- by Lapcinski, I. P., Petersen, A. J., Ashe, K. H., Liu, P.The amyloid cascade hypothesis posits that {beta}-amyloid (A{beta}) oligomers (A{beta}o) play a key role in the pathogenesis of Alzheimer's disease (AD). A{beta}o are believed to contribute to dementia in AD, and more than a dozen have been identified. While some oligomers are associated with amyloid plaques, others–such as A{beta}*56–are not. It remains unclear whether these plaque-independent oligomers contribute to dementia. A{beta}*56 is a non-fibrillar, sodium dodecyl sulfate-stable, brain-derived type of A{beta}o that impairs memory in mice. We recently confirmed and […]
- by Warrick, J. E., Attili, D., van Eeuwen, T., Hoffmann-Weitsman, S. E., Forsyth, N. C., Barmada, S. J., Kearse, M. G.The loss and mutation of Topoisomerase 3{beta} (TOP3B), the only known eukaryotic topoisomerase with the ability to catalyze RNA strand passage reactions, is linked to schizophrenia, autism, and intellectual disability. Uniquely, TOP3B primarily localizes to the cytoplasm and has been shown to regulate mRNA translation and stability of a subset of transcripts. Three neurological disease-linked de novo TOP3B point mutations outside of the active site have been identified but their impact on TOP3B activity in cells remains poorly understood. Upon […]
- by Shah, T., Fitzpatrick, J. A., Orsburn, B. C.Nearly all methods of mass spectrometry-based proteomics rely on knowing the proteome of the species. In less studied organisms without annotated genomes, it can seem impossible to perform proteomic analysis. In this study we sought to answer the question – does enough information exist to do proteomics on any organism we want? As a case study we started with material available due to an infestation of a home with black widow spiders. Thanks to the recent publication of an annotated […]
- by D'Anna, C., Di Sano, C., Li Petri, G., Angellotti, G., Ciriminna, R., Pagliaro, M.In vitro investigations of citrus IntegroPectin bioconjugates obtained through acoustic cavitation in water of different citrus fruit (lemon, red orange, and sweet orange) processing waste revealed the conjugate's ability to inhibit the migratory features of Caco-2 colon cancer and MCF-7 breast cancer cells. All tested pectins substantially reduced cell migration of both tumor cell lines already at 0.5 and 1.0 mg/mL concentration. Dissolved in aqueous phase, furthermore, red orange and lemon IntegroPec-tin phytocomplexes at 5 and 10 mg/mL load reduced […]
- by Zhao, H., Li, X., Yao, X., Zhang, S., Bao, Y., Lu, W., Xing, M., Wang, X., Wang, X., Zhao, Y., Chu, Q., Lu, X.Discovery of cyclic peptide hits using DNA-encoded libraries (DELs) has recently been extensively researched, with significant efforts directed toward developing DEL-compatible macrocyclization methods. To investigate how different cyclic linkers influence DEL selection outcomes, we constructed eight distinct sub-libraries and screened them against two protein targets, MDM2 and GIT1, resulting in two representative yet contrasting scenarios. Validation studies for MDM2 revealed that structural similarity patterns observed across multiple sub-libraries could enhance confidence in the authenticity of identified hits. Notably, cmp-10 demonstrated […]
- by Miller, S. T., Henzler-Wildman, K. A., Raman, S.Multidrug efflux pumps are dynamic molecular machines that drive antibiotic resistance by harnessing ion gradients to export chemically diverse substrates. Despite their clinical importance, the molecular principles underlying multidrug promiscuity and energy efficiency remain poorly understood. Using multiparametric deep mutational scanning across eight substrates and two energy conditions, we deconvolute the contributions of substrate recognition, energetic coupling, and protein stability, providing an integrated, high-resolution view of multidrug transport. We find that substrate specificity arises from a distributed network of residues […]
- by Kumar, R., Sykes, D. J., Band, V. I., Schaller, M. L., Patel, R., Vitvitsky, V., Sajjakulnukit, P., Singhal, R., Wong, H. K. A., Hourigan, S. K., Ichinose, F., Lyssiotis, C. A., Shah, Y. M., Banerjee, R.The host-microbiome interface is rich in metabolite exchanges and exquisitely sensitive to diet. Hydrogen sulfide (H2S) is present at high concentrations at this interface, and is a product of both microbial and host metabolism. The mitochondrial enzyme, sulfide quinone oxidoreductase (SQOR), couples H2S detoxification to oxidative phosphorylation; its inherited deficiency presents as Leigh disease. Since an estimated two thirds of systemic H2S metabolism originates in gut, it raises questions as to whether impaired sulfide clearance in this compartment contributes to […]
- by Violante, S., Kyaw, A., Kouatli, L., Paladugu, K., Apostolakis, L., Jenks, M., Johnson, A., Sheldon, R., Schilmiller, A., Visconti, P., Cross, J., Levin, L., Buck, J., Balbach, M.Prior to ejaculation, sperm are stored in the epididymis in a resting metabolic state. Upon ejaculation, sperm must alter their metabolism to generate the energy needed to support the motility and maturation process known as capacitation to reach and fertilize the oocyte. How sperm regulate the capacitation-induced increase in carbon flux is unknown. Here, we use 13C stable isotope labeling to follow glucose metabolism through sperm central carbon metabolic network before and after sperm activation. We identify regulatory steps which […]
- by Wesslowski, J., Safi, S., Rottmann, M., Rothley, M., Davidson, G.Upon engagement of one of the 19 secreted Wnt signalling proteins with one of the 10 Frizzled transmembrane Wnt receptors (FZD1-10), a wide variety of cellular Wnt signalling responses can be elicited, the selectivity of which depends on: 1) the specific Wnt-FZD pairing, 2) the participation of Wnt co-receptors, and 3) the cellular context. Co-receptors play a pivotal role in guiding the specificity of Wnt signaling, most notably between {beta}-catenin dependent and independent pathways, where co-receptors such as LRP5/6 and […]
- by Chagas, R. S., Marana, S. R.The mechanisms of reversible inhibitors with a single binding site on enzymes are usually divided into basic groups: linear and hyperbolic, also called partial. Each of them subdivided into types: competitive, non-competitive and mixed. These six mechanisms are often considered separate identities. Here, prompted by the characterization of the inhibition of the wild-type and mutant {beta}-glucosidase Sf{beta}gly by Imidazole and Tris (2-amino-2-(hydroxymethyl)-1,3-propanediol) we developed a unifying enzyme kinetic model that integrates these six basic inhibition mechanism onto a single one. […]
- by Chaturvedi, J., Zhang, F., Zhang, C., Badhe, S., Xiang, Y., Deng, J.Human SAMD9 and SAMD9L (collectively SAMD9/9L) are large cytoplasmic proteins with antiviral and antiproliferative activities, recently shown to regulate protein synthesis by specifically cleaving phenylalanine tRNA (tRNAPhe). The enzymatic activity of human SAMD9 (hSAMD9) resides within its N-terminal tRNase domain, which depends on three essential basic residues for tRNA binding and biological activity. While these residues are highly conserved across mammalian SAMD9/9L, lagomorph SAMD9 orthologs uniquely harbor a charge-reversal acidic residue at one of three sites, a change known to […]
- by Chatterjee, D., Dederer, V., Nguyen, L. V., Wendel, M., Abdul Azeez, K. R., Mahesula, S., Stengel, F., Reck-Peterson, S., Mathea, S.The Rab GTPase switch 2 region is a hotspot for post-translational modifications. Its phosphorylation can determine whether individuals develop Parkinson's disease or not. Other modifications of the same region are catalysed by enzymes from bacterial pathogens when they infect human cells. Here, we profiled a set of kinases including LRRK1, LRRK2, DYRK1A, MST1, and TBK1 for their capability of phosphorylating Rab GTPases. We identified several novel kinase:Rab pairs, such as LRRK1:Rab43 and TBK1:Rab29. Further, we comprehensively assessed what makes a […]
- by Ahern, W., Yim, J., Tischer, D., Salike, S., Woodbury, S., Kim, D., Kalvet, I., Kipnis, Y., Coventry, B., Altae-Tran, H., Bauer, M., Barzilay, R., Jaakkola, T., Krishna, R., Baker, D. A.De novo enzyme design starts from ideal active site descriptions consisting of constellations of catalytic residue functional groups around reaction transition state(s), and seeks to generate protein structures that can accurately hold the site in place. Highly active enzymes have been designed starting from such descriptions using the generative AI method RFdiffusion, but there are two current methodological limitations. First, the geometry of the active site can only be specified at the residue level, so for each catalytic residue functional […]
- by Noerremark, M. F., Petersen, R., Ruppert, P. M. M., Doktor, T. K., Nielsen, R., Kappel, J. F., Larsen, S., Kornfeld, J.-W., Mandrup, S., Andresen, B. S., Havelund, J. F., Neess, D., Faergeman, N. J.Acyl-CoA binding protein (ACBP) plays a vital role in lipid metabolism by mediating the intracellular flux and utilization of long-chain acyl-CoAs. In this study we generated brown- and white adipose tissue specific knockout mice (Adipoq-Acbp-/-) and brown adipose tissue specific knockout mice (Ucp1-Acbp-/-) to investigate the role of ACBP in adipose tissue function. Here we demonstrate that loss of ACBP does not affect body weight, fat and lean mass, food intake and systemic energy expenditure, even under cold stress. Transcriptomic […]
- by Massie, F., MacKenzie, A., Pandor, S., Cremonini, M. A., Moses, T.Metabolomics is the comprehensive study of small molecules that provides a snapshot of an organism's physiological state. Reflecting phenotype more closely than genes or proteins, metabolites reveal changes linked to diseases, mutations, genetic interventions, and environmental stimuli. Recent technological advancements in metabolomics analysis through the application of ion mobility mass spectrometry have enhanced the comprehensive analysis of complex metabolic mixtures. However, pre-analytical bottlenecks in throughput and consistent extraction persist. We developed an automated, sample-agnostic metabolite extraction workflow for diverse liquid […]
- by Perrard, J., Gao, K., Ring, K., Smith, S.AbstractADP-ribosylation is a key post-translational modification that impacts diverse cellular pathways. The modification can occur as mono-ADP-ribose (MAR) or be extended into poly-ADP- ribose (PAR). Tankyrase, a PAR transferase, adds PAR to itself and other proteins to influence their function and stability by tagging them for proteasomal degradation via the PAR-binding E3 ligase RNF146. This degradation can be counteracted by RING-UIM E3 ligases RNF114 and RNF166, though the process is unclear. Here we identify a new mechanism that can regulate […]
- by Chakraborti, S., Sistla, J. S.Mycobacterium tuberculosis (Mtb), the pathogenic bacterium that causes tuberculosis, has developed its own ways of evading defense mechanisms to counteract the lethal effects of reactive oxygen species (ROS) generated within the host macrophages during infection. The melH gene present in Mtb and Mycobacterium marinum (Mm) plays an important role to reduce ROS generated during infection. The melH gene encodes for an epoxide hydrolase. Bioinformatics data suggests that encoded enzyme utilizes lipid substrates for its function. Initially, we used a lipid […]
- by Astter, Y., Davis, D., Treco, E., Shrestha, P., Stream, A., Haque, M., Mulugeta, N., Yarchoan, R.We previously reported that Kaposi sarcoma-associated herpesvirus (KSHV) latency-associated nuclear antigen (LANA) acts as a pseudo-substrate for caspases-1 and 3, thereby interfering with their inflammatory and apoptotic activity, respectively. To determine if other KSHV proteins undergo caspase cleavage, we screened the KSHV proteome for potential caspase cleavage sites. Using SitePrediction (SP), 30 KSHV proteins with potential caspase-cleavage sites were identified. Among those with highest SP score was an early lytic protein, K5. Treatment of BJAB K5-FLAG cells with ?Fas, an […]
- by Kumari, A., Enache, T., Craggs, T. D., Pata, J. D., Lahiri, I.Plasmodium falciparum is a unicellular eukaryotic pathogen responsible for the majority of malaria-related fatalities. Plasmodium belongs to the phylum Apicomplexa and like most members of this phylum, contains a non-photosynthetic plastid called the apicoplast. The apicoplast has its own genome, which is replicated by a dedicated apicoplast replisome. Unlike other cellular replisomes, the apicoplast replisome uses a single DNA polymerase (apPol) for copying the apicoplast DNA. Being the only DNA polymerase in the apicoplast, apPol is expected to multitask, catalysing […]
- by Nemkov, T., Stauffer, E., Cendali, F., Stephenson, D., Nader, E., Robert, M., Skinner, S., Dzieciatkowska, M., Hansen, K. C., Robach, P., Millet, G., Connes, P., D'Alessandro, A.Ultra-endurance exercise places extreme physiological demands on oxygen transport, yet its impact on red blood cells (RBCs) remains underexplored. We conducted a multi-omics analysis of plasma and RBCs from endurance athletes before and after a 40-km trail race (MCC) and a 171-km ultramarathon (UTMB(R)). Ultra-running led to oxidative stress, metabolic shifts, and inflammation-driven RBC damage, including increased acylcarnitines, kynurenine accumulation, oxidative lipid and protein modifications, reduced RBC deformability, enhanced microparticle release, and decreased hematocrit – hallmarks of accelerated RBC aging […]
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