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Ubiquitin

Ubiquitin is a highly conserved, 76-amino acid protein found in all eukaryotic cells.
It plays a crucial role in the regulation of protein degradation, signal transduction, and various cellular processes.
Ubiquitin attaches to target proteins, marking them for destruction by the proteasome or triggering other cellular responses.
This versatile molecule is involved in a wide range of biological functions, including cell cycle control, DNA repair, immune response, and neurodegeneration.
Understanding the complex mechanisms of ubiquitin-mediated pathways is essential for developing new therapies for ubiquitin-related disorders, such as cancer, autoimmune diseases, and neurodegenerative conditions.
Reasearchers can utilize PubCompare.ai's AI-powered platform to effortlessly locate the best protocols from literature, pre-prints, and patents, enhancing the reproducibility and accuracy of ubiquitin studies.

Most cited protocols related to «Ubiquitin»

Validating Force Field for Diverse Proteins

The C36m FF was validated using a variety of systems including peptides, IDPs, unfolded states of proteins, and globular proteins. The CHARMM-modified TIP3P model³⁵ was used in all simulations, unless noted. All the systems studied here are in high dilution such that the systems did not test the force fields with respect to aggregation. A summary of the validation simulations is given in the Supplementary Table 1, and detailed information of setup and analysis for each simulation system is given in the Supplementary Note. Briefly, temperature replica exchange (T-REX) simulations were carried out with GROMACS³⁶ for the RS peptide (0.63 μs * 34 replica), the GB1 hairpin (0.8 μs * 32 replica), the Nrf2 hairpin (1 μs * 28 replica), Chignolin (6 μs * 29 replica) and CLN025 (6 μs * 29 replica). Hamiltonian replica exchange (HREX) simulation was carried out with CHARMM³⁷ for polyQ using the end-to-end distance as the biasing reaction coordinate. Harmonic umbrella potentials with a force constant of 0.2 kcal/mol/Å² were applied to target end-to-end distances ranging from 5 to 75 Å spaced at 5 Å intervals. Similar H-REX protocol using distance as the biasing reaction coordinate was applied to study the folding free energy of HP21. Conformations were also sampled using single, long MD trajectories with OpenMM,³⁸ including 5 μs simulations for the HEWL19 peptide, IN and CspTm, 10 μs simulations for the (AGQ)_n peptides, and 16 μs simulations for (AAQAA)₃. A 1.2 μs simulation of ubiquitin was carried out with NAMD to compare with previous results using the C36 FF.³⁹ Alternative water models were tested with the RS peptide using T-REX simulations (0.63 μs * 34 replica) and with IN and CspTm using 5 μs MD simulations.
Analysis of MD trajectories was carried out using GROMACS³⁶ or CHARMM.³⁷ A left-handed α-helix is defined as having at least three consecutive residues with φ, ψ~falling in the α_L region (30°<φ<100° and 7°<ψ< 67°, Supplementary Fig. 20). The α_L probability is computed as the fraction of the ensemble containing left α-helix as in Ref.³² We also compute the α_L fraction as the probability for residues to be in a left-handed α-helix, and the α_L propensity as the probability for residues’ φ, ψ to be in the α_L region, as additional measurement of α-left helix sampling.

Huang J., Rauscher S., Nawrocki G., Ran T., Feig M., de Groot B.L., Grubmüller H, & MacKerell AD J.r. (2016). CHARMM36m: An Improved Force Field for Folded and Intrinsically Disordered Proteins. Nature methods, 14(1), 71-73.

Publication 2016

chignolin Eye Helix (Snails) IDH2, human NFE2L2 protein, human Peptides polyglutamine Proteins Technique, Dilution Ubiquitin YYDPETGTWY

Molecular Dynamics Simulations of Proteins

MD simulations of hen egg white lysozyme (HEWL), bovine pancreatic trypsin inhibitor (BPTI), ubiquitin (Ubq), and the B3 domain of Protein G (GB3) were performed using Desmond version 2.1.0.1 and the Amber ff99SB or the modified Amber ff99SB-ILDN force fields. The TIP3P water model20 was used for simulations of HEWL, Ubq, and GB3, and the TIP4P-Ew water model21 (link) was used for simulations of BPTI. Simulation parameters were the same as in the simulations of small helical peptides, apart from the fact that a 64³ PME grid was used for HEWL and a 48³ grid was used for BPTI, Ubq, and GB3. Simulations of HEWL, BPTI, Ubq, and GB3 were initiated from PDB22 (link) entries 6LYT, 5PTI, 1UBQ, and 1P7E solvated in cubic water boxes containing 10,594, 4215, 6080, and 5156 water molecules, respectively. The net charge of the proteins was neutralized with sodium or chloride ions. Each system was initially subject to energy minimization, followed by 1.2 ns of MD simulation in the NPT ensemble during which the temperature was increased linearly from 10 to 300 K, and position restraints on the backbone atoms were annealed from 1.0 to 0.0 kcal mol⁻¹ Å⁻¹. After this initial relaxation, each system was simulated for 6 ns in the NPT ensemble. The frame of this simulation with the volume closest to the average volume was selected as the starting conformation for a production run of 1.2 μs in the NVT ensemble. The trajectories obtained from the NVT runs were used for subsequent data analysis.

Lindorff-Larsen K., Piana S., Palmo K., Maragakis P., Klepeis J.L., Dror R.O, & Shaw D.E. (2010). Improved side-chain torsion potentials for the Amber ff99SB protein force field. Proteins, 78(8), 1950-1958.

Publication 2010

Amber Aprotinin Chlorides Cuboid Bone Helix (Snails) hen egg lysozyme Ions Peptides Protein Domain Proteins Reading Frames Sodium Ubiquitin Vertebral Column

Protein Simulation with CHARMM-GUI and NAMD

Protein simulation systems were prepared with the CHARMM-GUI.^{28 (link)} Briefly, protein structures taken from corresponding protein data bank^{29 (link)} files were solvated in pre-equilibrated cubic TIP3P water boxes of suitable sizes and counter-ions were added to keep systems neutral as detailed in Table 1. Periodic boundary conditions were applied and Lennard-Jones (LJ) interactions were truncated at 12 Å with a force switch smoothing function from 10 Å to 12 Å. The non-bonded interaction lists were generated with a distance cutoff of 16 Å and updated heuristically. Electrostatic interactions were calculated using the particle mesh Ewald method³⁰ with a real space cutoff of 12 Å on an approximately 1 Å grid with 6th order spline. Covalent bonds to hydrogen atoms were constrained by SHAKE.³¹ After a 200 step Steepest Descent (SD) minimization with the protein fixed and another 200 steps without the protein fixed, the systems were first heated to 300 K and then subjected to a 100 ps NVT simulation followed by a 100 ps NPT simulation. The minimization, heating and initial equilibrium was performed with CHARMM,^{32 (link)} and the resultant structures were used to start simulations in NAMD.^{33 (link)} After a 1 ns NPT simulation as equilibration, the production simulations were run for 100 ns in the NVT ensemble (see Table 1). For HEWL NPT ensembles were generated to better compare with previous work that found CMAP helps to better reproduced order parameter S^{2,34 (link)} and simulations were extended to 200 ns to reduce the uncertainty of the computed S². Langevin thermostat with a damping factor of 5 ps⁻¹ was used for NVT simulation and the Nosé-Hoover Langevin piston method with a barostat oscillation time scale of 200 fs was further applied for the NPT simulation at 300 K and 1 atm. The time step equals 2 fs and coordinates were stored every 10 ps. For each protein the above simulation protocol was applied with the C36 and C22/CMAP FFs, while for ubiquitin an additional 1.2 μs trajectories with C36 was generated. This long simulation is used to check the convergence and also to examine whether computed NMR data deteriorate over a longer simulation time, as it was reported that RDCs significantly deviate from experimental values after approximately 500 ns simulations with the C22 FF.^{22 (link)}

Huang J, & MacKerell AD J.r. (2013). CHARMM36 all-atom additive protein force field: Validation based on comparison to NMR data. Journal of computational chemistry, 34(25), 2135-2145.

Publication 2013

Cuboid Bone Electrostatics factor A Factor V Familial Mediterranean Fever Hydrogen Bonds Ions Proteins Ring dermoid of cornea Staphylococcal Protein A STEEP1 protein, human Tremor Ubiquitin

Molecular Dynamics Simulations of Folded Proteins

Simulations using Gromacs 4.5.3 were carried out for the following four folded globular proteins: bovine pancreatic trypsin inhibitor (BPTI), ubiquitin, GB3 and hen Lysozyme, starting from the published experimental structures (PDB entries 5PTI^{48 (link)}, 1UBQ^{49 (link)}, 1P7E^{50 (link)}, 6LYT⁵¹ respectively). Each protein was solvated in a truncated octahedron simulation cell filled with TIP3P water, with nearest distance between images of 45 Å for all proteins except for lysozyme, for which the distance was 60 Å. Sodium and chloride ions were added as needed to yield a final salt concentrations of ~100 mM, with adjustments to ensure charge neutrality. For each protein, a 100-step SD energy minimization of the whole system was performed, followed by 200 ps of MD at a constant pressure of 1 bar and temperature of 300 K, in which harmonic positional restraints of 2.39 kcal/mol/Å² were applied to each Cartesian component of each protein non-hydrogen atom using the minimized structure as a reference. Each protein was then simulated at a constant pressure of 1 bar and a temperature of 300 K for 200 ns. Pressure was regulated by a Parinello-Rahman barostat⁵² with a coupling time of 2.5 ps; otherwise all details were as described for Ac-(AAQAA)₃-NH₂ above.

Best R.B., Zhu X., Shim J., Lopes P.E., Mittal J., Feig M, & MacKerell AD J.r. (2012). Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone φ, ψ and side-chain χ1 and χ2 dihedral angles. Journal of chemical theory and computation, 8(9), 3257-3273.

Publication 2012

A 300 Aprotinin Cells Chlorides Eye hen egg lysozyme Hydrogen Ions Muramidase Pressure Proteins Sodium Sodium Chloride Ubiquitin

Molecular Dynamics Simulations of Peptides

Simulations of Ala₅ were run using the simulation package Gromacs^{28 ,29} using a protocol similar to that used in our previous work,^{15 (link)} and with the implementation of the Amber force fields by Sorin and Pande.^{30 (link)} The peptide was unblocked and protonated at both N and C termini, corresponding to the experimental conditions of pH 2.^{14 (link)} Molecular dynamics simulations of each peptide in a 30 Å cubic simulation box of explicit TIP3P water³¹ were run at a constant temperature of 300 K and a constant pressure of 1 atm, with long range electrostatic terms evaluated using particle-mesh Ewald (PME) using a 1.0 Å grid spacing and a 9 Å cutoff for short-range interactions. For each force field, four runs of 50 ns each were initiated from different starting configurations. Further details of the simulation protocols are as published.^{15 (link)}Replica exchange molecular dynamics (REMD) simulations of the blocked peptide Ac-(AAQAA)₃-NH₂ were run using Gromacs^{28 ,29} with 32 replicas spanning a temperature range of 278 K to 595 K. The peptide was solvated in a truncated octahedron simulation cell of 1022 TIP3P water molecules with an initial distance of 35 Å between the nearest faces of the cell. This cell was equilibrated for 200 ps at 300 K and a constant pressure of 1 atm. Subsequently, all REMD simulations were done at constant volume, with long range electrostatics calculated using PME with a 1.2 Å grid spacing and 9 Å cutoff. Dynamics was propagated with a Langevin integration algorithm using a friction of 1 ps⁻¹, and replica exchange attempts every 1 ps (every 500 steps with a time step of 2 fs). Typical acceptance probabilities for the replica exchange were in the range 0.1–0.5. All replica exchange runs used the same set of initial configurations, which were taken from the final configurations of a preliminary replica exchange simulation with ff99SB. The simulations were run for at least 30 ns per replica, of which the first 10 ns were discarded in the analysis (with an aggregate of ≈ 1 µs for each force field). To test for possible system size dependence, additional simulations of Ac-(AAQAA)₃-NH₂ in a 45 Å truncated octahedron box solvated by 2268 water molecules were run for 30 ns using a similar protocol, in this case with 32 replicas at 5 K intervals between 278 and 433 K.
Additional simulations were performed for the unblocked peptide HEWL19, derived from hen egg-white lysozyme with sequence KVFGRC(SMe)ELAAAMKRHGLDN. The structure and parameters for the S-methylated Cys 6 were adapted from those for methionine and are given in Supporting Information (SI) Figure 1 and Table 1 respectively. Both termini as well as all acidic side chains were protonated, corresponding to the experimental conditions of pH 2.^{14 (link)} The peptide was solvated in a truncated octahedron simulation cell with a 42 Å distance between nearest faces, and equilibrated at constant pressure for 200 ps at 300 K. Constant volume REMD was run with 32 replicas spanning the temperature range 278 K to 472 K, for 27 ns, of which the first 10 ns were discarded in the analysis. All other parameters were the same as for Ac-(AAQAA)₃-NH₂.
Native state simulations of ubiquitin were run starting from the crystal structure 1UBQ.^{32 (link)} The protein was solvated by 2586 explicit TIP3P water molecules in a cubic simulation box of 45 Å length with long range electrostatics calculated using PME with a 1.2 Å grid spacing and 9 Å cutoff. To neutralize the system charge, 7 sodium and 8 chloride ions were added. Dynamics was propagated for 30 ns at constant pressure (1 atm) and temperature (300 K) using a Nosé-Hoover thermostat³³ and Parrinello-Rahman barostat.³⁴

Best R.B, & Hummer G. (2009). Optimized molecular dynamics force fields applied to the helix-coil transition of polypeptides. The journal of physical chemistry. B, 113(26), 9004-9015.

Publication 2009

Acids Amber Cells Chlorides Cuboid Bone Electrostatics Face Friction hen egg lysozyme Ions Methionine Molecular Dynamics Peptides Pressure Proteins Sodium Ubiquitin

Most recents protocols related to «Ubiquitin»

Micropeptides Identified from lncRNAs

Not available on PMC !

Example 1

The authors of the invention have identified 3 micropeptides corresponding to sequences SEQ ID NO: 1, 2 and 3.

The micropeptide of SEQ ID NO 1 is a highly conserved 87 aa micropeptide whose sequence is:

(FIG. 1A)

MEGLRRGLSRWKRYHIKVHLADEALLLPLTVRPRDTLSDLRAQLVGQGVSS

WKRAFYYNARRLDDHQTVRDARLQDGSVLLLVSDPR.

In silico analysis of the amino acid sequence predicts a 3D structure resembling the protein UBIQUITIN (FIG. 1B). SEQ ID NO 1 micropeptide is coded by the lncRNA TINCR (LINC00036 in humans and Gm20219 in mice).

The micropeptide of SEQ ID NO: 2 is a 64-amino acid micropeptide whose sequence is:

(FIG. 2A)

MVRRKSMKKPRSVGEKKVEAKKQLPEQTVQKPRQECREAGPLFLQSRRETR

DPETRATYLCGEG.

It is encoded by ZEB2 antisense 1 (ZEB2AS1) long non-coding RNA (lncRNA). ZEB2AS1 is a natural antisense transcript corresponding to the 5′ untranslated region (UTR) of zinc finger E-box binding homeobox 2 (ZEB2). The ORF encoding the micropeptide spams part of the second and third exons of the lncRNA. I-Tasser, a 3D protein structure predictor, has been used in order to build a model of SEQ ID NO: 2 micropeptide 3D structure (FIG. 2B). Further in-silico analysis has revealed high amino acidic sequence conservation across the species and a potential cytoplasmatic localization of the micropeptide of SEQ ID NO: 2.

The micropeptide of SEQ ID NO: 3 is a 78-amino acid micropeptide encoded by the first exon of LINC0086 lncRNA. Its sequence, highly conserved across evolution is:

(FIG. 3A)

MAASAALSAAAAAAALSGLAVRLSRSAAARGSYGAFCKGLTRTLLTFFDLA

WRLRMNFPYFYIVASVMLNVRLQVRIE.

In silico analysis of this sequence predicted a tertiary structure (FIG. 3B) with a transmembrane domain at C-terminal of the protein and a signal peptide in the first 25 amino acids.

US11858972B2. Micropeptides and uses thereof (2024-01-02). FUNDACIÓ PRIVADA INSTITUT D'INVESTIGACIÓ ONCOLÒGICA DE VALL HEBRON [ES]. Inventors: Maria Abad Méndez [ES], Olga Boix Sánchez [ES], Emanuela Greco [ES], Iñaki Merino Valverde [ES].

Patent 2024

Amino Acids Amino Acid Sequence Biological Evolution Cytoplasm Exons Homo sapiens Integral Membrane Proteins Mice, House Protein Domain Proteins RNA, Long Untranslated Sequence Analysis Sequence Analysis, Protein Signal Peptides Ubiquitin Zinc Finger E-box Binding Homeobox 2

Synthesis of Substituted Pyridine Derivative

Not available on PMC !

Example 5

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Example 50

[Figure (not displayed)]
[Figure (not displayed)]
wherein X^Xand Y^Aare each independently CH or N.

The title compound was synthesized using the procedure in Example 50A, but substituting 5-Chloro-2-nitropyridine, wherein Y^Ais CH and X^Xis N, for 2-chloro-5-nitropyridine. LCMS C₂₈H₄₀N₁₀O₂requires: 548, found: m/z=549 [M+H]⁺.

US11866442B2. Bifunctional compounds for degrading BTK via ubiquitin proteosome pathway (2024-01-09). NURIX THERAPEUTICS, INC. [US]. Inventors: Daniel W. Robbins [US], Arthur T. Sands [US], Joel McIntosh [US], Jeffrey Mihalic [US], Jeffrey Wu [US], Daisuke Kato [US], Dahlia Weiss [US], Ge Peng [US].

Patent 2024

Laser Capture Microdissection Multicatalytic Endopeptidase Complex Ubiquitin

Transgenic Zebrafish Line Generation

Not available on PMC !

Example 1

Adult fish were raised and maintained as described in [28] and in strict accordance with the recommendations in the Guide for the Care and Use of Laboratory Animals by University of Southern California, where the protocol was approved by the Institutional Animal Care and Use Committee (IACUC) (Permit Number: 12007 USC). Transgenic FlipTrap Gt(desm-citrine)^ct122a/+ line was obtained from a previously described screen in the lab [23], Tg(kdrl:eGFP)^s843line [24] was provided by the Stainier lab, and Tg(ubiq:membrane-Cerulean-2a-H2B-tdTomato) line was generated by injecting a construct containing tol2 transposable elements flanking the ubiquitin promoter, coding sequence for membrane localized cerulean, a short sequence encoding the ribosome-skipping peptide of Thosea asigna virus (2a) followed by H2B-tdTomato. Upon crossing appropriate adult lines, the embryos obtained were raised in Egg Water (about 60 μg/ml of Instant Ocean and about 75 μg/ml of CaSO₄in Milli-Q water) at about 28.5° C. with addition of about 0.003% (w/v) 1-phenyl-2-thiourea (PTU) about 18 hpf to reduce pigment formation [28].

US11869176B2. Hyperspectral imaging system (2024-01-09). UNIVERSITY OF SOUTHERN CALIFORNIA [US]. Inventors: Wen Shi [US], Eun Sang Koo [US], Scott E. Fraser [US], Francesco Cutrale [US].

Patent 2024

Adult Animals, Laboratory Animals, Transgenic DNA Transposable Elements Embryo Fishes Institutional Animal Care and Use Committees LINE-1 Elements Open Reading Frames Peptides Phenylthiourea Pigmentation Ribosomes tdTomato Tissue, Membrane Ubiquitin Virus Zebrafish

Exosome-mediated Ubiquitin Ligase Delivery

Not available on PMC !

Example 13

The binding of CIBN and CRY2 in cells expressing CIBN-EGFP-CD9 and Ubiquitin ligase-mCherry-Cry2 at 488 nm wavelength blue light, and the loading of Ubiquitin ligases within the exosome is evaluated.

For the massive production of Ubiquitin ligase-loaded exosomes, cells stably expressing CIBN-EGFP-CD9 gene and Ubiquitin ligase-mCherry-CRY2 gene are established, and exosomes are isolated and purified by Tangential Flow Filtration (TFF) method from culture supernatant.

Functional analysis of Ubiquitin ligase-loaded exosomes is performed in target cells:

Target cells are treated with the Ubiquitin ligase-loaded exosomes to show the functional activity.

Animal models are administered with the Ubiquitin ligase-loaded exosomes by i.p. or i.v. to show therapeutic effect.

US11872193B2. Compositions containing protein loaded exosome and methods for preparing and delivering the same (2024-01-16). ILIAS BIOLOGICS INC. [KR]. Inventors: Chulhee Choi [KR], Nambin Yim [KR], Won Do Heo [KR], Seung-Wook Ryu [KR], Hojun Choi [KR], Kyungsun Choi [KR].

Patent 2024

Animal Model Cells Exosomes Filtration Genes Ligase Light Therapeutic Effect Ubiquitin

Histological analysis of traumatic brain injury

Authorizations for reporting these three cases were granted by the Eastern Ontario Regional Forensic Unit and the Laboratoire de Sciences Judiciaires et de Médecine Légale du Québec.
The sampling followed a relatively standardized protocol for all TBI cases: samples were collected from the cortex and underlying white matter of the pre-frontal gyrus, superior and middle frontal gyri, temporal pole, parietal and occipital lobes, deep frontal white matter, hippocampus, anterior and posterior corpus callosum with the cingula, lenticular nucleus, thalamus with the posterior limb of the internal capsule, midbrain, pons, medulla, cerebellar cortex and dentate nucleus. In some cases, gross pathology (e.g. contusions) mandated further sampling along with the dura and spinal cord if available. The number of available sections for these three cases was 26 for case1, and 24 for cases 2 and 3.
For the detection of ballooned neurons, all HE or HPS sections, including contusions, were screened at 200×.
Representative sections were stained with either hematoxylin–eosin (HE) or hematoxylin-phloxin-saffron (HPS). The following histochemical stains were used: iron, Luxol-periodic acid Schiff (Luxol-PAS) and Bielschowsky. The following antibodies were used for immunohistochemistry: glial fibrillary acidic protein (GFAP) (Leica, PA0026,ready to use), CD-68 (Leica, PA0073, ready to use), neurofilament 200 (NF200) (Leica, PA371, ready to use), beta-amyloid precursor-protein (β-APP) (Chemicon/Millipore, MAB348, 1/5000), αB-crystallin (EMD Millipore, MABN2552 1/1000), ubiquitin (Vector, 1/400), β-amyloid (Dako/Agilent, 1/100), tau protein (Thermo/Fisher, MN1020 1/2500), synaptophysin (Dako/Agilent, ready to use), TAR DNA binding protein 43 (TDP-43) ((Protein Tech, 10,782-2AP, 1/50), fused in sarcoma binding protein (FUS) (Protein tech, 60,160–1-1 g, 1/100), and p62 (BD Transduc, 1/25). In our index cases, the following were used for the evaluation of TAI: β-APP, GFAP, CD68 and NF200; for the neurodegenerative changes: αB-crystallin, NF200, ubiquitin, tau protein, synaptophysin, TDP-43, FUS were used.
For the characterization of the ballooned neurons only, two cases of fronto-temporal lobar degeneration, FTLD-Tau, were used as controls. One was a female aged 72 who presented with speech difficulties followed by neurocognitive decline and eye movement abnormalities raising the possibility of Richardson’s disorder. The other was a male aged 67 who presented with a primary non-fluent aphasia progressing to fronto-temporal demαentia. In both cases, the morphological findings were characteristic of a corticobasal degeneration.

Michaud J., Plu I., Parai J., Bourgault A., Tanguay C., Seilhean D, & Woulfe J. (2023). Ballooned neurons in semi-recent severe traumatic brain injury. Acta Neuropathologica Communications, 11, 37.

Publication 2023

Amyloid beta-Protein Precursor Amyloid Proteins Antibodies Broca Aphasia Cloning Vectors Congenital Abnormality Contusions Corpus Callosum Cortex, Cerebellar Cortex, Cerebral Corticobasal Degeneration Crystallins Dura Mater Eosin Eye Abnormalities Eye Movements Frontotemporal Lobar Degeneration FUBP1 protein, human Glial Fibrillary Acidic Protein Hematoxylin Immunohistochemistry Internal Capsule Iron Males Medial Frontal Gyrus Medulla Oblongata Mesencephalon Movement Movement Disorders neurofilament protein H Neurons Nucleus, Dentate Nucleus, Lenticular Occipital Lobe Periodic Acid phloxine Pons Proteins protein TDP-43, human RNA-Binding Protein FUS Saffron Sarcoma Seahorses Speech Spinal Cord Staining Synaptophysin Temporal Lobe Thalamus Ubiquitin White Matter Woman

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More about "Ubiquitin"

Ubiquitin, a highly conserved 76-amino acid protein, is found in all eukaryotic cells and plays a crucial role in a wide range of biological processes.
This versatile molecule is involved in protein degradation, signal transduction, cell cycle control, DNA repair, immune response, and neurodegeneration.
Understanding the complex mechanisms of ubiquitin-mediated pathways is essential for developing new therapies for ubiquitin-related disorders, such as cancer, autoimmune diseases, and neurodegenerative conditions.
Researchers can leverage PubCompare.ai's AI-powered platform to effortlessly locate the best protocols from literature, pre-prints, and patents, enhancing the reproducibility and accuracy of ubiquitin studies.
This includes protocols and techniques related to MG132 (a proteasome inhibitor), TRIzol reagent (for RNA isolation), Lipofectamine 2000 (a transfection reagent), Cycloheximide (a protein synthesis inhibitor), and Anti-ubiquitin antibodies (for detection and purification of ubiquitinated proteins).
The RNeasy Plant Mini Kit, for example, can be used to isolate high-quality RNA from plant samples, which is particularly useful for studying ubiquitin-mediated pathways in plant systems.
By utilizing these powerful tools and techniques, researchers can enhance the reproducibility and accuracy of their ubiquitin studies, paving the way for groundbreaking discoveries and the development of novel therapeutic approaches.