VCP/p97-associated proteins are binders and debranching enzymes of K48-K63-branched ubiquitin chains.

Branched ubiquitin (Ub) chains constitute a sizable fraction of Ub polymers in human cells. Despite their abundance, our understanding of branched Ub function in cell signaling has been stunted by the absence of accessible methods and tools. Here we identify cellular branched-chain-specific binding proteins and devise approaches to probe K48-K63-branched Ub function.

Mechanism of human PINK1 activation at the TOM complex in a reconstituted system.

Loss-of-function mutations in PTEN-induced kinase 1 (PINK1) are a frequent cause of early-onset Parkinson's disease (PD). Stabilization of PINK1 at the translocase of outer membrane (TOM) complex of damaged mitochondria is critical for its activation. The mechanism of how PINK1 is activated in the TOM complex is unclear.

Correction: Biochemical characterization of protease activity of Nsp3 from SARS-CoV-2 and its inhibition by nanobodies.

[This corrects the article DOI: 10.1371/journal.pone.

UBE2A and UBE2B are recruited by an atypical E3 ligase module in UBR4.

UBR4 is a 574 kDa E3 ligase (E3) of the N-degron pathway with roles in neurodevelopment, age-associated muscular atrophy and cancer. The catalytic module that carries out ubiquitin (Ub) transfer remains unknown. Here we identify and characterize a distinct E3 module within human UBR4 consisting of a 'hemiRING' zinc finger, a helical-rich UBR zinc-finger interacting (UZI) subdomain, and an N-terminal region that can serve as an affinity factor for the E2 conjugating enzyme (E2).

Functional characterization of C21ORF2 association with the NEK1 kinase mutated in human in diseases.

The NEK1 kinase controls ciliogenesis, mitosis, and DNA repair, and mutations cause human diseases including axial spondylometaphyseal dysplasia and amyotrophic lateral sclerosis. mutations cause a similar pattern of human diseases, suggesting close functional links with Here, we report that endogenous NEK1 and C21ORF2 form a tight complex in human cells. A C21ORF2 interaction domain "CID" at the C-terminus of NEK1 is necessary for its association with C21ORF2 in cells, and pathogenic mutations in this region disrupt the complex.

Impact of 100 LRRK2 variants linked to Parkinson's disease on kinase activity and microtubule binding.

Mutations enhancing the kinase activity of leucine-rich repeat kinase-2 (LRRK2) cause Parkinson's disease (PD) and therapies that reduce LRRK2 kinase activity are being tested in clinical trials. Numerous rare variants of unknown clinical significance have been reported, but how the vast majority impact on LRRK2 function is unknown. Here, we investigate 100 LRRK2 variants linked to PD, including previously described pathogenic mutations.

Purification, crystallization and drug screening of the IRAK pseudokinases.

Pseudokinases are emerging as critical components of cell signaling pathways. Consequently, the ability to obtain large quantities of pure protein for structural characterization and drug discovery efforts has become essential for the study of these proteins. Small molecules binding to pseudokinases may induce allosteric changes and serve as valuable tools to study the physiological roles of these "dead" enzymes.

Deubiquitinases: From mechanisms to their inhibition by small molecules.

Deubiquitinases (DUBs) are specialized proteases that remove ubiquitin from substrates or cleave within ubiquitin chains to regulate ubiquitylation and therefore play important roles in eukaryotic biology. Dysregulation of DUBs is implicated in several human diseases, highlighting the importance of DUB function. In addition, many pathogenic bacteria and viruses encode and deploy DUBs to manipulate host immune responses and establish infectious diseases in humans and animals.

Mechanism of activation and regulation of deubiquitinase activity in MINDY1 and MINDY2.

Of the eight distinct polyubiquitin (polyUb) linkages that can be assembled, the roles of K48-linked polyUb (K48-polyUb) are the most established, with K48-polyUb modified proteins being targeted for degradation. MINDY1 and MINDY2 are members of the MINDY family of deubiquitinases (DUBs) that have exquisite specificity for cleaving K48-polyUb, yet we have a poor understanding of their catalytic mechanism. Here, we analyze the crystal structures of MINDY1 and MINDY2 alone and in complex with monoUb, di-, and penta-K48-polyUb, identifying 5 distinct Ub binding sites in the catalytic domain that explain how these DUBs sense both Ub chain length and linkage type to cleave K48-polyUb chains.

Biochemical characterization of protease activity of Nsp3 from SARS-CoV-2 and its inhibition by nanobodies.

Of the 16 non-structural proteins (Nsps) encoded by SARS CoV-2, Nsp3 is the largest and plays important roles in the viral life cycle. Being a large, multidomain, transmembrane protein, Nsp3 has been the most challenging Nsp to characterize. Encoded within Nsp3 is the papain-like protease domain (PLpro) that cleaves not only the viral polypeptide but also K48-linked polyubiquitin and the ubiquitin-like modifier, ISG15, from host cell proteins.

Dimeric Structure of the Pseudokinase IRAK3 Suggests an Allosteric Mechanism for Negative Regulation.

Interleukin-1 receptor associated kinases (IRAKs) are key players in innate immune signaling that mediate the host response to pathogens. In contrast to the active kinases IRAK1 and IRAK4, IRAK2 and IRAK3 are pseudokinases lacking catalytic activity and their functions are poorly understood. IRAK3 is thought to be a negative regulator of innate immune signaling and mutations in IRAK3 are associated with asthma and cancer.

Evaluation of Mechanical Properties of Segmented Esophageal Self-Expandable Metal Stents: Innovative Test Methods Are Needed.

Self-expanding metal stents (SEMSs) in different geometric shapes are well established treatment options in diseases of the esophagus. Mechanical properties and stent design may have an impact on patient comfort, migration rate, and removability. In this study, we evaluated mechanical properties of three segmented SEMSs (segSEMSs) for the esophagus with regard to distinct stent sections.

Graphene-Enhanced Raman Scattering from the Adenine Molecules.

An enhanced Raman scattering from a thin layer of adenine molecules deposited on graphene substrate was detected. The value of enhancement depends on the photon energy of the exciting light. The benzene ring in the structure of adenine molecule suggests π-stacking of adenine molecule on top of graphene.

The Interaction of CCDC104/BARTL1 with Arl3 and Implications for Ciliary Function.

Cilia are small antenna-like cellular protrusions critical for many developmental signaling pathways. The ciliary protein Arl3 has been shown to act as a specific release factor for myristoylated and farnesylated ciliary cargo molecules by binding to the effectors Unc119 and PDE6δ. Here we describe a newly identified Arl3 binding partner, CCDC104/CFAP36.

Mechanical properties of sol-gel derived SiO2 nanotubes.

The mechanical properties of thick-walled SiO2 nanotubes (NTs) prepared by a sol-gel method while using Ag nanowires (NWs) as templates were measured by using different methods. In situ scanning electron microscopy (SEM) cantilever beam bending tests were carried out by using a nanomanipulator equipped with a force sensor in order to investigate plasticity and flexural response of NTs. Nanoindentation and three point bending tests of NTs were performed by atomic force microscopy (AFM) under ambient conditions.

An energy transfer kinetic probe for OH-quenchers in the Nd(3+):YPO4 nanocrystals suitable for imaging in the biological tissue transparency window.

Tetragonal xenotime-type yttrium orthophosphate (YPO4) Nd(3+) doped nanoparticles suitable for biomedical applications were prepared by microwave-hydrothermal treatment. We applied the energy transfer probing based on the analysis of kinetics of impurity quenching to determine the presence and spatial position of -OH fluorescence quenching acceptors in the impurity-containing nanoparticles. We show that the impurity quenching kinetics of the 0.

A defined, controlled culture system for primary bovine chromaffin progenitors reveals novel biomarkers and modulators.

We present a method to efficiently culture primary chromaffin progenitors from the adult bovine adrenal medulla in a defined, serum-free monolayer system. Tissue is dissociated and plated for expansion under support by the mitogen basic fibroblast growth factor (bFGF). The cultures, although not homogenous, contain a subpopulation of cells expressing the neural stem cell marker Hes3 that also propagate.

Differentiation of chromaffin progenitor cells to dopaminergic neurons.

The differentiation of dopamine-producing neurons from chromaffin progenitors might represent a new valuable source for replacement therapies in Parkinson's disease. However, characterization of their differentiation potential is an important prerequisite for efficient engraftment. Based on our previous studies on isolation and characterization of chromaffin progenitors from adult adrenals, this study investigates their potential to produce dopaminergic neurons and means to enhance their dopaminergic differentiation.

Development of a compression molding process for three-dimensional tailored free-form glass optics.

Because of the limitation of manufacturing capability, free-form glass optics cannot be produced in a large volume using traditional processes such as grinding, lapping, and polishing. Very recently compression molding of glass optics became a viable manufacturing process for the high-volume production of precision glass optical components. An ultraprecision diamond-turning machine retrofitted with a fast tool servo was used to fabricate a free-form optical mold on a nickel-plated surface.