for their Mitochondrial Protein studies and elevate the accuracy and reproducibility of their research.
To study Mitochondrial Proteins, researchers often employ techniques like PVDF membrane-based protein transfer, Oxygraph-2k for measuring mitochondrial respiration, and specialized kits for isolating mitochondria from cells and tissues, such as the Cell Mitochondria Isolation Kit, Mitochondria Isolation Kit, and Tissue Mitochondria Isolation Kit.
Additionally, protein quantification methods like the Pierce BCA Protein Assay Kit, BCA protein assay kit, and Bradford assay are commonly used to determine the concentration of Mitochondrial Proteins.
The Qproteome Mitochondria Isolation Kit provides a streamlined approach for extracting and purifying Mitochondrial Proteins from various sample types.