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Protein Precursors

Protein Precursors are the preliminary forms of proteins that undergo various modifications to become the final, functional proteins.
These precursor molecules may undergo cleavage, folding, or other transformations to reach their mature state.
Understanding the structure and characteristics of protein precursors is crucial for researchers studying protein synthesis, cellular processes, and potential therapeutic interventions.
PubCompare.ai can help optimize your protein precursor research by locating the best protocols from literature, preprints, and patents, using intelligent comparisons to enhance reproducibility and accuarcy.
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Most cited protocols related to «Protein Precursors»

Mass spectrometric data were collected on an Orbitrap Fusion Lumos mass spectrometer in-line with a Proxeon NanoLC-1200 UHPLC. The 100 μm capillary column was packed with 35 cm of Accucore 150 resin (2.6 μm, 150Å; ThermoFisher Scientific). Spectra were converted to mzXML using a modified version of ReAdW.exe. Database searching included all entries from the Saccharomyces Genome Database (SGD; August 21, 2017). This database was concatenated with one composed of all protein sequences in the reversed order. Searches were performed using a 50-ppm precursor ion tolerance for total protein level profiling. The product ion tolerance was set to 0.9 Da. These wide mass tolerance windows were chosen to maximize sensitivity in conjunction with SEQUEST searches and linear discriminant analysis (16 (link), 17 (link)). TMT tags on lysine residues and peptide N termini (+229.163 Da) and carbamidomethylation of cysteine residues (+57.021 Da) were set as static modifications, while oxidation of methionine residues (+15.995 Da) was set as a variable modification. For phosphorylation analysis, deamidation (+0.984) on asparagine and glutamine and phosphorylation (+79.966) on serine, threonine, and tyrosine were set as variable modifications. Peptide-spectrum matches (PSMs) were adjusted to a 1% false discovery rate (FDR) (18 (link), 19 (link)). PSM filtering was performed using a linear discriminant analysis, as described previously (17 (link)) and then assembled further to a final protein-level FDR of 1% (19 (link)). Phosphorylation site localization was determined using the AScore algorithm (13 (link)). AScore is a probability-based approach for high-throughput protein phosphorylation site localization. Specifically, a threshold of 13 corresponded to 95% confidence in site localization. Proteins were quantified by summing reporter ion counts across all matching PSMs, as described previously (20 (link)). Reporter ion intensities were adjusted to correct for the isotopic impurities of the different TMT reagents according to manufacturer specifications. The signal-to-noise (S/N) measurements of peptides assigned to each protein were summed and these values were normalized so that the sum of the signal for all proteins in each channel was equivalent, to account for equal protein loading. Lastly, each protein was scaled such that the summed signal-to-noise for that protein across all channels was greater than 100, thereby generating a relative abundance (RA) measurement. A detailed description of the methods in a step-by-step outline is available in the Supplementary Materials.
Publication 2018
Amino Acid Sequence Asparagine Capillaries Cysteine Genome Glutamine Hypersensitivity Immune Tolerance Isotopes Lysine Mass Spectrometry Methionine Peptides Phosphorylation Protein Precursors Proteins Resins, Plant Saccharomyces Serine Signal Peptides Staphylococcal Protein A Threonine Tyrosine
To search for transcripts encoding putative neuropeptide or peptide hormone precursor proteins in A. rubens, the sequences of neuropeptide or peptide hormone precursors previously identified in the sea urchin S. purpuratus [5 (link),6 (link),11 (link),16 (link),17 (link),37 (link),38 (link)], the sea cucumber A. japonicus [10 (link)] and the starfish species Asterina pectinifera [39 (link)] were submitted individually as queries in tBLASTn searches of the contig database with the BLAST parameter e-value set to 1000. Contigs identified as encoding putative precursors were analysed after translation of their full-length DNA sequence into protein sequence using the ExPASy Translate tool (http://web.expasy.org/translate/). Proteins were assessed as potential precursors of secreted bioactive peptides by investigating: (i) the presence of a putative N-terminal signal peptide sequence, using the SignalP v. 3.0 online server [40 (link)], (ii) the presence of putative monobasic or dibasic cleavage sites N-terminal and C-terminal to the putative bioactive peptide(s), with reference to known consensus cleavage motifs [41 (link)–43 (link)], and (iii) the presence, in some cases, of a C-terminal glycine residue that is a potential substrate for amidation.
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Publication 2016
Amino Acid Sequence Asterina pectinifera Cytokinesis DNA Sequence Glycine Neuropeptides Peptide Hormone Peptides polypeptide C Protein Precursors Proteins Ruthenium Ben Sea Cucumbers Sea Urchin Signal Peptides Starfish
The recombinant plasmids for expression of the goat cathelicidins were constructed with the use of pET-based vector as described previously (Panteleev and Ovchinnikova, 2017 (link)). The target peptides were expressed in E. coli BL21 (DE3) as chimeric proteins that included 8 × His tag, the E. coli thioredoxin A with the M37L substitution (TrxL), methionine residue, and a mature cathelicidin. The ChMAP-28 amino acid sequence was translated from mRNA for the corresponding precursor protein (GenBank: AJ243126.1) as a 27-residue peptide without the C-terminal glycine, a common amidation signal in cathelicidins. The transformed E. coli BL21 (DE3) cells were grown up to OD600 1.0 at 37°C in lysogeny broth (LB) containing 20 mM glucose, 1 mM MgSO4, and 0.1 mM CaCl2, 100 μg/ml of ampicillin and then were induced with isopropyl β-D-1-thiogalactopyranoside (IPTG) at a final concentration of 0.3 mM. The cells were cultivated for 5 h at 30°C with intense agitation. Then the cells were pelleted by centrifugation and sonicated in immobilized metal affinity chromatography (IMAC) loading buffer containing 6 M guanidine hydrochloride. The clarified lysate was applied on a column packed with Ni Sepharose (GE Healthcare). The recombinant protein was eluted with the buffer containing 0.5 M imidazole. Then the eluate containing the fusion protein was acidified (up to pH 1.0) and cleaved by 100-fold molar excess of cyanogen bromide over methionine for 20 h at 25°C in the dark. The reaction products were lyophilized, dissolved in water, titrated to pH 5.0, and loaded on a semi-preparative Reprosil-pur C18-AQ column (10 mm × 250 mm, 5-μm particle size, Dr. Maisch GmbH). Reversed-phase high-performance liquid chromatography (RP-HPLC) was performed with a linear gradient of acetonitrile in water containing 0.1% trifluoroacetic acid. The peaks were monitored at 214 and 280 nm. The collected fractions were analyzed by MALDI-TOF mass-spectrometry using Reflex III instrument (Bruker Daltonics). The fractions containing the target peptides were lyophilized and dissolved in water. The synthetic melittin (>98% pure) was kindly provided by Dr. Sergey V. Sychev (M.M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia). The recombinant tachyplesin-1 was obtained as described previously (Panteleev and Ovchinnikova, 2017 (link)). The peptides concentrations were estimated using UV absorbance.
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Publication 2018
acetonitrile Amino Acid Sequence Ampicillin Buffers Cathelicidins Cells Centrifugation Chimera Chromatography, Affinity Chromatography, Reversed-Phase Liquid Cloning Vectors Cyanogen Bromide Escherichia coli Glucose Glycine Goat Hydrochloride, Guanidine imidazole Lysogeny Mass Spectrometry Melitten Metals Methionine Molar Peptides Plasmids polypeptide C Protein Precursors Proteins Recombinant Proteins Reflex Reprosil RNA, Messenger Sepharose Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization Sulfate, Magnesium tachyplesin peptide, Tachypleus tridentatus Trifluoroacetic Acid TXN protein, human

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Publication 2016
6H,8H-3,4-dihydropyrimido(4,5-c)(1,2)oxazin-7-one Amino Acid Sequence Biological Processes Cellular Structures Cysteine Cytokinesis Genome Hypersensitivity Immune Tolerance Ions isolation Lysine Mass Spectrometry Methionine Peptides Protein Precursors Proteins Saccharomyces Saccharomyces cerevisiae SET protein, human Staphylococcal Protein A
Extracts taken from tissue sections were pipetted directly into 3µL of the extraction solvent. Aliquots of 1–2µL, containing 25–50% of each tissue extract, were diluted 6-fold with 0.1% formic acid to reduce the organic composition in the solvent to 3% acetonitrile. For lens extract analysis, 1 µL (25%) of the tissue extract was used, and 2-µL aliquots (50%) of the kidney and brain extracts were analyzed by LC-MS/MS. The diluted protein extracts were loaded onto a reverse-phase capillary trap column using a helium-pressurized cell (pressure bomb). The trapping column (360µm × 150µm ID) was fritted with a filter end-fitting (IDEX Health & Science), and was packed with 5 cm of C8 material (15 µm material, 300Å Grace Vydac or 5µm, 300 Å YMC Co.). Once the sample was loaded, an M-520 microfilter union (IDEX Health & Science) was used to connect the trap column to an analytical column (360µm × 100µm ID, 8 cm or 20 cm of C8 stationary phase material), equipped with a laser-pulled emitter tip. Using an Eksigent NanoLC Ultra HPLC, peptides were gradient-eluted at a flow rate of 400 nL/min, and the mobile phase solvents consisted of 0.1% formic acid, 99.9% water (solvent A) and 0.1% formic acid, 99.9% acetonitrile (solvent B). The gradient consisted of 2–60 %B in 50 min, 60–90 %B in 10 min, 90 %B for 1 min, 90-2 %B in 1 min, and the column was equilibrated at 2 %B for 12 min. Upon gradient-elution, proteins were mass analyzed on a LTQ Velos mass spectrometer, equipped with a nanoelectrospray ionization source (Thermo Scientific). The instrument was operated using a data-dependent method or a combination method consisting of both data-dependent and targeted scan events. Dynamic exclusion was enabled allowing a repeat count of 4 within 15 s. For all LC-MS/MS analyses, full scan (m/z 360–2000) spectra were acquired as the initial scan event, and the seven or eight most abundant ions in each MS scan were selected for fragmentation in the LTQ. For electron transfer dissociation (ETD) of eluting protein species, an isolation width of 2.5 m/z and reaction times of 90–115 ms were used. The MSn AGC target value in the ion trap was set to 1e4, with a maximum injection time of 100 ms. The ETD reagent ion AGC target was 3e5 or 5e5 with a maximum inject time of 100 ms. For a subset of LC-MS/MS analyses, a data-dependent ETD/CID toggle method was used, where sequential ETD and CID spectra were acquired of the same protein precursors in back-to-back scan events. ETD and CID MS/MS spectra were interpreted manually with assistance by the TagIdent tool (http://web.expasy.org/tagident/).
Publication 2013
acetonitrile Brain Capillaries Cells Electron Transport formic acid Helium High-Performance Liquid Chromatographies isolation Kidney Lens, Crystalline Peptides Pressure Protein Precursors Proteins Radionuclide Imaging Solvents Tandem Mass Spectrometry Tissues Z-360

Most recents protocols related to «Protein Precursors»

Example 2

Table 1 below summarizes data obtained from Vero cells that were administered an HSV-1 TLR3 ROVV and TLR3 protein levels were compared against control Vero cells that did not receive the HSV-1 TLR3 ROVV (control). Specifically, about 2.5×106 Vero confluent cells were administered about 3×108 HSV-1 TLR3 ROVV. About 48 hours later, expression levels of human TLR3 mRNA were determined by qRT-PCR, and converted to expressed TLR3 protein levels.

TABLE 1
TLR3 Protein Levels
HSV-1 TLR3
ControlROVV recipient
Molecule(ag)(ag)P-value
TLR34450.0052
n.b. ag = attogram 1 × 10−18 grams

As shown in Table 1, cells that received the HSV-1 TLR3 ROVV that included SEQ ID No. 1 and that encoded for increased production of a TLR3 precursor protein demonstrated statistically significant higher amounts of TLR3 than the control cells that did not receive the HSV-1 TLR3 ROVV. Without being bound by any particular theory, the cells that were administered the HSV-1 TLR3 ROVV had higher levels of TLR3 than cells that did not receive the HSV-1 TLR3 ROVV.

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Patent 2024
Cells Homo sapiens Human Herpesvirus 1 Protein Precursors Proteins RNA, Messenger Vero Cells
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Example 1

Expression cassettes for expressing a precursor protein were synthesized. Each cassette contained a CMV promotor, followed by the sequence for the precursor protein. The synthesized precursor protein expression cassettes were cloned into the ROVV using the methods described by Law el al. (A New Approach to Assessing HSV-1 Recomination during Intracellular Spread. Viruses 2018, 10, 220), the disclosure of which is incorporated herein by reference.

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Patent 2024
Human Herpesvirus 1 Protein Precursors Protoplasm Virus
The reference genomes of O. polymorpha HU-11/CBS4732 (GenBank: CP073033-40), NCYC495 (GenBank: NW_017264698–704), DL-1 (GenBank: CP080316-22), C. elegans (RefSeq: NC_003279–84), M. piriformis (GenBank: OW971867-72) and S. cerevisiae (Assembly: GCF_000146045.2) were downloaded from the NCBI GenBank or RefSeq database for the analysis in local servers. The reference genome of C. elegans was analyzed using the UCSC genome browser and tools. Another genome of O. polymorpha DL-1 (RefSeq: NC_027860–66) was used to confirm the results obtained using the DL-1 genome (GenBank: CP080316-22). The nt sequences of Tc1-OP1, Tc1-MP1, Tc1-CE1, and IS630-AB1 are located in the genomes of O. polymorpha DL-1 (CP080317: 544314–549,972), M. piriformis (OW971871: 2795447–2,793,760), C. elegans (NC_003283: 17805799–17,807,409) and A. baumannii CAM180-1 (CP044356: 173741–174,626). InterProScan (Jones et al., 2014 (link)) v5.56–89.0 was used to predict protein domains against InterPro consortium member databases with default parameter setting. The repeats in all the analyzed genomes were detected using the software RepeatMasker v4.1.2 with the RepBase v20181026 and Dfam v3.6 databases. The software BLAST v2.12.0 was used to search for homologs in a local NCBI NR database with default parameter setting. Signal peptides of protein precursors were detected using SignalP v5.0. The secondary structures of putative proteins were predicted using PSIPRED (Buchan and Jones, 2019 (link)) v4.0. The 3D structures of putative proteins were predicted using trRosetta (Yang et al., 2020 (link)), trRosettaX, AlphaFold v2.2.0 and RoseTTAFold v1.1.0. The top 5 models of the Tc1-OP1 protein predicted by AlphaFold had low per-residue confidence scores (pLDDTs) around 50 which indicated that most of the protein regions may be unstructured, likewise, those predicted by RoseTTAFold also had low quality scores about 0.3. We had to use trRosetta to improve the prediction of the Tc1-OP1 protein for a better performance. The top 1 model (Supplementary File S2) of the Tc1-OP1 protein (139–1,155 aa) predicted by trRosettaX had the best template modeling (TM) score of 0.334, although it was much lower than the TM scores of Tc1-MP1 and Tc1-CE1 transposases that are 0.62 and 0.688, respectively. DaliLite v5 and 3D-BLAST vbeta102 were used for protein structural alignment and structure database search. The analysis and plotting of protein structures were performed using PyMOL v2.5.26; The neighbor joining (NJ) analyses were performed using MEGA (Kumar et al., 1994 (link)) v7.0.26; The maximum likelihood (ML) and Bayesian inference (BI) analyses were performed using PhyloSuite (Zhang et al., 2020 (link)) v1.2.2. Statistics and plotting were conducted using the software R v2.15.3 with the Bioconductor packages (Gao et al., 2014 ). All other data processing were carried out using Perl scripts.
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Publication 2023
Caenorhabditis elegans Genome Protein Domain Protein Precursors Proteins Saccharomyces cerevisiae Signal Peptides Tc1 transposase
All raw MS files were processed using MaxQuant (version 1.6.1.0) (19 (link)). MS/MS spectra were searched against the Human UniprotKB protein sequence database (December 2014, with 88,657 entries of 20,459 human genes) using the Andromeda search engine (20 (link)). Primary searches were performed using 6 ppm precursor ion tolerance for total protein-level analysis. MS/MS ion tolerance was set at 20 ppm. Cysteine carbamidomethylation was used as a fixed modification. Protein N-acetylation and methionine oxidation are considered variable modifications. Enzyme specificity was set to full tryptic digestion. Peptides with a minimum length of six amino acids and up to two missed cleavages were considered. The required false discovery rate (FDR) was set to 1% at peptide, protein, and modification levels. To maximize the number of quantification events across samples, we enabled the “Match between Runs” options on the MaxQuant platform. The MS proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE (21 (link)) partner repository with the dataset identifier PXD034646. Annotated MS/MS spectra can be accessed through MS-Viewer (22 (link)) (https://msviewer.ucsf.edu/cgi-bin/mssearch.cgi?report_title=MS-Viewer&search_key=bzgazjrsgb&search_name=msviewer) with the following search keys: bzgazjrsgb.
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Publication 2023
Acetylation Amino Acids Cysteine Cytokinesis Digestion Enzymes Homo sapiens Immune Tolerance Methionine nucleoprotein, Measles virus Peptides Protein Precursors Proteins Tandem Mass Spectrometry Trypsin
The cDNA and translated protein of each neuropeptide were selected by searching for the sequences of closely related orthopteran species against the in-house database of G. bimaculatus transcripts constructed in previous reports [12 (link)]. Among the 43 neuropeptides that were reported in insects, 35 neuropeptides were provisionally determined as the reference neuropeptide sequences, which are the mature, precursor, or cDNA sequences (Table S1). In particular, the sequences of ACP [7 (link)], Ast B [12 (link)], corazonin [6 (link)], elevenin [6 (link)], myosuppressin [13 (link)], and PDF [14 (link)] were used as seed sequences as described in previously published studies. These selected proteins, except for sequences published in previous studies, were submitted with BLASTP [24 (link)] on the NCBI website (https://blast.ncbi.nlm.nih.gov/Blast.cgi (accessed on 16 July 2022)) with the clustered nr database to confirm homology with the sequences of closely related orthopteran species. These precursor proteins and their amino acid sequences deduced from cDNA were confirmed to belong to that they belong to appropriate protein clusters (Table S2).
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Publication 2023
Amino Acid Sequence corazonin protein, insect DNA, Complementary Homologous Sequences Insecta Neuropeptides Protein Precursors Proteins

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[35S]-methionine is a radioactive isotope of the amino acid methionine. It is commonly used as a labeling agent in various biochemical and molecular biology applications.
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The TNT Quick Coupled Transcription/Translation kit is a laboratory tool that enables the concurrent synthesis of both mRNA and its corresponding protein from a DNA template in a single reaction vessel. The kit provides the necessary components, including RNA polymerase, amino acids, and energy sources, to facilitate this coupled transcription and translation process.
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More about "Protein Precursors"

Protein precursors are the initial forms of proteins that undergo various modifications to become the final, functional proteins.
These precursor molecules may be subjected to cleavage, folding, or other transformations to reach their mature state.
Understanding the structure and characteristics of protein precursors is crucial for researchers studying protein synthesis, cellular processes, and potential therapeutic interventions.
PubCompare.ai can help optimize your protein precursor research by locating the best protocols from literature, preprints, and patents, using intelligent comparisons to enhance reproducibility and accuracy.
Streamline your research and find the right solutions with PubCompare.ai.
Protein precursors, also known as proproteins or preproteins, are the preliminary forms of proteins that undergo a series of modifications to become the final, functional proteins.
These precursor molecules may undergo cleavage, folding, or other transformations to reach their mature state.
Understanding the structure and characteristics of protein precursors is crucial for researchers studying protein synthesis, cellular processes, and potential therapeutic interventions.
PubCompare.ai, an AI-driven platform, can help researchers optimize their protein precursor research by locating the best protocols from literature, preprints, and patents.
The platform uses intelligent comparisons to enhance reproducibility and accuracy, allowing researchers to streamline their research and find the right solutions.
Researchers studying protein precursors may utilize tools and techniques such as Rabbit reticulocyte lysate, TNT Coupled Reticulocyte Lysate System, Cobas 8000, ÄKTA FPLC system, [35S]-methionine, SIG-39320, TNT Quick Coupled Transcription/Translation kit, Amicon 10,000 MWCO concentrator, and A8717 Complete protease inhibitor mixture.
These resources can aid in the analysis, purification, and modification of protein precursors, as well as the study of their synthesis and processing pathways.
By leveraging the insights and capabilities of PubCompare.ai, researchers can streamline their protein precursor research, enhance reproducibility, and ultimately accelerate the advancement of knowledge in this crucial field of study.