High-Performance Workflow for Identifying Site-Specific Crosslinks Originating from a Genetically Incorporated, Photoreactive Amino Acid.

In conventional crosslinking mass spectrometry, proteins are crosslinked using a highly selective, bifunctional chemical reagent, which limits crosslinks to residues that are accessible and reactive to the reagent. Genetically incorporating a photoreactive amino acid offers two key advantages: any site can be targeted, including those that are inaccessible to conventional crosslinking reagents, and photoreactive amino acids can potentially react with a broad range of interaction partners. However, broad reactivity imposes additional challenges for crosslink identification. In this study, we incorporate benzoylphenylalanine (BPA), a photoreactive amino acid, at selected sites in an intrinsically disordered region of the human protein HSPB5. We report and characterize a workflow for identifying and visualizing residue-level interactions originating from BPA. We routinely identify 30 to 300 crosslinked peptide spectral matches with this workflow, which is up to ten times more than existing tools for residue-level BPA crosslink identification. Most identified crosslinks are assigned to a precision of one or two residues, which is supported by a high degree of overlap between replicate analyses. Based on these results, we anticipate that this workflow will support the more general use of genetically incorporated, photoreactive amino acids for characterizing the structures of proteins that have resisted high-resolution characterization.

The Impact of a CMV Infection on the Expression of Selected Immunological Parameters in Liver Tissue in Children with Biliary Atresia.

The pathogenesis of biliary atresia (BA) is still not clear. The aim of this study was to evaluate the expression of selected immunological parameters in liver tissue in BA children based on CMV/EBV infection status. Eight of thirty-one children with newly diagnosed BA were included in this prospective study and assigned to two groups (I with active infection, II without active or past infection). All studies were performed on surgical liver biopsies. To visualize CD8+ T cells and CD56 expression, immunohistochemical staining was performed. The viral genetic material in the studied groups was not found, but CMV infection significantly affected the number of CD8+ lymphocytes in both the portal area and the bile ducts. The average number of CD8+ cells per mm2 of portal area in Groups I and II was 335 and 200 (p = 0.002). The average number of these cellsthat infiltrated the epithelium of the bile duct per mm2 in Group I and II was 0.73 and 0.37 (p = 0.0003), respectively. Expression of CD56 in the bile ducts corresponded to the intensity of the inflammatory infiltrate of CD8+ cells. Our results suggest that active CMV infection induces an increased infiltration of CD8+ lymphocytes, which could play a role in BA immunopathogenesis. Increased CD56 expression can be a sign of a newly formed bile structure often without lumen, suggesting inhibition of the maturation process in BA.

Analysis of the Nutritional Value of the Diets Presented in Women's and Sports Magazines before and during the COVID-19 Pandemic.

For consumers, among the most important sources of information related to nutrition are popular journals and magazines, including women's and sports, but the diets presented there may lead to unhealthy weight-control behaviors. The aim of the study was to assess the nutritional value of regular and low-calorie diets presented in Polish women's and sports magazines before and during COVID-19 pandemic. The study was based on two popular Polish magazines­one women's magazine and one sports magazine, which regularly present various types of diets. The nutritional value of all the diets published from January 2014 to May 2022 was analyzed. The total number of included single-day menus was n = 119, while for analysis they were stratified based on: type of magazine (published in the women's magazine n = 41 and in the sports magazine n = 78), year of publication (before the COVID-19 pandemic n = 78 and during n = 41), and type of diet (regular n = 61 and low-calorie n = 58). The analysis included the energy value and nutritional value. For the type of magazine, the diets published in the sports magazine were characterized by a higher intake of fat (p < 0.0001 for intake in grams and in % of energy) and calcium (p = 0.0330), whereas the diets published in the women's magazine were characterized by a higher intake of carbohydrates (p = 0.0226 for intake in grams, and p = 0.0002 for intake in % of energy) and fiber (p = 0.0163). For the year of publication, the diets published during the COVID-19 pandemic were characterized by a higher intake of protein (p = 0.0166 for intake in grams), sodium (p = 0.0465), calcium (p < 0.0001), vitamin D (p = 0.0197), vitamin B6 (p = 0.0207), and vitamin B12 (p = 0.0277), whereas the diets published before the COVID-19 pandemic were characterized by a higher intake of carbohydrates (p = 0.0243 for intake in % of energy). For the type of diet, the regular diets were characterized by a higher energy value (p = 0.0020), as well as by a higher intake of fat (p = 0.0162 for intake in grams), carbohydrates (p = 0.0390 for intake in grams), mono- and oligosaccharides (p = 0.0084 for intake in % of energy), fiber (p < 0.0001), magnesium (p = 0.0323), iron (p = 0.0307), and vitamin B6 (p = 0.0204). The nutritional value of the diets presented in the Polish women's and sports magazines was not justified by the type of magazine or type of diet, associated with the target group, which may cause the following of improperly balanced diets. However, the changes in the typical nutritional value of diets presented in the Polish women's and sports magazines during the COVID-19 pandemic were justified by some specific needs for the prevention and treatment of COVID-19.

Cullin-independent recognition of HHARI substrates by a dynamic RBR catalytic domain.

RING-between-RING (RBR) E3 ligases mediate ubiquitin transfer through an obligate E3-ubiquitin thioester intermediate prior to substrate ubiquitination. Although RBRs share a conserved catalytic module, substrate recruitment mechanisms remain enigmatic, and the relevant domains have yet to be identified for any member of the class. Here we characterize the interaction between the auto-inhibited RBR, HHARI (AriH1), and its target protein, 4EHP, using a combination of XL-MS, HDX-MS, NMR, and biochemical studies. The results show that (1) a di-aromatic surface on the catalytic HHARI Rcat domain forms a binding platform for substrates and (2) a phosphomimetic mutation on the auto-inhibitory Ariadne domain of HHARI promotes release and reorientation of Rcat for transthiolation and substrate modification. The findings identify a direct binding interaction between a RING-between-RING ligase and its substrate and suggest a general model for RBR substrate recognition.

Cold Ischemia Time and Graft Fibrosis Are Associated with Autoantibodies after Pediatric Liver Transplantation: A Retrospective Cohort Study of the European Reference Network TransplantChild.

The reported prevalence of autoantibodies (AAB) (ANA, SMA, LKM, SLA) after pediatric liver transplantation (pLTX) varies considerably from 26-75%, but their clinical impact on outcome is uncertain. We aimed to study the prevalence of AAB after pLTX, their association with donor-, transplant-, and recipient-characteristics, and their relation to outcome. In our multicenter retrospective study, we aimed to clarify conflicting results from earlier studies. Six ERN TransplantChild centers reported data on 242 patients, of whom 61% were AAB positive. Prevalence varied across these centers. Independent of the interval between pLTX and AAB analysis, a one-hour increase in CIT resulted in an odds ratio (OR) of 1.37 (95% CI 1.11-1.69) for SMA positivity and an OR of 1.42 (95%CI 1.18-1.72) for ANA positivity. Steroid-free immunosuppression (IS) versus steroid-including IS (OR 5.28; 95% CI 1.45-19.28) was a risk factor for SMA positivity. Liver enzymes were not associated with ANA or SMA positivity. We did not observe an association of rejection activity index with ANA or SMA. However, the liver fibrosis score in follow-up biopsies was associated with ANA titer and donor age. In conclusion, this first multicenter study on AAB after pLTX showed high AAB prevalence and varied widely between centers. Longer CIT and prednisolone-free-IS were associated with AAB positivity, whereas AAB were not indicative of rejection, but instead were associated with graft fibrosis. The detection of AAB may be a marker of liver fibrosis and may be taken into consideration when indications for liver biopsy and immunosuppressive regimes, or reduction of immunosuppression in long-term follow-up, are being discussed. Prospective immunological profiling of pLTX patients, including AAB, is important to further improve our understanding of transplant immunology and silent graft fibrosis.

Successful Liver Transplantation in Two Polish Brothers with Transaldolase Deficiency.

Transaldolase deficiency (TALDO; OMIM 606003) is a rare inborn autosomal-recessive error of the pentose phosphate pathway. It is an early-onset multisystem disease with dysmorphic features, anaemia, coagulopathy, thrombocytopenia, tubulopathy, hepatosplenomegaly and end-stage liver disease. We present a case of two Polish brothers, born to consanguineous parents, with early-onset TALDO. The dominant feature of disease was an early severe liver injury, with subsequent renal tubulopathy. Nodular liver fibrosis developed in the course of the underlying disease. The older brother presented stable liver function, however, he was qualified for deceased donor liver transplantation (DDLT) because of a liver tumour and suspicion of hepatocarcinoma. The boy was transplanted at the age of 14. The younger brother was qualified for DDLT due to end-stage liver disease and transplanted at the age of 11. Currently, both our patients are alive and in a good condition with normal graft function 23 and 20 months after DDLT respectively. Liver transplantation can be a therapeutic option in TALDO and should be considered in patients with coexisting severe chronic and end-stage liver disease. Long term follow-up is necessary to assess the impact of liver transplantation for quality of life, survival time and the course of the disease.

The usefulness of immunohistochemical staining of bile tracts in biliary atresia.

AIM OF THE STUDY: To assess ductular proliferation (DP) and ductal plate malformation (DPM) in biliary atresia (BA) by means of immunohistochemical staining using cytokeratins CK7 and CK19 and neural cell adhesion molecule (NCAM) antibody CD56. MATERIAL AND METHODS: In 10 cases of BA, liver surgical biopsies obtained at the time of hepatoportoenterostomy were stained with H&E, PAS, Gomori and Azan methods. Immunohistochemical technique was used to outline bile ducts, ductular reaction, reactive bile duct/ductules and DPM by CK7, CK19 and NCAM antibody CD56. RESULTS: We found fibrosis, bile stasis and mild inflammation in all cases. In the routine staining DP was not seen in 3 cases. The immunohistochemical staining by means of CK19 was helpful in the detection of DP, and allowed it to be demonstrated in all cases. The biliary epithelial cell markers for CD56, CK7, CK19 were used for demonstration of bile duct cell but not hepatocyte alterations in the structure of intrahepatic biliary ducts and different stages of maturation. CD56 as a marker of immature bile ducts was expressed on biliary epithelium of bile ducts and bizarre forms of DPM in 6 cases. The positive expression of CD56 corresponded to the co-localization of CK19 of DPM, but not CK7, to the ductular reaction at the limiting plate of portal tracts. CD7, considered as a marker of DP, also stained ductal hepatocytes and multipotential oval cells, and was a marker of DPM in 3 cases. CONCLUSIONS: Use of CK7, CK19 and CD56 is helpful in BA diagnosis and allows differentiation of the stage of developing bile duct cells according to the expression pattern.

Who with whom: functional coordination of E2 enzymes by RING E3 ligases during poly-ubiquitylation.

Protein modification with poly-ubiquitin chains is a crucial process involved in a myriad of cellular pathways. Chain synthesis requires two steps: substrate modification with ubiquitin (priming) followed by repetitive ubiquitin-to-ubiquitin attachment (elongation). RING-type E3 ligases catalyze both reactions in collaboration with specific priming and elongating E2 enzymes. We provide kinetic insight into poly-ubiquitylation during protein quality control by showing that priming is the rate-determining step in protein degradation as directed by the yeast ERAD RING E3 ligases, Hrd1 and Doa10. Doa10 cooperates with the dedicated priming E2, Ubc6, while both E3s use Ubc7 for elongation. Here, we provide direct evidence that Hrd1 uses Ubc7 also for priming. We found that Ubc6 has an unusually high basal activity that does not require strong stimulation from an E3. Doa10 exploits this property to pair with Ubc6 over Ubc7 during priming. Our work not only illuminates the mechanisms of specific E2/E3 interplay in ERAD, but also offers a basis to understand how RING E3s may have properties that are tailored to pair with their preferred E2s.

Isoxazole-containing 5' mRNA cap analogues as inhibitors of the translation initiation process.

Herein we describe a synthesis of new isoxazole-containing 5' mRNA cap analogues via a cycloaddition reaction. The obtained analogues show a capability to inhibit cap-dependent translation in vitro and are characterized by a new binding mode in which an isoxazolic ring, instead of guanine, is involved in the stacking effect. Our study provides valuable information toward designing new compounds that can be potentially used as anticancer therapeutics.

Mechanisms of Small Heat Shock Proteins.

Small heat shock proteins (sHSPs) are ATP-independent chaperones that delay formation of harmful protein aggregates. sHSPs' role in protein homeostasis has been appreciated for decades, but their mechanisms of action remain poorly understood. This gap in understanding is largely a consequence of sHSP properties that make them recalcitrant to detailed study. Multiple stress-associated conditions including pH acidosis, oxidation, and unusual availability of metal ions, as well as reversible stress-induced phosphorylation can modulate sHSP chaperone activity. Investigations of sHSPs reveal that sHSPs can engage in transient or long-lived interactions with client proteins depending on solution conditions and sHSP or client identity. Recent advances in the field highlight both the diversity of function within the sHSP family and the exquisite sensitivity of individual sHSPs to cellular and experimental conditions. Here, we will present and highlight current understanding, recent progress, and future challenges.

A pH-dependent switch promotes ß-synuclein fibril formation via glutamate residues.

α-Synuclein (αS) is the primary protein associated with Parkinson's disease, and it undergoes aggregation from its intrinsically disordered monomeric form to a cross-ß fibrillar form. The closely related homolog ß-synuclein (ßS) is essentially fibril-resistant under cytoplasmic physiological conditions. Toxic gain-of-function by ßS has been linked to dysfunction, but the aggregation behavior of ßS under altered pH is not well-understood. In this work, we compare fibril formation of αS and ßS at pH 7.3 and mildly acidic pH 5.8, and we demonstrate that pH serves as an on/off switch for ßS fibrillation. Using αS/ßS domain-swapped chimera constructs and single residue substitutions in ßS, we localized the switch to acidic residues in the N-terminal and non-amyloid component domains of ßS. Computational models of ßS fibril structures indicate that key glutamate residues (Glu-31 and Glu-61) in these domains may be sites of pH-sensitive interactions, and variants E31A and E61A show dramatically altered pH sensitivity for fibril formation supporting the importance of these charged side chains in fibril formation of ßS. Our results demonstrate that relatively small changes in pH, which occur frequently in the cytoplasm and in secretory pathways, may induce the formation of ßS fibrils and suggest a complex role for ßS in synuclein cellular homeostasis and Parkinson's disease.

The loss of inhibitory C-terminal conformations in disease associated P123H ß-synuclein.

ß-synuclein (ßS) is a homologue of α-synuclein (αS), the major protein component of Lewy bodies in patients with Parkinson's disease. In contrast to αS, ßS does not form fibrils, mitigates αS toxicity in vivo and inhibits αS fibril formation in vitro. Previously a missense mutation of ßS, P123H, was identified in patients with Dementia with Lewy Body disease. The single P123H mutation at the C-terminus of ßS is able to convert ßS from a nontoxic to a toxic protein that is also able to accelerate formation of inclusions when it is in the presence of αS in vivo. To elucidate the molecular mechanisms of these processes, we compare the conformational properties of the monomer forms of αS, ßS and P123H-ßS, and the effects on fibril formation of coincubation of αS with ßS, and with P123H-ßS. NMR residual dipolar couplings and secondary structure propensities show that the P123H mutation of ßS renders it more flexible C-terminal to the mutation site and more αS-like. In vitro Thioflavin T fluorescence experiments show that P123H-ßS accelerates αS fibril formation upon coincubation, as opposed to wild type ßS that acts as an inhibitor of αS aggregation. When P123H-ßS becomes more αS-like it is unable to perform the protective function of ßS, which suggests that the extended polyproline II motif of ßS in the C-terminus is critical to its nontoxic nature and to inhibition of αS upon coincubation. These studies may provide a basis for understanding which regions to target for therapeutic intervention in Parkinson's disease.

Intermolecular Paramagnetic Relaxation Enhancement (PRE) Studies of Transient Complexes in Intrinsically Disordered Proteins.

NMR interchain paramagnetic relaxation enhancement (PRE) techniques are a very powerful approach for detecting transient interchain interactions between intrinsically disordered proteins. These experiments, requiring a mixed sample containing a 1:1 ratio of isotope-labeled (15)N protein and natural abundance (14)N protein with a paramagnetic spin label, provide data that is limited to interchain interactions only. Application of these experiments to weakly associated transient species such as those that are present in the very early stages of self-assembly processes will aid our understanding of protein aggregation or fibril formation processes.

Unveiling transient protein-protein interactions that modulate inhibition of alpha-synuclein aggregation by beta-synuclein, a pre-synaptic protein that co-localizes with alpha-synuclein.

Pathology in Parkinson's disease is linked to self-association of α-Synuclein (αS) into pathogenic oligomeric species and highly ordered amyloid fibrils. Developing effective therapeutic strategies against this debilitating disease is critical and ßS, a pre-synaptic protein that co-localizes with αS, can act as an inhibitor of αS assembly. Despite the potential importance of ßS as an inhibitor of αS, the nature, location and specificity of the molecular interactions between these two proteins is unknown. Here we use NMR paramagnetic relaxation enhancement experiments, to demonstrate that ßS interacts directly with αS in a transient dimer complex with high specificity and weak affinity. Inhibition of αS by ßS arises from transient αS/ßS heterodimer species that exist primarily in head- to- tail configurations while αS aggregation arises from a more heterogeneous and weaker range of transient interactions that include both head-to-head and head-to-tail configurations. Our results highlight that intrinsically disordered proteins can interact directly with one another at low affinity and that the transient interactions that drive inhibition versus aggregation are distinct by virtue of their plasticity and specificity.

Mechanistic insight into the relationship between N-terminal acetylation of α-synuclein and fibril formation rates by NMR and fluorescence.

Aggregation of α-synuclein (αSyn), the primary protein component in Lewy body inclusions of patients with Parkinson's disease, arises when the normally soluble intrinsically disordered protein converts to amyloid fibrils. In this work, we provide a mechanistic view of the role of N-terminal acetylation on fibrillation by first establishing a quantitative relationship between monomer secondary structural propensity and fibril assembly kinetics, and secondly by demonstrating in the N-terminal acetylated form of the early onset A53T mutation, that N-terminal transient helices formed and/or inhibited by N-terminal acetylation modulate the fibril assembly rates. Using NMR chemical shifts and fluorescence experiments, we report that secondary structural propensity in residues 5-8, 14-31, and 50-57 are highly correlated to fibril growth rate. A four-way comparison of secondary structure propensity and fibril growth rates of N-terminally acetylated A53T and WT αSyn with non-acetylated A53T and WT αSyn present novel mechanistic insight into the role of N-terminal acetylation in amyloid fibril formation. We show that N-terminal acetylation inhibits the formation of the "fibrillation promoting" transient helix at residues 14-31 resulting from the A53T mutation in the non-acetylated variant and supports the formation of the "fibrillation inhibiting" transient helix in residues 1-12 thereby resulting in slower fibrillation rates relative to the previously studied non-acetylated A53T variant. Our results highlight the critical interplay of the region-specific transient secondary structure of the N-terminal region with fibrillation, and the inhibitory role of the N-terminal acetyl group in fibril formation.

Exploring the accessible conformations of N-terminal acetylated α-synuclein.

Alpha synuclein (αsyn) fibrils are found in the Lewy Bodies of patients with Parkinson's disease (PD). The aggregation of the αsyn monomer to soluble oligomers and insoluble fibril aggregates is believed to be one of the causes of PD. Recently, the view of the native state of αsyn as a monomeric ensemble was challenged by a report suggesting that αsyn exists in its native state as a helical tetramer. This review reports on our current understanding of αsyn within the context of these recent developments and describes the work performed by a number of groups to address the monomer/tetramer debate. A number of in depth studies have subsequently shown that both non-acetylated and acetylated αsyn purified under mild conditions are primarily monomer. A description of the accessible states of acetylated αsyn monomer and the ability of αsyn to self-associate is explored.