- Journal article
Authors : Henning, Nathaniel J. (2021) - Targeted protein degradation is a powerful therapeutic modality that uses heterobifunctional small-molecules to
induce proximity between E3 ubiquitin ligases and target proteins to ubiquitinate and degrade specific proteins
of interest. However, many proteins are ubiquitinated and degraded to drive disease pathology; in these cases
targeted protein stabilization (TPS), rather than degradation, of the actively degraded target using a smallmolecule
would be ther...
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- Journal article
Authors : Trainor, Brandon M. (2021) - The conventional view regarding regulation of gene expression is based on transcription control.
However, a growing number of recent studies has revealed the important additional impact of
translational regulation. Eukaryotic translational machinery appears to be capable of
reprogramming mRNA translation to generate proteins required to maintain a healthy cellular
proteostasis under particular physiological conditions or to adapt to stress. Altho...
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- Journal Article
Authors : Muir, Tom W. (2023) - The post-translational regulation of protein function is involved in most cellular processes.
As such, synthetic biology tools that operate at this level provide opportunities for manipulating
cellular states. Here, we deploy a proximity-triggered protein trans-splicing technology to enable
the time-resolved synthesis of target proteins from pre-made parts. The modularity of the strategy
allows for the addition or removal of various control elements as&#x...
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- Journal Article
Authors : Ashok, Yashwanth (2023) - The DNA damage response involves a complex protein network with members mediating different post-translational modifications such as ubiquitination and deubiquitination. Thereby the E3 ubiquitin ligase DTX3L as well as the deubiquitinase USP28 are recruited especially to DNA double strand breaks (DSBs) suggesting mutual functional interactions. Here we present evidence for the existence of such crosstalk. Mechanistically we show that DTX3L interacts with USP28 and ubiq...
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- Ebooks (Sách điện tử)
Authors : Karaś, Piotr (2023) - Evolution can tinker with multi-protein machines and replace them with simpler single-protein systems performing equivalent functions in equally efficient manner. It is unclear how, on a molecular level, such simplification can arise. With ancestral reconstruction and biochemical analysis we have traced the evolution of bacterial small heat shock proteins (sHsp), which help to refold proteins from aggregates using either two proteins with different functions (IbpA ...
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- Journal Article
Authors : Baboo, Sabyasachi (2023) - It has been three years since SARS-CoV-2 emerged and the world plunged into a “once in a century”
pandemic. Since then, multiple waves of infection have swept through the human population, led by
variants that were able to evade any acquired immunity. The co-evolution of SARS-CoV-2 variants with
human immunity provides an excellent opportunity to study the interaction between viral pathogens and
their human hosts. The heavily N-gl...
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- Journal Article
Authors : Baboo, Sabyasachi (2023) - UBR4 is an E3 ligase (E3) of the N-degron pathway and is involved in
neurodevelopment, age-associated muscular atrophy and cancer progression. The location
and mechanistic classification of the E3 module within the 600 kDa protein UBR4 remains
unknown. Herein, we identify and characterize, at a biochemical and structural level, a distinct
E3 module within human UBR4 consisting of a novel “hemiRING” zinc finger, a helical-rich
UBR ...
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- Journal Article
Authors : Mendes, Luis Felipe S.; Costa-Filho, Antonio J. (2023) - Eukaryotic cells evolved to possess efficient secretory machinery capable of transporting a significant fraction of their proteome. The number of proteins predicted to enter the secretory pathway can reach up to 36% of the total proteome in humans (1). Proteins entering the secretory pathway are efficiently sorted to a specific destination: the extracellular space, the plasma membrane, or the interior of the endomembrane system. The machinery also has&#x...
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- Journal article
Authors : Ball, Eric H. (2023) - AbstractF
ilter paper provides an excellent matrix for retention of proteins containing a cellulose binding
domain. To use this capability for manipulating recombinant fusion proteins, binding and elution
parameters were explored and procedures developed for small scale purification, modification and
assay. Proteins were tagged with the cellulose binding domain from the C thermocellum CipB gene via
a cleavable linker. Filter paper disks of 6mm&...
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- Journal Article
Authors : Cordoba, John J (2023) - In eukaryotes, DNA polymerase α-primase (pol-prim) initiates DNA synthesis during replication, generating the first ~30 nucleotides of nascent strands.1–5 Pol-prim is unique among replicative polymerases in its ability to perform de novo synthesis from a single-stranded DNA template; the primers it creates are required for further synthesis by the processive polymerases ε and δ that perform the bulk of nascent strand synthesis6,7. Pol-prim plays a particularly...
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- Journal article
Authors : Frei, Michelle S. (2021) - HaloTag9 is an engineered variant of HaloTag7 with up to 40% higher brightness and increased
fluorescence lifetime when labeled with fluorogenic rhodamines. Moreover, combining HaloTag9
with HaloTag7 and other fluorescent probes enabled live-cell multiplexing using a single
fluorophore and the generation of a fluorescence lifetime-based biosensor. The increased
brightness of HaloTag9 and its use in fluorescence lifetime multiplexing makes it a...
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- Journal article
Authors : witucki (2023) - The loss of cystathionine β-synthase (CBS), an important homocysteine (Hcy)-metabolizing enzyme or
the loss of PHF8, an important histone demethylase participating in epigenetic regulation, causes severe
mental retardation in humans. Similar neuropathies were also observed in Cbs-/- and Phf8-/- mice. How
CBS or PHF8 depletion can cause neuropathy was unknown. To answer this question, we examined a
possible interaction between PHF8 and CBS u...
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- Journal article
Authors : Barik, Sushanta Kumar (2021) - Acquired immunodeficiency syndrome is one of the most
important diseases caused by human immunodeficiency virus. Understanding its molecular
pathogenesis is essential to manage the disease at the population level. In this study, a quantitative analysis of plasma proteins was carried out in drug resistant and drug respondent patients using the SWATH-MS. Sequential window acquisition of all theoretical mass spectra (SWATH-MS) is a prime technique to seek...
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- Journal Article
Authors : Enustun, Eray (2023) - In the arms race between bacteria and bacteriophages (phages), some large-genome jumbo
phages have evolved a protein shell that encloses their replicating genome to protect it
against DNA-targeting immune factors. By segregating the genome from the host cytoplasm,
however, the “phage nucleus” introduces the need to specifically transport mRNA and
proteins through the nuclear shell, and to dock capsids on the shell for genome packaging.
�...
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- Journal Article
Authors : Sahil, Mohammad (2023) - Bacterial transcription initiation mainly occurs via two diverse RNA polymerases, namely
70 and 54. While 70 polymerase transcribes housekeeping genes and does not require
any external activation to form transcriptionally competent open complex, the alternate
polymerase 54 require regulatory proteins, typically AAA+ ATPases, that aid in converting
the closed RNA polymerase complex to an active open state.1,2 External stimuli and
enviro...
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- Journal article
Authors : Manikandan, Amrutha (2023) - The AMP-activated protein kinase (AMPK) is known to be activated by the protein tyrosine
phosphatase non-receptor type 12 (PTP-PEST) under hypoxic conditions. This activation is
mediated by tyrosine dephosphorylation of the AMPKα subunit. However, the identity of the
phosphotyrosine residues remains unknown. In this study we first predicted the structure of
the complex of the AMPKα2 subunit and PTP-PEST catalytic domain using bioinformatics
too...
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- Journal article
Authors : Bageshwar, Umesh K. (2021) - The twin-arginine translocation (Tat) pathway transports folded proteins across energetic membranes.
Numerous Tat substrates contain co-factors that are inserted before transport with the assistance of redox
enzyme maturation proteins (REMPs), which bind to the signal peptide of precursor proteins. How signal
peptides are transferred from a REMP to a binding site on the Tat receptor complex remains unknown.
Since the signal peptide mediates both ...
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- Journal article
Authors : Park, Sang Ho (2021) - SARS-CoV-2 is the novel coronavirus that is the causative agent of COVID-19, a sometimes-lethal respiratory infection responsible for a world-wide pandemic. The envelope (E) protein, one of four structural proteins encoded in the viral genome, is a 75-residue integral membrane protein whose transmembrane domain exhibits ion channel activity and whose cytoplasmic domain participates in protein-protein interactions. These activities contribute to several aspects ...
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- Journal Article
Authors : Doulidis, Pavlos G. (2023) - Bloodwork is a widely used diagnostic tool in veterinary medicine, as diagnosis and therapeutic 15 interventions often rely on blood biomarkers. However, biomarkers available in veterinary medicine 16 often lack sensitivity or specificity. Mass spectrometry (MS)-based proteomics technology has been 17 extensively used in biological fluids and offers excellent potential for a more comprehensive 18 characterization of the plasma proteome in veterinary medicine. In this&#...
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- Journal Article
Authors : Henrion, André (2023) - Quantitative analysis depends on pure-substance primary calibrators with known mass fractions of impurity. Here, label-free quantification (LFQ) is being evaluated as a readily available, reliable method for determining the mass fraction of host-cell proteins (HCPs) in bioengineered proteins. For example, hemoglobin-A2 (HbA2) is being used as obtained through overexpression in E.coli. Two different materials had been produced: natural, and U-15N-labeled HbA2. For quantification&...
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