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> Chemicals & Drugs > Amino Acid > Proteins

Proteins

Proteins are large, complex molecules that play a vital role in the structure and function of all living organisms.
They are composed of amino acids, which are linked together in a specific sequence to form a unique three-dimensional structure.
Proteins are involved in a wide range of biological processes, including catalyzing chemical reactions, transporting and storing other molecules, providing structural support, and regulating cellular processes.
They can be found in a variety of forms, such as enzymes, hormones, antibodies, and structural proteins.
Understanding the structure and function of proteins is crucial for advancing our knowledge of biology and developing new therapies for a range of diseases.
Reseachers can leverage the power of PubCompare.ai to optimize their protein research and enhance reproducibility.

Most cited protocols related to «Proteins»

1
Simulating 16S Sequence Alignments
Cited 3990 times
The simulated protein alignments and the genuine COG alignments were described previously [2] (link). The 16S alignment with 237,882 distinct sequences was taken from GreenGenes [33] (link) (http://greengenes.lbl.gov). The 16S alignment with 15,011 distinct “families” is a non-redundant subset of these sequences ( identical). 16S alignments with 500 sequences are also non-redundant random subsets ( identical). Other large 16S alignments are from [11] (link).
For the 16S-like simulations with 78,132 distinct sequences, we used a maximum-likelihood tree inferred from a non-redundant aligned subset of the full set of 16S sequences ( % identity) by an earlier version of FastTree (1.9) with the Jukes-Cantor model (no CAT). To ensure that the simulated trees were resolvable, which facilitates comparison of methods (but inflates the accuracy of all methods), branch lengths of less than 0.001 were replaced with values of 0.001, which corresponds to roughly one substitution across the internal branch, as the 16S alignment has 1,287 positions. Evolutionary rates for each site were randomly selected from 16 rate categories according to a gamma distribution with a coefficient of variation of 0.7. Given the tree and the rates, sequences were simulated with Rose [34] (link) under the HKY model and no transition bias. To allow Rose to handle branch lengths of less than 1%, we set “MeanSubstitution = 0.00134” and multiplied the branch lengths by 1,000.
Price M.N., Dehal P.S, & Arkin A.P. (2010). FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments. PLoS ONE, 5(3), e9490.
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Publication 2010
Biological Evolution Cantor Gamma Rays Proteins Sequence Alignment Trees
2
Molecular Dynamics Protocol for Biomolecular Simulations
Cited 2064 times
Initial helical conformations were defined as all amino acids having (φ, ψ)=(−60°, −40°). Initial extended conformations were defined as all (φ, ψ)=(180°, 180°). Native conformations, as appropriate, were defined for each system as below. Explicit solvation was achieved with truncated octahedra of TIP3P water16 with a minimum 8.0 Å buffer between solute atoms and box boundary. All structures were built via the LEaP module of Ambertools. Except where otherwise indicated, equilibration was performed with a weak-coupling (Berendsen) thermostat33 and barostat targeted to 1 bar with isotropic position scaling as follows. With 100 kcal mol−1 Å−2 positional restraints on protein heavy atoms, structures were minimized for up to 10000 cycles and then heated at constant volume from 100 K to 300 K over 100 ps, followed by another 100 ps at 300 K. The pressure was equilibrated for 100 ps and then 250 ps with time constants of 100 fs and then 500 fs on coupling of pressure and temperature to 1 bar and 300 K, and 100 kcal mol−1 Å−2 and then 10 kcal mol−1 Å−2 Cartesian positional restraints on protein heavy atoms. The system was again minimized, with 10 kcal mol−1 Å−2 force constant Cartesian restraints on only the protein main chain N, Cα, and C for up to 10000 cycles. Three 100 ps simulations with temperature and pressure time constants of 500 fs were performed, with backbone restraints of 10 kcal mol−1 Å−2, 1 kcal mol−1 Å−2, and then 0.1 kcal mol−1 Å−2. Finally, the system was simulated unrestrained with pressure and temperature time constants of 1 ps for 500 ps with a 2 fs time step, removing center-of-mass translation and rotation every picosecond.
SHAKE34 was performed on all bonds including hydrogen with the AMBER default tolerance of 10−5 Å for NVT and 10−6 Å for NVE. Non-bonded interactions were calculated directly up to 8 Å. Beyond 8 Å, electrostatic interactions were treated with cubic spline switching and the particle-mesh Ewald approximation35 in explicit solvent, with direct sum tolerances of 10−5 for NVT or 10−6 for NVE. A continuum model correction for energy and pressure was applied to long-range van der Waals interactions. The production timesteps were 2 fs for NVT and 1 fs for NVE.
Maier J.A., Martinez C., Kasavajhala K., Wickstrom L., Hauser K.E, & Simmerling C. (2015). ff14SB: Improving the accuracy of protein side chain and backbone parameters from ff99SB. Journal of chemical theory and computation, 11(8), 3696-3713.
Publication 2015
Amber Amino Acids Buffers Cuboid Bone Debility Electrostatics Helix (Snails) Hydrogen-5 Immune Tolerance nucleoprotein, Measles virus Pressure Proteins Solvents Vertebral Column
3
Benchmarking Transcriptome Reconstruction Methods
Cited 1869 times
Current gene annotations for S. pombe were downloaded as file ‘pombe_290110.gff’ from GeneDB (http://old.genedb.org/genedb/pombe/). RefSeq transcript gene annotations were downloaded for mouse at the UCSC mouse genome browser gateway (http://genome.ucsc.edu/cgi-bin/hgGateway?db=mm9) in BED format. Protein coding nucleotide sequences were extracted from the genome sequences based on the gene annotations using custom PERL scripts. The mouse reference coding sequences were further distilled to remove entirely identical sequences corresponding to isoforms encoding identical proteins and paralogous sequences: the original 19,947 genes encoding 23,881 transcripts were reduced to 19,857 genes encoding 22,717 on-identical coding transcripts.
Reconstructed transcript sequences (via de novo assembly, Scripture, or Cufflinks) were mapped to the reference coding sequences using BLAT35 (link). Full-length reference annotation mappings were defined as having at least 95% sequence identity covering the entire reference coding sequence and containing at most 5% insertions or deletions (cumulative gap content). In evaluating methods that leverage the strand-specific data (Trinity and Cufflinks), proper sense-strand mapping of sequences was required. Transcripts reconstructed by the alternative methods (Scripture, ABySS, and SOAPdenovo) were allowed to map to either strand. Fusion transcripts were identified as individual reconstructed transcripts that mapped as full-length to multiple reference coding sequences and lacked overlap among the matching regions within the reconstructed transcript. One-to-one mappings were required between reconstructed transcripts and reference transcripts, including alternatively spliced isoforms, with the exception of fusion transcripts.
Grabherr M.G., Haas B.J., Yassour M., Levin J.Z., Thompson D.A., Amit I., Adiconis X., Fan L., Raychowdhury R., Zeng Q., Chen Z., Mauceli E., Hacohen N., Gnirke A., Rhind N., di Palma F., Birren B.W., Nusbaum C., Lindblad-Toh K., Friedman N, & Regev A. (2011). Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data. Nature biotechnology, 29(7), 644-652.
Publication 2011
Exons Gene Annotation Gene Deletion Genes Genome Insertion Mutation Mus Open Reading Frames Protein Isoforms Proteins
4
Benchmarking Transcriptome Reconstruction Methods
Cited 1780 times
Current gene annotations for S. pombe were downloaded as file ‘pombe_290110.gff’ from GeneDB (http://old.genedb.org/genedb/pombe/). RefSeq transcript gene annotations were downloaded for mouse at the UCSC mouse genome browser gateway (http://genome.ucsc.edu/cgi-bin/hgGateway?db=mm9) in BED format. Protein coding nucleotide sequences were extracted from the genome sequences based on the gene annotations using custom PERL scripts. The mouse reference coding sequences were further distilled to remove entirely identical sequences corresponding to isoforms encoding identical proteins and paralogous sequences: the original 19,947 genes encoding 23,881 transcripts were reduced to 19,857 genes encoding 22,717 on-identical coding transcripts.
Reconstructed transcript sequences (via de novo assembly, Scripture, or Cufflinks) were mapped to the reference coding sequences using BLAT35 (link). Full-length reference annotation mappings were defined as having at least 95% sequence identity covering the entire reference coding sequence and containing at most 5% insertions or deletions (cumulative gap content). In evaluating methods that leverage the strand-specific data (Trinity and Cufflinks), proper sense-strand mapping of sequences was required. Transcripts reconstructed by the alternative methods (Scripture, ABySS, and SOAPdenovo) were allowed to map to either strand. Fusion transcripts were identified as individual reconstructed transcripts that mapped as full-length to multiple reference coding sequences and lacked overlap among the matching regions within the reconstructed transcript. One-to-one mappings were required between reconstructed transcripts and reference transcripts, including alternatively spliced isoforms, with the exception of fusion transcripts.
Grabherr M.G., Haas B.J., Yassour M., Levin J.Z., Thompson D.A., Amit I., Adiconis X., Fan L., Raychowdhury R., Zeng Q., Chen Z., Mauceli E., Hacohen N., Gnirke A., Rhind N., di Palma F., Birren B.W., Nusbaum C., Lindblad-Toh K., Friedman N, & Regev A. (2011). Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data. Nature biotechnology, 29(7), 644-652.
Publication 2011
Exons Gene Annotation Gene Deletion Genes Genome Insertion Mutation Mus Open Reading Frames Protein Isoforms Proteins
5
KOBAS 2.0: Pathway and Disease Annotation
Cited 1486 times
KOBAS 2.0 has two consecutive programs ‘annotate’ and ‘identify’, which is similar to KOBAS 1.0 (1 (link),2 (link)). The first program ‘annotates’ each input gene with putative pathways and diseases by mapping the gene to genes in KEGG GENES or terms in KO which are linked to pathway and disease terms in backend databases. For ID mapping, input IDs are mapped directly to genes using the cross-links we parsed from KEGG GENES. Then, if necessary, IDs are mapped to KO terms. For sequence similarity mapping, each input sequence is BLASTed against all sequences in KEGG GENES. The default cutoffs are BLAST E-value <10−5 and rank ≤5. They mean that an input sequence is assigned KO term(s) of the first BLAST hit that (i) has known KO assignments; (ii) has BLAST E-value <10−5; and (iii) has less than five other hits with a lower E-value that do not have KO assignments (1 (link)). A new option in KOBAS 2.0 is that users can map against genes in user-specified species instead of all genes by BLASTing against only sequences of the user-specified species. In order to reduce possible false positives due to multidomain proteins, we added a new option to allow users to set a cutoff of BLAST subject coverage. Another new option allows users to restrict sequence mapping to only orthologs as defined by Ensembl Compara (38 (link)).
The second program ‘identifies’ statistically significantly enriched pathways and diseases by comparing results from the first program against the background (usually genes from the whole genome, or all probe sets on a microarray). Users can define their own background distribution in KOBAS 2.0 (for example, result from the first program to ‘annotate’ all probe sets on a microarray). If users do not upload a background file, KOBAS 2.0 uses the genes from whole genome as the default background distribution. Here, we consider only pathways and diseases for which there are at least two genes mapped in the input. Users can choose to perform statistical test using one of the following four methods: binomial test, chi-square test, Fisher's exact test and hypergeometric test, and perform FDR correction. The purpose of performing FDR correction is to reduce the Type-1 errors. When a large number of pathway and disease terms are considered, multiple hypotheses tests are performed, which leads to a high overall Type-1 error even for a relatively stringent P-value cutoff. KOBAS 1.0 supports the FDR correction method QVALUE (39 ). In KOBAS 2.0, we add two more popular FDR correction methods: Benjamini-Hochberg (40 ) and Benjamini-Yekutieli (41 ).
Xie C., Mao X., Huang J., Ding Y., Wu J., Dong S., Kong L., Gao G., Li C.Y, & Wei L. (2011). KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases. Nucleic Acids Research, 39(Web Server issue), W316-W322.
Publication 2011
Chromosome Mapping Genes Genome Microarray Analysis Proteins

Most recents protocols related to «Proteins»

1
PD-1/PD-L1 Blocking Antibody Assay
Not available on PMC !

Example 10

This example provides in vitro IC50 data for the blocking of the interaction between recombinant human PD-1 (PD-1-Fc Chimera; Sino Biologics) and human PD-L1 expressed CHO cells by anti-PD-L1 antibody G12. Here, CHO cells expressing PD-L1 were pre-incubated with G12 prior to the addition of rhPD-1-Fc chimeric protein. After incubation and washing, PD-1 binding to cell surface expressed PD-L1 was detected using an Alexa-Fluor 647 tagged anti-PD-1 antibody by flow cytometry (Intellicyt HTFC; FL-4H). This example shows that anti-PD-L1 monoclonal antibody G12 was able to inhibit efficiently the binding of PD-1 to PD-L1 expressed on the surface of CHO cells.

Results: As shown in FIG. 8 and Table 4, the IC50 for blocking of the PD-1/PD-L1 cellular interaction by G12 is 1.76E-09 M. Data was collected on the Intellicyt HTFC flow cytometer, processed using FlowJo software, and analyzed and plotted in Graph Pad Prizm using non-linear regression fit. Data points are shown as the median fluorescence detected in the FL-4H channel+/−Std Error.

TABLE 4
G12
Inhibition of PD-1/PD-L1CHO-PD-L1/1.76E−09
Interaction IC50 (M)rhPD-1-Fc

US11878058B2. Antigen binding proteins that bind PD-L1 (2024-01-23). Sorrento Therapeutics, Inc. [US]. Inventors: Heyue Zhou [US], Randy Gastwirt [US], Barbara A. Swanson [US], John Dixon Gray [US], Gunnar F. Kaufmann [US].
Full text: Click here
Patent 2024
Alexa Fluor 647 Antibodies, Anti-Idiotypic Antigens Binding Proteins Biological Factors CD274 protein, human Cell Communication Cells Chimera CHO Cells Flow Cytometry Fluorescence Homo sapiens Immunoglobulins isononanoyl oxybenzene sulfonate Monoclonal Antibodies Proteins Psychological Inhibition
2
Preparation of Cell-free Lactobacillus Fractions
Not available on PMC !

Example 1

Cell-free fractions were prepared as previously described (25). Briefly, Lactobacillus acidophilus strain La-5 was grown overnight in modified DeMann, Rogosa and Sharpe medium. (mMRS; 10 g peptone from casein, 8 g meat extract, 4 g yeast extract, 8 g D(+)-glucose, 2 g dipotassium hydrogen phosphate, 2 g di-ammonium hydrogen citrate, 5 g sodium acetate, 0.2 g magnesium sulfate, 0.04 g manganese sulfate in 1 L distilled water) (MRS; BD Diagnostic Systems, Sparks, MD). The overnight culture was diluted 1:100 in fresh medium. When the culture grew to an optical density at 600 nm (OD600) of 1.6 (1.2×108 cells/ml), the cells were harvested by centrifugation at 6,000×g for 10 min at 4° C. The supernatant was sterilized by filtering through a 0.2-μm-pore-size filter (Millipore, Bioscience Division, Mississauga, ON, Canada) and will be referred to as cell-free spent medium (CFSM). Two litres of L. acidophilus La-5 CFSM was collected and freeze-dried (Unitop 600 SL, VirTis Co., Inc. Gardiner, NY., USA). The freeze-dried CFSM was reconstituted with 200 ml of 18-Ω water. The total protein content of the reconstituted CFSM was quantified using the BioRad DC protein assay kit II (Bio-Rad Laboratories Ltd., Mississauga, ON, Canada). Freeze-dried CFSM was stored at −20° C. prior to the assays.

US11857581B2. Antiviral methods and compositions comprising probiotic bacterial molecules (2024-01-02). MicroSintesis Inc. [CA]. Inventors: Mansel Griffiths [CA].
Full text: Click here
Patent 2024
ammonium citrate Biological Assay casein peptone Cells Centrifugation Diagnosis Freezing Glucose Hydrogen Lactobacillus acidophilus L Cells manganese sulfate Meat potassium phosphate, dibasic Proteins Sodium Acetate Sulfate, Magnesium Unitop Yeast, Dried
3
Lyophilized Silk Powder Formulations
Not available on PMC !

Example 19

TABLE 37
Embodiments of lyophilized silk powders
Silk SolutionTreatmentSoluble
~60 kDa silk, 6% silk, pH = 7-8lyopholize and cut withno
blender
~60 kDa silk, 6% silk, pH = 10lyopholize and cut withno
blender
~25 kDa silk, 6% silk, pH = 7-8lyopholize and cut withyes
blender
~25 kDa silk, 6% silk, pH = 10lyopholize and cut withyes
blender

The above silk solutions were transformed to a silk powder through lyophilization to remove bulk water and chopping to small pieces with a blender. pH was adjusted with sodium hydroxide. Low molecular weight silk (−25 kDa) was soluble while high molecular weight silk (−60 kDa) was not.

The lyophilized silk powder can be advantageous for enhanced storage control ranging from 10 days to 10 years depending on storage and shipment conditions. The lyophilized silk powder can also be used as a raw ingredient in the pharmaceutical, medical, consumer, and electronic markets. Additionally, lyophilized silk powder can be re-suspended in water, HFIP, or an organic solution following storage to create silk solutions of varying concentrations, including higher concentration solutions than those produced initially.

In an embodiment, aqueous pure silk fibroin-based protein fragment solutions of the present disclosure comprising 1%, 3%, and 5% silk by weight were each dispensed into a 1.8 L Lyoguard trays, respectively. All 3 trays were placed in a 12 ft2 lyophilizer and a single run performed. The product was frozen with a shelf temperature of ≤−40° C. and held for 2 hours. The compositions were then lyophilized at a shelf temperature of −20° C., with a 3 hour ramp and held for 20 hours, and subsequently dried at a temperature of 30° C., with a 5 hour ramp and held for about 34 hours. Trays were removed and stored at ambient conditions until further processing. Each of the resultant lyophilized silk fragment compositions were able to dissolve in aqueous solvent and organic solvent to reconstitute silk fragment solutions between 0.1 wt % and 8 wt %. Heating and mixing were not required but were used to accelerate the dissolving rate. All solutions were shelf-stable at ambient conditions.

In an embodiment, an aqueous pure silk fibroin-based protein fragment solution of the present disclosure, fabricated using a method of the present disclosure with a 30 minute boil, has a molecular weight of about 57 kDa, a polydispersity of about 1.6, inorganic and organic residuals of less than 500 ppm, and a light amber color.

In an embodiment, an aqueous pure silk fibroin-based protein fragment solution of the present disclosure, fabricated using a method of the present disclosure with a 60 minute boil, has a molecular weight of about 25 kDa, a polydispersity of about 2.4, inorganic and organic residuals of less than 500 ppm, and a light amber color.

US11878070B2. Silk-based moisturizer compositions and methods thereof (2024-01-23). Evolved By Nature, Inc. [US]. Inventors: Gregory H. Altman [US], Dylan S. Haas [US], Kevin T. Healy [US].
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Patent 2024
Amber ARID1A protein, human Dietary Fiber Fibroins Freeze Drying Freezing Furuncles Light Pharmaceutical Preparations Powder Proteins Silk Sodium Hydroxide Solvents
4
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
5
Recombinant Chimeric Protein Purification
Not available on PMC !

Example 3

Recombinant Protein Purification

FIG. 5 shows the steps of one of the purifications carried out on the chimera. In the case of GRNLY, this process was shown in an earlier paper [Ibáñez, R., University of Zaragoza. 2015]. It can be seen in FIG. 5A that the P. Pastoris supernatant obtained after induction (lane 1) contains rather diluted proteins. After concentrating same with Pellicom, protein bands are not seen in the permeate (lane 3), but proteins that are much more concentrated than in the supernatant are seen in the concentrate (lane 2). After dialysis (lane 4), the band profile remains similar to the concentrate. Furthermore, protein bands are not seen in the buffer in which the dialysis bag (lane 5) was introduced. Upon addition of the nickel resin, the chimera binds to said resin as it has a histidine tag. After adding the resin (lane 6), the intensity of a band corresponding to a protein of about 40 kDa decreases with respect to the concentrate and dialysate. This band may correspond to the chimera. The fact that this band does not altogether disappear may indicate that the nickel resin was saturated. In the washes performed on the resin, particularly in the first wash (lane 7), it can be seen how the residues of other proteins are removed. Finally, after the elution of the nickel column, a major protein with a molecular weight of about 40 kDa corresponding to the molecular weight of the chimera (lane 11) is clearly observed. As shown in FIG. 5B, it was confirmed by means of immunoblot that this band of about 40 kDa corresponds to the chimera (lane 11). It is also confirmed that the resin was saturated because a band appears in the post-resin dialysis phase (lane 6).

FIG. 6 shows different elution fractions and the pooling of all of them with the exception of elution fraction 1. FIG. 6A shows several bands in the different elution fractions and in the total eluate. The band with the highest intensity has a molecular weight corresponding to the chimera. Furthermore, other bands having intermediate molecular weights are observed, which means that the chimera undergoes partial proteolysis. The band with the second highest intensity has a molecular weight of about 10 kDa, which corresponds to 9-kDa GRNLY, as its molecular weight increases since it is bound to a histidine tag. In FIG. 6B, it was confirmed by means of immunoblot that these bands of about 40 and 10 kDa correspond to the chimeric recombinant protein and to recombinant GRNLY, respectively.

Once the chimera is generated, its functionality must be assured, that is, on one hand the scFv still recognizes the CEA antigen, and on the other hand GRNLY is still cytotoxic.

US11858973B2. Granulysin, method of obtaining same, and uses (2024-01-02). UNIVERSIDAD DE ZARAGOZA [ES], FUNDACIÓN AGENCIA ARAGONESA PARA LA INVESTIGACIÓN Y EL DESARROLLO (ARAID) [ES], FUNDACIÓN PARA LA INVESTIGACIÓN BIOMÉDICA HOSPITAL UNIVERSITARIO PUERTA DE HIERRO MAJADAHONDA [ES]. Inventors: Luis Alberto Anel Bernal [ES], Raquel Ibañez Perez [ES], Patricia Guerrero Ochoa [ES], Luis Martinez Lostao [ES], Blanca Conde Guerri [ES], Ramón Hurtado Guerrero [ES], Ana Laura Sanz Alcober [ES], Rocio Navarro Ortiz [ES].
Full text: Click here
Patent 2024
Antigens Buffers Chimera Chimeric Proteins, Recombinant Dialysis Dialysis Solutions GNLY protein, human Histidine Immunoblotting Nickel One-Step dentin bonding system Proteins Proteolysis Recombinant Proteins Resins, Plant Staphylococcal Protein A Vision

Top products related to «Proteins»

1
Pvdf membrane by Merck Group
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PVDF membranes are a type of laboratory equipment used for a variety of applications. They are made from polyvinylidene fluoride (PVDF), a durable and chemically resistant material. PVDF membranes are known for their high mechanical strength, thermal stability, and resistance to a wide range of chemicals. They are commonly used in various filtration, separation, and analysis processes in scientific and research settings.
2
Bca protein assay kit by Thermo Fisher Scientific
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The BCA Protein Assay Kit is a colorimetric detection and quantification method for total protein concentration. It utilizes bicinchoninic acid (BCA) for the colorimetric detection and quantification of total protein. The assay is based on the reduction of Cu2+ to Cu1+ by protein in an alkaline medium, with the chelation of BCA with the Cu1+ ion resulting in a purple-colored reaction product that exhibits a strong absorbance at 562 nm, which is proportional to the amount of protein present in the sample.
3
Pierce bca protein assay kit by Thermo Fisher Scientific
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The Pierce BCA Protein Assay Kit is a colorimetric-based method for the quantification of total protein in a sample. It utilizes the bicinchoninic acid (BCA) reaction, where proteins reduce Cu2+ to Cu+ in an alkaline environment, and the resulting purple-colored reaction is measured spectrophotometrically.
4
Protease inhibitor cocktail by Roche
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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.
5
Protease inhibitor cocktail by Merck Group
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The Protease Inhibitor Cocktail is a laboratory product designed to inhibit the activity of proteases, which are enzymes that can degrade proteins. It is a combination of various chemical compounds that work to prevent the breakdown of proteins in biological samples, allowing for more accurate analysis and preservation of protein integrity.
6
Bca protein assay kit by Beyotime
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The BCA protein assay kit is a colorimetric-based method for the quantitative determination of total protein concentration in a sample. It uses bicinchoninic acid (BCA) to detect and quantify the presence of protein.
7
Ripa lysis buffer by Beyotime
Sourced in China, United States, Switzerland, Germany, Japan, United Kingdom
RIPA lysis buffer is a detergent-based buffer solution designed for the extraction and solubilization of proteins from cells and tissues. It contains a mixture of ionic and non-ionic detergents that disrupt cell membranes and solubilize cellular proteins. The buffer also includes additional components that help to maintain the stability and activity of the extracted proteins.
8
β actin by Merck Group
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β-actin is a protein that is found in all eukaryotic cells and is involved in the structure and function of the cytoskeleton. It is a key component of the actin filaments that make up the cytoskeleton and plays a critical role in cell motility, cell division, and other cellular processes.
9
Pvdf membrane by Bio-Rad
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PVDF membranes are a type of laboratory equipment used for protein transfer and detection in Western blot analysis. They provide a stable and durable surface for the immobilization of proteins, enabling effective identification and quantification of target proteins in complex biological samples.
10
Nitrocellulose membrane by Bio-Rad
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Nitrocellulose membranes are a type of laboratory equipment designed for use in protein detection and analysis techniques. These membranes serve as a support matrix for the immobilization of proteins, enabling various downstream applications such as Western blotting, dot blotting, and immunodetection.

More about "Proteins"

Proteins are the building blocks of life, playing vital roles in the structure and function of all living organisms.
These large, complex molecules are composed of amino acids, linked together in a specific sequence to form a unique three-dimensional structure.
Proteins come in a variety of forms, such as enzymes, hormones, antibodies, and structural proteins, and are involved in a wide range of biological processes, including catalyzing chemical reactions, transporting and storing other molecules, providing structural support, and regulating cellular processes.
Understanding the structure and function of proteins is crucial for advancing our knowledge of biology and developing new therapies for a range of diseases.
Researchers can leverage the power of AI-driven platforms like PubCompare.ai to optimize their protein research and enhance reproducibility.
These platforms can help researchers locate the best protocols from literature, pre-prints, and patents using intelligent comparisons to identify the optimal solutions.
This can be especially useful when working with techniques and tools like PVDF membranes, BCA protein assay kits, Pierce BCA Protein Assay Kits, protease inhibitor cocktails, RIPA lysis buffers, and β-actin, as well as nitrocellulose membranes.
By streamlining the research process and identifying the most effective protocols, researchers can enhance the reproducibility of their protein studies and accelerate the development of new therapies and treatments.
This innovative AI-driven approach to protein research can help advance our understanding of these vital molecules and their role in human health and disease.