-
Human Pannexin 1 Channel is NOT Phosphorylated by Src Tyrosine Kinase at Tyr199 and Tyr309 bioRxiv. Biochem. Pub Date : 2024-03-18 Zheng Ruan, Juan Du, Wei Lu, Junuk Lee, Yangyang Li
Protein phosphorylation is one of the major molecular mechanisms regulating protein activity and function throughout the cell. Pannexin 1 (PANX1) is a large-pore channel permeable to ATP and other cellular metabolites. Its tyrosine phosphorylation and subsequent activation have been found to play critical roles in diverse cellular conditions, including neuronal cell death, acute inflammation, and smooth
-
Naa80 is required for actin N-terminal acetylation and normal hearing in zebrafish bioRxiv. Biochem. Pub Date : 2024-03-17 Rasmus Ree, Sheng-Jia Lin, Lars Ole Sti Dahl, Kevin Huang, Cassidy Petree, Gaurav K Varshney, Thomas Arnesen
Actin is a key component of the cytoskeleton of eukaryotic cells and is involved in numerous cellular functions. In animal cells, actins are uniquely N-terminally processed by a dedicated enzyme machinery to generate their mature acidic and acetylated forms. The final step of this maturation process involves N-terminal acetylation, a reaction catalyzed by NAA80 in humans. In human cell lines, N-terminal
-
Spec2Class: Accurate Prediction of Plant Secondary Metabolite Class using Deep Learning bioRxiv. Biochem. Pub Date : 2024-03-17 Victoria Poltorak, Nir Shachaf, Asaph Aharoni, David Zeevi
Mass spectrometry (MS)-based data is commonly used in studying metabolism and natural products, but typically requires domain-specific skill and experience to analyze. Existing computational tools for non-targeted metabolite analysis (i.e., metabolomics) mostly rely on comparison to reference MS spectral libraries for metabolite identification, limiting the annotation of metabolites for which reference
-
Orthogonal IMiD-Degron Pairs Induce Selective Protein Degradation in Cells bioRxiv. Biochem. Pub Date : 2024-03-16 Patrick J Brennan, Rebecca E Saunders, Mary Spanou, Marta Serafini, Liang Sun, Guillaume P Heger, Agnieszka Konopacka, Ryan D Beveridge, Laurie Gordon, Shenaz B Bunally, Aurore Saudemont, Andrew B Benowitz, Carlos Martinez-Fleites, Markus A Queisser, Heeseon An, Charlotte M Deane, Michael M Hann, Lewis L Brayshaw, Stuart J Conway
Immunomodulatory imide drugs (IMiDs) including thalidomide, lenalidomide, and pomalidomide, can be used to induce degradation of a protein of interest that is fused to a short zinc finger (ZF) degron motif. These IMiDs, however, also induce degradation of endogenous neosubstrates, including IKZF1 and IKZF3. To improve degradation selectivity, we took a bump-and-hole approach to design and screen bumped
-
Protein disulfide isomerase disassembles stress granules and blocks cytoplasmic aggregation of TDP-43 in ALS bioRxiv. Biochem. Pub Date : 2024-03-16 Jia-Qi Liu, Hao Liu, Yuying Li, Xiangyi Liu, Li-Qiang Wang, Kan Wang, Zhaofei Yang, Qi Fu, Xiaojiao Xu, Jie Chen, Yingshuang Zhang, Jun Zhou, Weidong Le, Mengchao Cui, Yi Liang
Cytoplasmic aggregation of the transactive response DNA-binding protein-43 (TDP-43) in neurons, a pathological feature common to amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration, has been found in some Alzheimer's patients. Protein disulfide isomerase (PDI) functions as both an enzyme and a molecular chaperone to correct or eliminate misfolded proteins under pathological conditions
-
Structural basis for allosteric regulation of human phosphofructokinase-1 bioRxiv. Biochem. Pub Date : 2024-03-16 Eric M Lynch, Heather Hansen, Lauren E Salay, Madison Cooper, Stepan Timr, Justin M Kollman, Bradley A Webb
Phosphofructokinase-1 (PFK1) catalyzes the rate-limiting step of glycolysis, committing glucose to conversion into cellular energy. PFK1 is highly regulated to respond to the changing energy needs of the cell. In bacteria, the structural basis of PFK1 regulation is a textbook example of allostery; molecular signals of low and high cellular energy promote transition between an active R-state and inactive
-
Mechanistic principles of hydrogen evolution in the membrane-bound hydrogenase bioRxiv. Biochem. Pub Date : 2024-03-16 Abhishek Sirohiwal, Ana P. Gamiz-Hernandez, Ville R. I. Kaila
The membrane-bound hydrogenase (Mbh) from Pyrococcus furiosus is an archaeal member of the Complex I superfamily. It catalyzes the reduction of protons to H2 gas powered by a [NiFe] active site and transduces the free energy into proton pumping and Na+/H+-exchange across the membrane. Despite recent structural advances, the mechanistic principles of H2 catalysis and ion transport in Mbh remain elusive
-
Loss of Lamin A leads to the nuclear translocation of AGO2 and compromised RNA interference bioRxiv. Biochem. Pub Date : 2024-03-16 Vivian Lobo, Iwona Nowak, Carola Fernandez, Ana Iris Correa Muler, Jakub O Westholm, Hsiang-Chi Huang, Ivo Fabrik, Hang Thuy Huynh, Evgeniia Shcherbinina, Melis Poyraz, Anetta Hartlova, Daniel Benhalevy, Davide Angeletti, Aishe A Sarshad
In mammals, RNA interference (RNAi) was historically studied as a cytoplasmic event; however, in the last decade, a growing number of reports convincingly show the nuclear localization of the Argonaute (AGO) proteins. Nevertheless, the extent of nuclear RNAi and its implication in biological mechanisms remain to be elucidated. We found that reduced Lamin A levels significantly induce nuclear influx
-
Elongation capacity of polyunsaturated fatty acids in the annelid Platynereis dumerilii bioRxiv. Biochem. Pub Date : 2024-03-16 Marc Ramos-Llorens, Khalida Bainour, Leonie Adelmann, Francisco Hontoria, Juan C Navarro, Florian Raible, Oscar Monroig
In animals, elongation of very long-chain fatty acid (Elovl) proteins play pivotal functions in the biosynthesis of fatty acids, including the physiologically essential long-chain polyunsaturated fatty acids (LC-PUFA). Polychaetes have important roles in marine ecosystems, contributing not only to nutrient recycling but also exhibiting a distinctive capacity for biosynthesising LC-PUFA, as emphasised
-
Photoactivatable Blue Fluorescent Protein bioRxiv. Biochem. Pub Date : 2024-03-16 Paul Gaytan, Abigail Roldan-Salgado
Photoactivable and photoswitchable fluorescent proteins (FPs) are sophisticated molecular tools that in combination with super-resolution microscopy are helping to elucidate many biological processes. Through the Y66H mutation in the chromophore of the violet fluorescent protein sumireF we created the first photoactivatable blue fluorescent protein (PA[ndash]BFP). This protein is rapidly activated
-
Welding PROxAb Shuttles: A modular approach for generating bispecific antibodies via site-specific protein-protein conjugation bioRxiv. Biochem. Pub Date : 2024-03-15 Tanja Lehmann, Hendrik Schneider, Jason Tonillo, Jennifer Schanz, Daniel Schwarz, Christian Schroeter, Harald Kolmar, Stefan Hecht, Jan Anderl, Nicolas Rasche, Marcel Rieker, Stephan Dickgiesser
Targeted protein degradation is an innovative therapeutic strategy to selectively eliminate disease-causing proteins. Exemplified by proteolysis-targeting chimeras (PROTACs), it has shown promise in overcoming drug resistance and targeting previously undruggable proteins. However, PROTACs face challenges such as low oral bioavailability and limited selectivity. The recently published PROxAb Shuttle
-
Phase separation of polyubiquitinated proteins in UBQLN2 condensates controls substrate fate bioRxiv. Biochem. Pub Date : 2024-03-15 Isabella M Valentino, Jeniffer G Llivicota-Guaman, Thuy P Dao, Erin O Mulvey, Andrew M Lehman, Sarasi K. K. Galagedera, Erica L Mallon, Carlos A Castañeda, Daniel A Kraut
Ubiquitination is one of the most common post-translational modifications in eukaryotic cells. Depending on the architecture of polyubiquitin chains, substrate proteins can meet different cellular fates, but our understanding of how chain linkage controls protein fate remains limited. UBL-UBA shuttle proteins, such as UBQLN2, bind to ubiquitinated proteins and to the proteasome or other protein quality
-
Undruggable oncoproteins cMyc and NMyc bind to mediator of transcription with superior high affinity bioRxiv. Biochem. Pub Date : 2024-03-15 Andrea Knight, Josef Houser, Tomas Otasevic, Vilem Juran, Vaclav Vybihal, Martin Smrcka, Dr martin
The overexpression of MYC genes is frequently found in many human cancers including adult and pediatric malignant brain tumors. Targeting MYC genes continues to be challenging due to their undruggable nature. The nine-amino-acid activation domain (9aaTAD) has been identified using our prediction algorithm in all four Yamanaka factors including c-Myc and showed to activate transcription as short peptides
-
14-3-3 binding regulates Tau assembly and microtubule association. bioRxiv. Biochem. Pub Date : 2024-03-15 Janine Hochmair, Maxime C. M. van den Oetelaar, Lisa Diez, Lenne J. M. Lemmens, Renata Ponce, Leandre Ravatt, Maximilian W. Franck, Ekaterina Semenova, Satabdee Mohapatra, Christian Ottmann Ottmann, Luc Brunsveld, Susanne Wegmann
14-3-3 proteins are among the most abundant proteins in the brain and bind a large number of proteins in a phosphorylation dependent manner, including proteins prone to aggregate in neurodegenerative diseases. Binding of 14-3-3 is reported to facilitate the function, promote solubility, and coordinate the assembly of client proteins. For the microtubule-associated protein Tau, a neuronal client of
-
Biochemical analysis of the endoribonuclease activity of the human mitochondrial topoisomerase 1 bioRxiv. Biochem. Pub Date : 2024-03-15 Cyrielle P.J. Bader, Erika Kasho, Josefin M.E. Forslund, Malgorzata Wessels, Paulina H Wanrooij
The incorporation of ribonucleotides (rNMPs) into the nuclear genome leads to severe genomic instability, including strand breaks and short 2-5 bp deletions at repetitive sequences. Curiously, the detrimental effects of rNMPs are not observed for the human mitochondrial genome (mtDNA) that typically contains several rNMPs per molecule. Given that the nuclear genome instability phenotype is dependent
-
Functional exploration of in vivo and in vitro lignocellulose-fed rumen bacterial microbiomes reveals novel enzymes involved in polysaccharide breakdown bioRxiv. Biochem. Pub Date : 2024-03-15 Lisa Ufarte, Elisabeth Laville, Adele Lazuka, Sophie Lajus, Emna Bouhajja, Davide Cecchini, Angeline Rizzo, Emilie Amblard, Elodie Drula, Vincent Lombard, Nicolas Terrapon, Bernard Henrissat, Megane Cleret, Diego P. Morgavi, Claire Dumon, Patrick Robe, Christophe Klopp, Sophie Bozonnet, Guillermina Hernandez-Raquet, Gabrielle Potocki-Veronese
Background: Plant cell walls are the main carbon sources for ruminal bacteria, which have evolved to produce sophisticated multi-functional enzyme cocktails in response to the structural diversity of lignocelulloses. Since a large proportion of ruminal bacteria are not yet cultured, we developed a high-throughput activity-based metagenomic approach to gain insight into this enzymatic diversity. Results:
-
R6G narrows BmrA conformational spectrum for a more efficient use of ATP bioRxiv. Biochem. Pub Date : 2024-03-15 Alexia Gobet, Loick Moissonnier, Eleftherios Zarkadas, Sandrine Magnard, Emmanuel Bettler, Juliette Martin, Raphael Terreux, Guy Schoehn, Cedric Orelle, Jean-Michel Jault, Pierre Falson, vincent Chaptal
Multidrug ABC transporters harness the energy of ATP binding and hydrolysis to change conformation and thereby translocate substrates out of the cell to detoxify them. While this general access mechanism scheme is well accepted, molecular details of this interplay is still elusive. Rhodamine6G binding on a catalytic mutant of the homodimeric multidrug ABC transporter BmrA triggers a cooperative binding
-
Revisiting the activity of two poly(vinyl chloride)- and polyethylene-degrading enzymes bioRxiv. Biochem. Pub Date : 2024-03-15 Anton A. Stepnov, Esteban Lopez-Tavera, Ross Klauer, Clarissa L. Lincoln, Ravindra R. Chowreddy, Gregg T. Beckham, Vincent G.H. Eijsink, Kevin Solomon, Mark Blenner, Gustav Vaaje-Kolstad
Biocatalytic degradation of non-hydrolyzable plastics is a rapidly growing field of research, driven by the global accumulation of waste. Enzymes capable of cleaving the carbon-carbon bonds in synthetic polymers are highly sought-after as they may provide tools for environmentally friendly plastic recycling. Despite some reports of oxidative enzymes acting on non-hydrolyzable plastics, including polyethylene
-
Solvation Free Energy in Governing Equations for DNA Hybridization, Protein–Ligand Binding, and Protein Folding bioRxiv. Biochem. Pub Date : 2024-03-15 Caroline Harmon, Austin Bui, Jasmin M Espejo, Marc Gancayco, Jennifer M Le, Juan Rangel, Daryl K Eggers
This work examines the thermodynamics of model biomolecular interactions using a governing equation that accounts for the participation of bulk water in the balanced reaction. In the first example, the binding affinities of two model DNA duplexes, one of nine and one of ten base pairs in length, are measured and characterized by isothermal titration calorimetry as a function of concentration. The results
-
Allosteric activation of the co-receptor BAK1 by the EFR receptor kinase initiates immune signaling bioRxiv. Biochem. Pub Date : 2024-03-15 Henning Mühlenbeck, Yuko Tsutsui, Mark Lemmon, Kyle W Bender, Cyril Zipfel
Transmembrane signaling by plant receptor kinases (RKs) has long been thought to involve reciprocal trans-phosphorylation of their intracellular kinase domains. The fact that many of these are pseudokinase domains, however, suggests that additional mechanisms must govern RK signaling activation. Non-catalytic (pseudo)kinase signaling mechanisms have been described in metazoans, but information is scarce
-
idh-1 neomorphic mutation confers sensitivity to vitamin B12 via increased dependency on one-carbon metabolism in Caenorhabditis elegans bioRxiv. Biochem. Pub Date : 2024-03-14 Olga Ponomarova, Alyxandra N Starbard, Alexandra Belfi, Amanda V Anderson, Meera V Sundaram, Albertha JM Walhout
The isocitrate dehydrogenase neomorphic mutation (idh-1neo) generates increased levels of cellular D-2-hydroxyglutarate (D-2HG), a proposed oncometabolite. However, the physiological effects of increased D-2HG and whether additional metabolic changes occur in the presence of an idh-1neo mutation are not well understood. We created a C. elegans model to study the effects of the idh-1neo mutation in
-
Polymorphic positions 349 and 725 of the autoimmunity-protective allotype 10 of ER aminopeptidase 1 are key in determining its unique enzymatic properties bioRxiv. Biochem. Pub Date : 2024-03-14 Galateia Georgaki, Anastasia Mpakali, Myrto Trakada, Athanasios Papakyriakou, Efstratios Stratikos
ER aminopeptidase 1 (ERAP1) is a polymorphic intracellular aminopeptidase with key roles in antigen presentation and adaptive immune responses. ERAP1 allotype 10 is highly protective towards developing some forms of autoimmunity and displays unusual functional properties, including very low activity versus some substrates. To understand the molecular mechanisms that underlie the biology of allotype
-
Bioluminescence Imaging of Potassium Ion Using a Sensory Luciferin and an Engineered Luciferase bioRxiv. Biochem. Pub Date : 2024-03-14 Shengyu Zhao, Ying Xiong, Ranganayakulu Sunnapu, Yiyu Zhang, Xiaodong Tian, Huiwang Ai
Bioluminescent indicators are power tools for studying dynamic biological processes. In this study, we present the generation of novel bioluminescent indicators by modifying the luciferin molecule with an analyte-binding moiety. Specifically, we have successfully developed the first bioluminescent indicator for potassium ions (K+), which are critical electrolytes in biological systems. Our approach
-
Chalkophomycin Biosynthesis Revealing Unique Enzyme Architecture for a Hybrid Nonribosomal Peptide Synthetase and Polyketide Synthase bioRxiv. Biochem. Pub Date : 2024-03-14 Long Yang, Liwei Yi, Bang Gong, Lili Chen, Miao Li, Xiangcheng Zhu, Yanwen Duan, Yong Huang
Chalkophomycin is a novel chalkophore with antibiotic activities isolated from Streptomyces sp. CB00271, while its potential in studying cellular copper homeostasis makes it an important probe and drug lead. The constellation of N-hydroxylpyrrole, 2H-oxazoline, diazeniumdiolate, and methoxypyrrolinone functional groups into one compact molecular architecture capable to coordinate cupric ion draws interest
-
Slippery sequences stall the 26S proteasome at multiple points along the translocation pathway bioRxiv. Biochem. Pub Date : 2024-03-14 Edwn R Ragwan, Faith M Kisker, Amelia R Mornin, Kaya R Weiser, Athena V Lago, Daniel A Kraut
In eukaryotes, the ubiquitin-proteasome system is responsible for intracellular protein degradation. Proteins tagged with ubiquitin are recognized by ubiquitin receptors on the 19S regulatory particle (RP) of the 26S proteasome, unfolded, routed through the translocation channel of the RP, and are then degraded in the 20S core particle (CP). Aromatic paddles on the pore-1 loops of the RP's Rpt subunits
-
Unexpected transformations during pyrroloiminoquinone biosynthesis bioRxiv. Biochem. Pub Date : 2024-03-14 Josseline Ramos Figueroa, Lingyang Zhu, Wilfred van der Donk
Pyrroloiminoquinone containing natural products have long been known for their biological activities. They are derived from tryptophan, but their biosynthetic pathways have remained elusive. Studies on the biosynthetic gene cluster (BGC) that produces the ammosamides revealed that the first step is attachment of Trp to the C-terminus of a scaffold peptide in an ATP and tRNA dependent manner catalyzed
-
Initial amino acid:codon assignments and strength of codon:anticodon binding bioRxiv. Biochem. Pub Date : 2024-03-14 Meng Su, Samuel James Roberts, John D Sutherland
The ribosome brings 3′-aminoacyl-tRNA and 3′-peptidyl-tRNAs together to enable peptidyl transfer by binding them in two major ways. Firstly, their anticodon loops are bound to mRNA, itself anchored at the ribosomal subunit interface, by contiguous anticodon:codon pairing augmented by interactions with the decoding centre of the small ribosomal subunit. Secondly, their acceptor stems are bound by the
-
Chemical modification of hyaluronan oligosaccharides differentially modulates hyaluronan- hyaladherin interactions. bioRxiv. Biochem. Pub Date : 2024-03-14 Rebecca J Dodd, Charles D Blundell, Benedict M Sattelle, Jan J Enghild, Caroline M Milner, Anthony J Day
The glycosaminoglycan hyaluronan (HA) is a ubiquitous, non-sulphated polysaccharide with diverse biological roles mediated through its interactions with HA-binding proteins (HABPs). Most HABPs belong to the Link module superfamily, including the major HA receptor, CD44, and secreted protein TSG-6, which catalyzes the covalent transfer of Heavy Chains (HC) from inter-a-inhibitor (IαI) onto HA. The structures
-
SARS-CoV-2 methyltransferase nsp10-16 in complex with natural and drug-like purine analogs for guiding structure-based drug discovery bioRxiv. Biochem. Pub Date : 2024-03-13 Viviane Kremling, Sven Falke, Yaiza Fernandez-Garcia, Christiane Ehrt, Antonia Kiene, Bjarne Klopprogge, T. Emilie S. Scheer, Fabian Barthels, Philipp Middendorf, Sebastian Kuehn, Stephan Guenther, Matthias Rarey, Henry N Chapman, Dominik Oberthuer, Janina Sprenger
Non-structural protein 10 (nsp10) and non-structural protein 16 (nsp16) are part of the RNA synthesis complex, which is crucial for the replication of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Nsp16 exhibits 2-O-methyltransferase activity during viral messenger RNA capping and is active in a heterodimeric complex with enzymatically inactive nsp10. It has been shown that inactivation
-
Structural basis for Retriever-SNX17 assembly and endosomal sorting bioRxiv. Biochem. Pub Date : 2024-03-13 Amika Singla, Daniel J. Boesch, Ho Yee Joyce Fung, Chigozie Ngoka, Avery S. Enriquez, Ran Song, Daniel A. Kramer, Yan Han, Puneet Juneja, Daniel D. Billadeau, Xiaochen Bai, Zhe Chen, Emre E. Turer, Ezra Burstein, Baoyu Chen
During endosomal recycling, Sorting Nexin 17 (SNX17) facilitates the transport of numerous membrane cargo proteins by tethering them to the Retriever complex. Despite its importance, the mechanisms underlying this interaction have remained elusive. Here, we report the structure of the Retriever-SNX17 complex determined using cryogenic electron microscopy (cryo-EM). Our structure reveals that the C-terminal
-
Anti-fungal recombinant psoriasin effectively inhibits Candida albicans growth on denture base bioRxiv. Biochem. Pub Date : 2024-03-13 Lucia Adriana Lifshits, Edward Brohnshtein, May Attias, Yoav Breuer, Adi Cohen, Matan Gabay, Marina Sova, Evgeny Weinberg, Eran Zenziper, Daniel Zvi Bar, Nir Sterer, Maayan Gal
Oral candidiasis leading to denture stomatitis is a fungal infection resulting from unregulated growth and adhesion mainly of Candida albicans onto acrylic denture base. Once the biofilm is formed, it is immune resistant and mainstay treatments involve toxic chemical antifungal agents or mechanical cleaning techniques, both offer limited efficacy. Consequently, there is an urgent need for more effective
-
Differences in Protein Capture by SP3 and SP4 Demonstrate Mechanistic Insights of Proteomics Clean-up Techniques bioRxiv. Biochem. Pub Date : 2024-03-13 Jessica M. Conforti, Amanda M. Ziegler, Charli S. Worth, Adhwaitha M. Nambiar, Jacob T. Bailey, Joseph H. Taube, Elyssia S. Gallagher
The goal of proteomics experiments is to identify proteins to observe changes in cellular processes and diseases. One challenge in proteomics is the removal of contaminants following protein extraction, which can limit protein identification. Single-pot, solid-phase-enhanced sample preparation (SP3) is a clean-up technique in which proteins are captured on carboxylate-modified particles through a proposed
-
A multi-modal image fusion workflow incorporating MALDI imaging mass spectrometry and microscopy for the study of small pharmaceutical compounds bioRxiv. Biochem. Pub Date : 2024-03-13 Zhongling Liang, Yingchan Guo, Abhisheak Sharma, Christopher R McCurdy, Boone M. Prentice
Multi-modal imaging analyses of dosed tissue samples can provide more comprehensive insight into the effects of a therapeutically active compound on a target tissue compared to single-modal imaging. For example, simultaneous spatial mapping of pharmaceutical compounds and endogenous macromolecule receptors is difficult to achieve in a single imaging experiment. Herein, we present a multi-modal workflow
-
Sulfite oxidase deficiency causes persulfidation loss and H2S release bioRxiv. Biochem. Pub Date : 2024-03-13 Chun-Yu Fu, Joshua Benedict Kohl, Filip Liebsch, Davide D`Andrea, Max Mai, Anna Theresa Mellis, Emilia Kouroussis, Tamás Ditrói, José Angel Santamaria-Araujo, Sin Yuin Yeo, Heike Endepols, Michaela Křížkov, Viktor Kožich, Uladzimir Barayeu, Takaaki Akaike, Julia B. Hennermann, Peter Nagy, Milos Filipovic, Günter Schwarz
Sulfite oxidase (SOX) deficiency is a rare inborn error of cysteine metabolism resulting in severe neurological damage. In patients, sulfite accumulates to toxic levels causing a raise in downstream products S-sulfocysteine (SSC), mediating excitotoxicity, and thiosulfate, a catabolic intermediate/product of H2S metabolism. Here, we report a full-body knock-out mouse model for SOX deficiency (SOXD)
-
The chromokinesin Kid forms a homodimer and moves processively along microtubules bioRxiv. Biochem. Pub Date : 2024-03-13 Shinsuke Niwa, Natsuki Furusaki, Tomoki Kita, Kyoko Chiba
During prometaphase in mitosis, chromosomes are pushed toward the spindle equator. The chromokinesin Kid moves chromosomes along spindle microtubules during prometaphase. Kid has long been considered as a monomeric and non-processive motor, different from typical kinesins that use two motor domains to transport cargos. However, this notion raises a question about how Kid transports chromosomes along
-
Development and application of GlycanDIA workflow for glycomic analysis bioRxiv. Biochem. Pub Date : 2024-03-13 Yixuan Xie, Xingyu Liu, Chenfeng Zhao, Siyu Chen, Shunyang Wang, Zongtao Lin, Faith M Robison, Benson M George, Ryan A Flynn, Carlito B Lebrilla, Benjamin A Garcia
Glycans modify protein, lipid, and even RNA molecules to form the regulatory outer coat on cells called the glycocalyx. The changes in glycosylation have been linked to the initiation and progression of many diseases. Thus, while the significance of glycosylation is well established, a lack of accessible methods to characterize glycans has hindered the ability to understand their biological functions
-
PrgE: an OB-fold protein from plasmid pCF10 with striking differences to prototypical bacterial SSBs bioRxiv. Biochem. Pub Date : 2024-03-13 Annika Breidenstein, Anais Lamy, Cyrielle P.J. Bader, Wei-Sheng Sun, Paulina H Wanrooij, Ronnie Per-Arne Berntsson
A major pathway for horizontal gene transfer is the transmission of DNA from donor to recipient cells via plasmid-encoded Type 4 Secretion Systems (T4SS). Many conjugative plasmids encode for a single-stranded DNA-binding protein (SSB) together with their T4SS. Some of these SSBs have been suggested to aid in establishing the plasmid in the recipient cell, but for many their function remains unclear
-
Single Cell MALDI-MS Imaging of Lipids and Proteins in Senescent Fibroblasts bioRxiv. Biochem. Pub Date : 2024-03-13 Emily R. Sekera, Lorena Rosas, Joseph H. Holbrook, Quetzalli D. Angeles, Timur Khaliullin, Mauricio Rojas, Ana L. Mora, Amanda B. Hummon
In this study, we evaluate the lipidomic and proteomic profiles of human lung fibroblasts (hLFs) to interrogate changes occurring due to senescence. To study single cell populations, a comparison of cell adhered onto slides utilizing poly-D-lysine versus centrifugal force deposition was first analyzed to determine whether specific alterations were observed be-tween preparations. The poly-D-lysine approach
-
Chemoproteomic profiling of serine hydrolases reveals the dynamic role of lipases in Phaeodactylum tricornutum bioRxiv. Biochem. Pub Date : 2024-03-13 Achintya Kumar Dolui, Beery Yaakov, Weronika Jasinska, Simon Barak, Yariv Brotman, Inna Khozin-Goldberg
Phaeodactylum tricornutum is a model oleaginous pennate diatom, widely investigated for the accumulation of triacylglycerols (TAG) in lipid droplets during nitrogen (N) starvation. However, lipid droplet breakdown, TAG catabolism, and remobilization upon N replenishment during growth restoration are less studied. Serine hydrolases (SH) constitute a diverse family encompassing proteases, amidases, esterases
-
The conserved membrane-proximal domain of Sbh1/ Sec61β guides signal peptides into the Sec61 channel bioRxiv. Biochem. Pub Date : 2024-03-13 Lalitha Yadhanapudi, Pratiti Bhadra, Guido Barbieri, Martin Jung, Mark Lommel, Volkhard Helms, Karin Romisch
Protein secretion begins with protein translocation through the universally conserved Sec61 channel in the endoplasmic reticulum (ER) membrane. The function of its β-subunit, called Sbh1 in yeast, remains poorly understood. Sbh1/Sec61β has a cytosolic domain consisting of two parts: the N-terminal approximately 40 amino acids are intrinsically unstructured, followed by a conserved membrane proximal
-
Mutational Profiling of SARS-CoV-2 PLpro in human cells reveals requirements for function, structure, and drug escape bioRxiv. Biochem. Pub Date : 2024-03-12 Xinyu Wu, Margareta Go, Julie V. Nguyen, Nathan W. Kuchel, Bernadine G.C. Lu, Kym N. Lowes, Dale J. Calleja, Jeffrey P. Mitchell, Guillaume Lessene, David Komander, Matthew E. Call, Melissa J. Call
SARS-CoV-2, the causative agent of COVID-19, is responsible for the recent global pandemic and remains a major source of mortality. Papain-like protease (PLpro) is a target for SARS-CoV-2 inhibitor development, as it is not only essential for viral replication through cleavage of the viral poly-proteins pp1a and pp1ab, but also has de-ubiquitylation and de-ISGylation activities, which can affect innate
-
SARS-CoV-2 Omicron XBB lineage spike structures, conformations, antigenicity, and receptor recognition bioRxiv. Biochem. Pub Date : 2024-03-12 Qianyi E Zhang, Jared Lindenberger, Ruth Parsons, Bhishem Thakur, Rob Parks, Chan Soo Park, Xiao Huang, Salam Sammour, Katarzyna Janowska, Taylor N Spence, Robert J. Edwards, Mitchell Martin, Wilton B Williams, Sophie Gobeil, David C Montefiori, Bette Korber, Kevin O'Neil Saunders, Barton F Haynes, Barton F. Haynes, Rory Henderson, Priyamvada Acharya
A recombinant lineage of the SARS-CoV-2 Omicron variant, named XBB, appeared in late 2022 and evolved descendants that successively swept local and global populations. XBB lineage members were noted for their improved immune evasion and transmissibility. Here, we determine cryo-EM structures of XBB.1.5, XBB.1.16, EG.5 and EG.5.1 spike (S) ectodomains to reveal reinforced 3-RBD-down receptor inaccessible
-
Metabolism of FAD, FMN and riboflavin (vitamin B2) in the human parasitic blood fluke Schistosoma mansoni bioRxiv. Biochem. Pub Date : 2024-03-12 Akram Da'dara, Catherine Nation, Patrick Skelly
Schistosomiasis is a parasitic disease caused by trematode worms of the genus Schistosoma. The intravascular worms acquire the nutrients necessary for their survival from host blood. Since all animals are auxotrophic for riboflavin (vitamin B2), schistosomes too must import it to survive. Riboflavin is an essential component of the coenzymes flavin mononucleotide (FMN) and flavin adenine dinucleotide
-
Exploring RNA modifications in infectious non-coding circular RNAs bioRxiv. Biochem. Pub Date : 2024-03-12 Pavel Vopalensky, Anton Skriba, Michela Chiumenti, Lucia Duricekova, Anna Simonova, Ondrej Luksan, Francesco Di Serio, Beatriz Navarro, Hana Cahova
Viroids, small circular non-coding RNAs, act as infectious pathogens in higher plants, demonstrating high stability despite consisting solely of naked RNA. Their dependence of replication on host machinery poses the question of whether RNA modifications play a role in viroid biology. Here, we explore RNA modifications in the avocado sunblotch viroid (ASBVd) and the citrus exocortis viroid (CEVd), representative
-
The carrier proteome limit should be reassessed for each mass analyzer architecture bioRxiv. Biochem. Pub Date : 2024-03-12 Ben Orsburn
A clever utilization of classic proteomics reagents now allows the effective amplification of peptide sequencing potential in shotgun proteomics. The application of this method has helped usher in the exciting new field of single cell proteomics. While it was easy to first think that the discovery of Budnik et al., was finally the answer for protein PCR, limitations were carefully described by the
-
Molecular mechanism for regulating APOBEC3G DNA editing function by the non-catalytic domain bioRxiv. Biochem. Pub Date : 2024-03-12 Hanjing Yang, Josue Pacheco, Kyumin Kim, Diako Ebrahimi, Fumiaki Ito, Xiaojiang S Chen
APOBEC3G (A3G) belongs to the AID/APOBEC cytidine deaminase family and is essential for antiviral immunity. It contains two zinc-coordinated cytidine-deaminase (CD) domains. The N-terminal CD1 domain is non-catalytic but has a strong affinity for nucleic acids, whereas the C-terminal CD2 domain catalyzes C-to-U editing in single-stranded DNA. The interplay between the two domains in DNA binding and
-
Phenylphenalenones and Linear Diarylheptanoid Derivatives are Biosynthesized via Parallel Routes in Musella lasiocarpa, the Chinese Dwarf Banana bioRxiv. Biochem. Pub Date : 2024-03-12 Hui Lyu, Lukas Ernst, Yoko Nakamura, Yu Okamura, Tobias Koellner, Katrin Luck, Benye Liu, Yu Chen, Ludger Beerhues, Jonathan Gershenzon, Christian Paetz
Phenylphenalenones (PPs) are complex polycyclic natural products that play an important role in the chemical defense system of banana and plantain (Musaceae). Although suggestions for how plants synthesize the PP scaffold were first proposed more than 50 years ago, no biosynthetic information is yet available at the enzyme level. Here, we use transcriptomic data from seeds of Musella lasiocarpa, the
-
High-throughput determination of RNA tertiary contact thermodynamics by quantitative DMS chemical mapping bioRxiv. Biochem. Pub Date : 2024-03-12 Bret W Lange, Ricardo G Gil, Joseph David Yesselman
Structured RNAs often contain long-range tertiary contacts that are critical to their function. Despite the importance of tertiary contacts, methods to measure their thermodynamics are low throughput or require specialized instruments. Here, we introduce a new quantitative chemical mapping method (qDMS-MaPseq) to measure Mg2+-induced formation of tertiary contact thermodynamics in a high-throughput
-
Uncovering the BIN1-SH3 interactome underpinning centronuclear myopathy bioRxiv. Biochem. Pub Date : 2024-03-12 Boglarka Zambo, Evelina Edelweiss, Bastien Morlet, Luc Negroni, Matyas Pajkos, Zsuzsanna Dosztanyi, Soren Ostergaard, Gilles Trave, Jocelyn Laporte, Gergo Gogl
Truncation of the protein-protein interaction SH3 domain of the membrane remodeling Bridging Integrator 1 (BIN1, Amphiphysin 2) protein leads to centronuclear myopathy. Here, we assessed the impact of a set of naturally observed, previously uncharacterized BIN1 SH3 domain variants using conventional in vitro and cell-based assays monitoring the BIN1 interaction with dynamin 2 (DNM2) and identified
-
Human primosome requires replication protein A when copying DNA with inverted repeats bioRxiv. Biochem. Pub Date : 2024-03-11 Andrey Baranovskiy, Lucia Morstadt, Nigar Babayeva, Tahir H. Tahirov
The human primosome, a four-subunit complex of primase and DNA polymerase alpha (Polα), initiates DNA synthesis on both chromosome strands by generating chimeric RNA-DNA primers for loading DNA polymerases delta and epsilon (Polε). Replication protein A (RPA) tightly binds to single-stranded DNA strands, protecting them from nucleolytic digestion and unauthorized transactions. We report here that RPA
-
Molecular basis of proteolytic cleavage regulation by the extracellular matrix receptor dystroglycan bioRxiv. Biochem. Pub Date : 2024-03-11 Michael JM Anderson, Amanda N Hayward, Adam T Smiley, Ke Shi, Matthew R Pawlak, Eric J Aird, Eva Grant, Lauren Greenberg, Hideki Aihara, Chris Ulens, Robert L Evans, Wendy R Gordon
The dystrophin glycoprotein complex (DGC), anchored by the transmembrane protein dystroglycan, functions to mechanically link the extracellular matrix to the actin cytoskeleton to drive critical aspects of development and adult homeostasis. Breaking this connection via mutation of the actin adaptor protein dystrophin or impaired glycosylation of dystroglycan are strongly associated with diseases such
-
Structural and biophysical characterisation of ubiquitin variants that specifically inhibit the ubiquitin conjugating enzyme Ube2d2 bioRxiv. Biochem. Pub Date : 2024-03-11 Jeffery MRB McAlpine, Jingyi Zhu, Nicholas Pudjihartono, Joan Teyra, Michael J Currie, Renwick CJ Dobson, Sachdev S Sidhu, Catherine L Day, Adam J Middleton
The ubiquitin conjugating E2 enzymes play a central role in ubiquitin transfer. Disruptions to the ubiquitin system are implicated in multiple diseases and as a result, molecules that modulate the activity of the ubiquitin system are of interest. E2 enzyme function is reliant on interactions with partner proteins and disruption of these is an effective way of modulating activity. Here, we report the
-
Structural basis of substrate transport and drug recognition by the human thiamine transporter SLC19A3 bioRxiv. Biochem. Pub Date : 2024-03-11 Florian Gabriel, Lea Spriestersbach, Antonia Fuhrmann, Katharina E. J. Jungnickel, Siavash Mostafavi, Els Pardon, Jan Steyaert, Christian Loew
Thiamine (vitamin B1) functions as an essential coenzyme in cells. Humans and other mammals cannot synthesise this vitamin de novo and thus have to take it up from their diet. Eventually, every cell needs to import thiamine across its plasma membrane which is mainly mediated by two specific thiamine transporters SLC19A2 and SLC19A3. Loss of function mutations in either of these transporters leads to
-
SIDERITE: Unveiling Hidden Siderophore Diversity in the Chemical Space Through Digital Exploration bioRxiv. Biochem. Pub Date : 2024-03-11 Ruolin He, Shaohua Gu, Jiazheng Xu, Xuejian Li, Haoran Chen, Zhengying Shao, Haofan Wang, Jiqi Shao, Wen-Bing Yin, Long Qian, Zhong Wei, Zhiyuan Li
Siderophores, a highly diverse family of secondary metabolites, play a crucial role in facilitating the acquisition of the essential iron. However, the current discovery of siderophore relies largely on manual approaches. In this work, we introduced SIDERTE, a digitized siderophore information database containing 872 siderophore records with 649 unique structures. Leveraging this digitalized dataset
-
EXCRETE enables deep proteomics of the microbial extracellular environment bioRxiv. Biochem. Pub Date : 2024-03-11 David A. Russo, Denys Oliinyk, Georg Pohnert, Florian Meier, Julie A. Z. Zedler
Extracellular proteins play a significant role in shaping microbial communities which, in turn, can impact ecosystem function, human health, and biotechnological processes. Yet, for many ubiquitous microbes, there is limited knowledge regarding the identity and function of secreted proteins. Here, we introduce EXCRETE (enhanced exoproteome characterization by mass spectrometry), a workflow that enables
-
LPOR and the membranes – evolutionary pathway towards prolamellar body formation bioRxiv. Biochem. Pub Date : 2024-03-11 Wiktoria Ogrodzinska, Katarzyna Szafran, Mateusz Luszczynski, Olga Woznicka, Michal Gabruk
Light-dependent protochlorophyllide oxidoreductase (LPOR) has captivated the interest of the research community for decades. One reason is the photocatalytic nature of the reaction catalyzed by the enzyme, and the other is the involvement of LPOR in the formation of a paracrystalline lattice called a prolamellar body (PLB) that disintegrates upon illumination, initiating a process of photosynthetic
-
Supramolecular complexes of GCAP1: towards the development of effective biologics for inherited retinal dystrophies bioRxiv. Biochem. Pub Date : 2024-03-11 Amedeo Biasi, Valerio Marino, Giuditta Dal Cortivo, Daniele Dell'Orco
Guanylate Cyclase Activating Protein 1 (GCAP1) is a neuronal Ca2+-sensor protein expressed in photoreceptors where it regulates the enzymatic activity of retinal Guanylate Cyclase 1 (GC1) in a Ca2+-dependent manner. Recently, over 20 missense mutations in GUCA1A (encoding for GCAP1) have been associated with inherited autosomal dominant retinal diseases, namely cone dystrophy (COD) and cone-rod dystrophy
-
Differentiating specific and non-specific protein-metabolite interactions using gradient open port probe electrospray ionization mass spectrometry bioRxiv. Biochem. Pub Date : 2024-03-09 Xiaobo Tian, Gerard Hopfgartner
Native electrospray ionization mass spectrometry (ESI-MS) using nano ESI or desorption electrospray ionization (DESI) has been widely used to study interactions between macromolecules and ligands, usually protein-metabolite interactions (PMIs). In MS spectra the charge state distributions (CSD) of proteins differ between native and non-native conditions and based on this, we report a method that can
-
Effect of pH on the thermostability and redox properties of cytochrome c552 from Wolinella succinogenes bioRxiv. Biochem. Pub Date : 2024-03-09 Vitor H. Mordido, Marta S. P. Carepo, Cristina M. Cordas, Navendu Paul, Jorg Simon, Isabel Moura, Sofia R. Pauleta
Cytochrome c552 from Wolinella succinogenes is one of the few examples of a low reduction potential class I c-type cytochrome with a mixture of high/low spin state populations observed in its visible spectrum. Analysis of its structural model suggests that the heme is Met/His coordinated and highly solvent-exposed. This supports the hypothesis that it is the solvent accessibility of the propionate
-
Cooperative involvement of zipper-interacting protein kinase (ZIPK) and the dual-specificity cell division cycle 14A phosphatase (CDC14A) in vascular smooth muscle cell migration bioRxiv. Biochem. Pub Date : 2024-03-09 Abdulhameed Al-Ghabkari, David A Carlson, Timothy AJ Haystead, Justin A MacDonald
Zipper-interacting protein kinase (ZIPK) is a Ser/Thr protein kinase with regulatory involvement in vascular smooth muscle cell (VSMC) actin polymerization and focal adhesion assembly dynamics. ZIPK silencing can induce cytoskeletal remodeling with disassembly of actin stress fiber networks and coincident loss of focal adhesion kinase (FAK)-pY397 phosphorylation. The link between ZIPK inhibition and