- Journal article
Authors : Stoeber, Jonathan (2021) - α-Synuclein (αS) is an intrinsically disordered protein (IDP) that aggregates into amyloid fibrils
during the progression of Parkinson’s Disease and other synucleinopathies. The N-terminal
domain (residues 1-60) is now understood to play a critical role in the initial nucleation of
aggregation, as well as a pivotal role in the monomer-fibril interaction underlying amyloid seeding.
Here we report on the interaction between αS and&#x...
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- Journal article
Authors : Dhenin, Jonathan (2021) - Top-down proteomics (TDP) is a powerful technology allowing the char acterization of proteins at the proteoform level using high-resolution tan dem mass spectrometry (MS/MS). Proteoforms correspond to the different
forms of a protein arising from all combinatorial sources of variation from
a single gene (including combinations of genetic variation, alternative
splicing, and post-translational modifications)(Smith and Kelleher, 2018).
The complete...
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- Journal article
Authors : Borvinskaya, Ekaterina V. (2021) - The protein composition (proteome) of cestode Schistocephalus solidus was measured in an experiment simulating the transition of the parasite from a cold-blooded to a warm-blooded host. Infective S. solidus plerocercoids obtained from the three-spined stickleback Gasterosteus aculeatus were heated at 40 °C for 1 hour or cultured in vitro at 40 °C and 22 °C for 48 hours. In the short-term experiment, the content of only one tegument prote...
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- Journal article
Authors : Thompson, Reece (2023) - The quantity of each protein in a cell only is only partially correlated with its gene transcription
rate. Independent influences on protein synthesis levels include mRNA sequence motifs,
amino acyl-tRNA synthesis levels, elongation factor action, and protein susceptibility to
degradation. Here we report two novel forms of interaction between the amino acid
composition of a protein and its expression level.
In animals, the differing origin...
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- Journal article
Authors : Kampourakis, Thomas (2023) - Phosphorylation of cardiac myosin binding protein-C (cMyBP-C) is a crucial determinant of
cardiac myofilament function. Although cMyBP-C phosphorylation by various protein kinases
has been extensively studied, the influence of protein phosphatases on cMyBP-C’s multiple
phosphorylation sites has remained largely obscure. Here we provide a detailed biochemical
characterization of cMyBP-C dephosphorylation by protein phosphatases 1 and 2A (PP1 and
PP2A) and deve...
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- Journal article
Authors : LaFrance, Benjamin (2021) - Bacterial nanocompartments, also known as encapsulins, are an emerging class of
protein-based ‘organelles’ found in bacteria and archaea. Encapsulins are virus-like
icosahedral particles comprising a ~25-50 nm shell surrounding a specific cargo
enzyme. Compartmentalization is thought to create a unique chemical environment to
facilitate catalysis and isolate toxic intermediates. Many questions regarding
nanocompartment structure-function remain unanswered, including how...
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- Journal article
Authors : Sennett, Michael A. (2023) - Ancestral sequence resurrection (ASR) is the inference of extinct biological sequences from extant sequences, the most popular of which are based on probabilistic models of evolution. ASR is becoming a popular method for studying the evolution of enzyme characteristics. The properties of ancestral enzymes are biochemically and biophysically characterized to gain some knowledge regarding the origin of some enzyme property. Current methodology relies on resurrection ...
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- Journal article
Authors : Knoke, Lisa R. (2023) - The thiol redox balance in the periplasm of E. coli depends on the DsbA/B pair for oxidative
14 power and the DsbC/D system as its complement for isomerization of non-native disulfides.
15 While the standard redox potentials of those systems are known, the in vivo redox potential
16 imposed onto protein thiol disulfide pairs in the periplasm remains unknown. Here, we used
17 genetically encoded redox probes (roGFP2 ...
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- Journal article
Authors : Knoke, Lisa R. (2023) - The thiol redox balance in the periplasm of E. coli depends on the DsbA/B pair for oxidative
14 power and the DsbC/D system as its complement for isomerization of non-native disulfides.
15 While the standard redox potentials of those systems are known, the in vivo redox potential
16 imposed onto protein thiol disulfide pairs in the periplasm remains unknown. Here, we used
17 genetically encoded redox probes (roGFP2 ...
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- Journal Article
Authors : Loughlin, Jennie O’ (2023) - The cis/trans isomerization of peptidyl-prolyl peptide bonds is often the bottleneck of the refolding reaction for proteins containing cis proline residues in the native state. Proline (Pro) analogues, especially C4-substituted fluoroprolines, have been widely used in protein engineering to enhance the thermodynamic stability of peptides and proteins and to investigate folding kinetics. 4-thiaproline (Thp) has been shown to bias the ring pucker of Pro, to inc...
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- Journal article
Authors : Ruedas, Rémi (2023) - RNA polymerases (RNAPs) involved in gene transcription are found in all living organisms with
degrees of complexity ranging from single polypeptide chains to multimeric enzymes. In the
chloroplasts, the nuclear-encoded RNA polymerase and the plastid-encoded RNA polymerase (PEP)
are both involved in the selective transcription of the plastid genome. The PEP is a prokaryotic-type
multimeric RNAP found in different states depending on light stimuli ...
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- Journal article
Authors : Ginn, Helen Mary (2023) - Present understanding of protein structure dynamics trails behind that of static structures. A torsionangle
based approach, called representation of protein entities (RoPE), derives an interpretable conformational
space which correlates with data collection temperature, resolution and reaction coordinate.
For more complex systems, atomic coordinates fail to separate functional conformational states, which
are still preserved by torsion angle-derived space. This indicates...
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- Journal Article
Authors : Steens, Jurre A. (2023) - Type III CRISPR-Cas systems provide a sequence-specific adaptive immune response that protects prokaryotic hosts against viruses and other foreign genetic invaders. These crRNA-guided Cas effector complexes bind and cleave complementary RNA targets. Specific target binding stimulates the Cas10 subunit to generate cyclic oligoadenylate (cOA) signaling molecules, that in turn allosterically activate proteins carrying cognate sensory domains: CARF or SAVED. Here, we characterize an...
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- Journal Article
Authors : Katzschmann, Anja (2023) - Affilin proteins (artificial binding proteins based on the ubiquitin scaffold) were generated using
directed protein evolution to yield de‐novo variants that bind the extra‐domain B (EDB) of oncofetal
fibronectin, an abundant tumor marker in fetal and neoplastic tissues. Structures of two EDB‐specific
Affilin molecules reveal striking structural plasticity of the ubiquitin scaffold, characterized by β‐strand
slippage, leading to diverse register shifts of ...
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- Journal Article
Authors : Govender, Ireshyn (2023) - The study of the human urinary proteome is becoming increasingly popular in clinical proteomics studies. Large volumes of samples are readily available with minimal invasiveness, and, in addition, soluble proteins and peptides de- rived from various tissues and organs are also filtered in urine, which can reflect more general health problems [1].
Plasma was long considered the best biofluid choice for biomarker discovery studies. However, the main ...
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- Journal Article
Authors : Gan, Jin (2023) - The ubiquitin-like modifier ISG15 can modulate host and viral proteins to restrict viral and
microbial infections, and act as a cytokine. Its expression and conjugation are strongly upregulated
by type I interferons. Here we identify the deubiquitinating enzyme USP16 as an
ISG15 cross-reactive protease. Ubiquitin-specific protease 16 (USP16) was found to react
with an ISG15 activity-based probe in pull-down experiments using chronic myeloid
leu...
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- Journal Article
Authors : Gubensäk, N. (2023) - Cholera represents a diarrheal disease caused by the Gram-negative bacterium Vibrio cholerae. Its environmental persistence causing recurring sudden outbreaks is enabled by V. cholerae’s rapid adaption to changing environments involving sensory proteins like ToxR and ToxS. Located at the inner membrane, ToxR and ToxS react to environmental stimuli like bile acid, thereby inducing survival strategies e.g. bile resistance and virulence regulation. Currently, transcript...
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- Journal article
Authors : Müller, Henrik (2021) - αB-crystallin (ABC) is a human small heat shock protein that is strongly linked to Alzheimer’s
disease (AD). In vitro, it can inhibit the aggregation and amyloid formation of a range of proteins
including Aβ(1-40), a primary component of AD amyloid plaques. Despite the strong links, the
mechanism by which ABC inhibits amyloid formation has remained elusive, in part due to the
notorious irreproducibility of aggregation assays involving&...
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