Top 7 Biorxiv Papers Today in Biochemistry


2.0 Mikeys
#1. In-depth and 3-Dimensional Exploration of the Budding Yeast Phosphoproteome
Michael C Lanz, Kumar Yugandhar, Shagun Gupta, Ethan Sanford, Vitor Faça, Stephanie Vega, Aaron Joiner, Chris Fromme, Haiyuan Yu, Marcus B. Smolka
Phosphorylation is one of the most dynamic and widespread post-translational modifications regulating virtually every aspect of eukaryotic cell biology. Here we present a comprehensive phosphoproteomic dataset for budding yeast, comprised of over 30,000 high confidence phosphorylation sites identified by mass spectrometry. This single dataset nearly doubles the size of the known phosphoproteome in budding yeast and defines a set of cell cycle-regulated phosphorylation events. With the goal of enhancing the identification of functional phosphorylation events, we performed computational positioning of phosphorylation sites on available 3D protein structures and systematically identified events predicted to regulate protein complex architecture. Results reveal a large number of phosphorylation sites mapping to or near protein interaction interfaces, many of which result in steric or electrostatic clashes predicted to disrupt the interaction. Phosphorylation site mutants experimentally validate our predictions and support a role for...
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biorxivpreprint: In-depth and 3-Dimensional Exploration of the Budding Yeast Phosphoproteome https://t.co/zPKmSieX4g #bioRxiv
cryoEM_Papers: In-depth and 3-Dimensional Exploration of the Budding Yeast Phosphoproteome https://t.co/QPuOhaIyYw
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Authors: 10
Total Words: 13194
Unqiue Words: 3110

1.998 Mikeys
#2. Use of extracellular polymer substances as additives for improving biogas yield and digestion performance
Haitong Ma, Chenyan Guo, Ming Wu, Hui Liu, Zhiwei Wang, Shuangfei Wang
To understand how extracellular polymer substances (EPS) as additives promotes methanogenesis, batch tests of methane production potential in anaerobic reactors with the addition of EPS or not were conducted. Research showed that EPS increased remarkably methane production during anaerobic digestion (36.5% increase compared with the control). EPS enriched functional microorganisms such as Firmicutes, Actinobacteria, Synergistetes , and Chloroflexi . Among them, 8.86% OTUs from the important hydrolysis and acidification phyla, which may be an important reason for the enhanced methanogenic capacity of anaerobic granular sludge. Additionally, EPS also improved the abundance of cytochrome c (c-Cyts), accelerating the direct interspecies electron transfer (DIET) between syntrophic bacteria and methanogens, thus enhancing the methane production. Interestingly, the average particle size, volatile suspended solids/total suspended solids (VSS/TSS) and EPS content of anaerobic granular sludge (AnGS) in the EPS reactor were approximately...
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Authors: 6
Total Words: 6507
Unqiue Words: 2331

1.998 Mikeys
#3. Metabolic dependency of chorismate in Plasmodium falciparum
Ana Lisa Valenciano, Maria L. Fernandez-Murga, Emilio F. Merino, Nicole R. Holderman, Grant J. Butschek, Karl J. Shaffer, Peter C. Tyler, Maria B. Cassera
The shikimate pathway, a metabolic pathway absent in humans, is responsible for the production of chorismate, a branch point metabolite. In the malaria parasite, chorismate is postulated to be a direct precursor in the synthesis of p-aminobenzoic acid (folate biosynthesis), p-hydroxybenzoic acid (ubiquinone biosynthesis), menaquinone, and aromatic amino acids. While the potential value of the shikimate pathway as a drug target is debatable, the metabolic dependency of chorismate in P. falciparum remains unclear. Current evidence suggests that the main role of chorismate is folate biosynthesis despite ubiquinone biosynthesis being active and essential in the malaria parasite. Our goal in the present work was to expand our knowledge of the ubiquinone head group biosynthesis and its potential metabolic dependency on chorismate in P. falciparum. These data led us to further characterize the mechanism of action of MMV688345, a compound from the open-access Pathogen Box collection from Medicine for Malaria Venture. We systematically...
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Authors: 8
Total Words: 0
Unqiue Words: 0

1.998 Mikeys
#4. Horse gluteus is a null-sarcolipin muscle with enhanced sarcoplasmic reticulum calcium transport
Joseph M. Autry, Bengt Svensson, Samuel F. Carlson, Zhenhui Chen, L. Michel Espinoza-Fonseca, David D. Thomas
We have analyzed gene transcription, protein expression, and enzymatic activity of the Ca2+-transporting ATPase (SERCA) in horse gluteal muscle. Horses are bred for peak athletic performance but exhibit a high incidence of exertional rhabdomyolysis, suggesting Ca2+ as a correlative linkage. To assess Ca2+ regulation in horse gluteus, we developed an improved protocol for isolating horse sarcoplasmic reticulum (SR) vesicles. RNA-seq and immunoblotting determined that the ATP2A1 gene (protein product SERCA1) is the predominant Ca2+ ATPase expressed in horse gluteus, as in rabbit muscle. Gene expression was assessed for four regulatory peptides of SERCA, finding that sarcolipin (SLN) is the predominant regulatory peptide transcript expressed in horse gluteus, as in rabbit muscle. Surprisingly, the RNA transcription ratio of SLN-to-ATP2A1 in horse gluteus is an order of magnitude higher than in rabbit muscle, but conversely, the protein expression ratio of SLN-to-SERCA1 in horse gluteus is an order of magnitude lower than in rabbit....
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biorxivpreprint: Horse gluteus is a null-sarcolipin muscle with enhanced sarcoplasmic reticulum calcium transport https://t.co/RGalglhsUZ #bioRxiv
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Authors: 6
Total Words: 34237
Unqiue Words: 7273

1.998 Mikeys
#5. A nanobody that recognizes a 14-residue peptide epitope in the E2 ubiquitin-conjugating enzyme UBC6e modulates its activity
Jingjing Ling, Ross W Cheloha, Nicholas McCaul, Zhen-Yu J Sun, Gerhard Wagner, Hidde L Ploegh
A substantial fraction of eukaryotic proteins is folded and modified in the endoplasmic reticulum (ER) prior to export and secretion. Proteins that enter the ER but fail to fold correctly must be degraded, mostly in a process termed ER-associated degradation (ERAD). Both protein folding in the ER and ERAD are essential for proper immune function. Several E2 and E3 enzymes localize to the ER and are essential for various aspects of ERAD, but their functions and regulation are incompletely understood. Here we identify and characterize single domain antibody fragments derived from the variable domain of alpaca heavy chain-only antibodies (VHHs or nanobodies) that bind to the ER-localized E2 UBC6e, an enzyme implicated in ERAD. One such VHH, VHH05 recognizes a 14 residue stretch and enhances the rate of E1-catalyzed ubiquitin E2 loading in vitro and interferes with phosphorylation of UBC6e in response to cell stress. Identification of the peptide epitope recognized by VHH05 places it outside the E2 catalytic core, close to the...
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Authors: 6
Total Words: 10018
Unqiue Words: 3274

1.997 Mikeys
#6. Molecular mechanism of mitochondrial phosphatidate transfer by Ups1/Mdm35
Jiuwei Lu, Kevin Chan, Leiye Yu, Jun Fan, Yujia Zhai, Fei Sun
Cardiolipin plays many important roles for mitochondrial physiological function and is synthesized from phosphatidic acid (PA) at inner mitochondrial membrane (IMM). PA synthesized from endoplasmic reticulum needs to transfer to IMM via outer mitochondrial membrane (OMM). The transfer of PA between IMM and OMM is mediated by Ups1/Mdm35 protein family. Although there are many structures of this family available, the detailed molecular mechanism of how PA is transferred between membranes is yet unknown. Here, we report another crystal structures of Ups1/Mdm35 in the authentic monomeric apo state and the DHPA bound state. By combining subsequent all-atom molecular dynamics simulations, extensive structural comparisons and biophysical assays, we discovered the conformational changes of Ups1/Mdm35, identified key structural elements and residues during membrane binding and PA entry. We found the monomeric Ups1 on membrane is an important transit for the success of PA transfer, and the equilibrium between monomeric Ups1 and Ups1/Mdm35...
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biorxivpreprint: Molecular mechanism of mitochondrial phosphatidate transfer by Ups1/Mdm35 https://t.co/2iPe4Mo0HT #bioRxiv
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Authors: 6
Total Words: 0
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1.995 Mikeys
#7. The PAX3 and 7 homeodomains have evolved unique determinants that influence DNA-binding, structure and communication with the paired domain
Gareth N. Corry, Brian D. Sykes, D. Alan Underhill
The PAX (paired box) family is a collection of metazoan transcription factors defined by the paired domain, which confers sequence-specific DNA-binding. Ancestral PAX proteins also contained a homeodomain, which can communicate with the paired domain to modulate DNA-binding. In the present study, we sought to identify determinants of this functional interaction using the paralogous PAX3 and 7 proteins. First, we evaluated a group of heterologous paired domains and homeodomains for the ability to bind DNA cooperatively through formation of a ternary complex (paired domain:homeodomain:DNA). This revealed that capacity for ternary complex formation was unique to the PAX3 and 7 homeodomains and therefore not simply a consequence of DNA-binding. We also found PAX3 and 7 were distinguished by an extended region of conservation N-terminal to the homeodomain (NTE). Phylogenetic analyses established the NTE was restricted to PAX3/7 orthologs of segmented metazoans, indicating it arose in a bilaterian precursor prior to separation of...
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Authors: 3
Total Words: 7346
Unqiue Words: 2180

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