bims-mimbat Biomed News
on Mitochondrial metabolism in brown adipose tissue
Issue of 2023–03–26
fiveteen papers selected by
José Carlos de Lima-Júnior, Washington University
  1. ATF4 Expression in Thermogenic Adipocytes is Required for Cold-Induced Thermogenesis in Mice via FGF21-Independent Mechanisms.
  2. Involvement of a novel cAMP signaling mediator for beige adipogenesis.
  3. Resting mitochondrial complex I from Drosophila melanogaster adopts a helix-locked state.
  4. A FRET sensor for the real-time detection of long chain acyl-CoAs and synthetic ABHD5 ligands.
  5. Structure of mycobacterial respiratory complex I.
  6. TonB-Dependent Transport Across the Bacterial Outer Membrane.
  7. Balanced mitochondrial function at low temperature is linked to cold adaptation in Drosophila species.
  8. A cooperative knock-on mechanism underpins Ca2+-selective cation permeation in TRPV channels.
  9. Inhibition of nucleotide biosynthesis disrupts lipid accumulation and adipogenesis.
  10. Pharmacologic Activation of an Integrated Stress Response Kinase Promotes Mitochondrial Remodeling.
  11. Hydrogen peroxide production by epidermal dual oxidase 1 regulates nociceptive sensory signals.
  12. The yeast Gdt1 protein mediates the exchange of H+ for Ca2+ and Mn2+ influencing the Golgi pH.
  13. Influence of Electronic Polarization on the Binding of Anions to a Chloride-Pumping Rhodopsin.
  14. A quantitative fluorescence-based approach to study mitochondrial protein import.
  15. Lipid hydroperoxides promote sarcopenia through carbonyl stress.
  1. bioRxiv. 2023 Mar 10. pii: 2023.03.09.531964. [Epub ahead of print]
    ATF4 Expression in Thermogenic Adipocytes is Required for Cold-Induced Thermogenesis in Mice via FGF21-Independent Mechanisms.
    Sarah H Bjorkman, Alex Marti, Jayashree Jena, Luis Miguel García-Peña, Eric T Weatherford, Kevin Kato, Jivan Koneru, Jason H Chen, Ayushi Sood, Matthew J Potthoff, Christopher M Adams, E Dale Abel, Renata O Pereira.
      In brown adipose tissue (BAT), short-term cold exposure induces the integrated stress response (ISR) main effector, activating transcription factor 4 (ATF4), and its downstream target fibroblast growth factor 21 (FGF21). We recently demonstrated that induction of ATF4 in BAT in response to mitochondrial stress is required for thermoregulation, at least in part, via induction of FGF21. In the present study, we tested the hypothesis that Atf4 and Fgf21 induction in BAT are both required for BAT thermogenesis by generating mice selectively lacking either Atf4 (ATF4 BKO) or Fgf21 (FGF21 BKO) in UCP1-expressing adipocytes. After 3 days of cold exposure, core body temperature was significantly reduced in ad-libitum -fed ATF4 BKO mice, which correlated with Fgf21 downregulation in brown and beige adipocytes, and impaired browning of white adipose tissue (WAT). Conversely, although Fgf21 deletion in thermogenic adipocytes also reduced cold-induced browning of WAT, ad libitum -fed FGF21 BKO mice had preserved core body temperature after cold exposure. When cold-exposed under fasting conditions, both ATF4 BKO and FGF21 BKO mice had reduced cold tolerance. Mechanistically, ATF4 downregulation in thermogenic adipocytes decreased amino acid import and metabolism in BAT, likely contributing to impaired brown adipocyte thermogenic capacity under ad libitum-fed conditions. Thus, Atf4 regulates Fgf21 expression in thermogenic adipocytes during cold stress, which is required to mediate cold-induced browning of iWAT but is dispensable for thermoregulation in the fed state. In contrast, in the fasted state, both Atf4 and Fgf21 expression in thermogenic adipocytes are required for thermoregulation in mice.
    DOI:  https://doi.org/10.1101/2023.03.09.531964
  2. Metabolism. 2023 Mar 16. pii: S0026-0495(23)00139-7. [Epub ahead of print]143 155536
    Involvement of a novel cAMP signaling mediator for beige adipogenesis.
    Jun Seok Kim, Hye-Sook Han, Je Kyung Seong, Young-Gyu Ko, Seung-Hoi Koo.
       BACKGROUND: Exposure to cold temperature stimulates the sympathetic nervous system that activates β-adrenergic receptor signals in brown and beige adipocytes, leading to the induction of adaptive thermogenesis in mammals. Prominin-1 (PROM1) is a pentaspan transmembrane protein that is widely identified as a marker for stem cells, although the role of this protein as a regulator of many intracellular signaling cascades has been recently delineated. The main focus of the current study is to identify the previously unknown role of PROM1 in beige adipogenesis and adaptive thermogenesis.
    METHODS: Prom1 whole body knockout (Prom1 KO) mice, Prom1 adipogenic progenitor (AP) cell-specific knockout (Prom1 APKO) mice and Prom1 adipocyte-specific knockout (Prom1 AKO) mice were constructed and were subject for the induction of adaptive thermogenesis. The effect of systemic Prom1 depletion was evaluated by hematoxylin and eosin staining, immunostaining, and biochemical analysis in vivo. Flow cytometric analysis was performed to determine the identity of PROM1-expressing cell types, and the resultant cells were subject to beige adipogenesis in vitro. The potential role of PROM1 and ERM in cAMP signaling was also assessed in undifferentiated AP cells in vitro. Finally, the specific effect of Prom1 depletion on AP cell or mature adipocytes on adaptive thermogenesis was evaluated by hematoxylin and eosin staining, immunostaining, and biochemical analysis in vivo.
    RESULTS: Prom1 KO mice displayed an impairment in cold- or β3-adrenergic agonist-induced adaptive thermogenesis in subcutaneous adipose tissues (SAT) but not in brown adipose tissues (BAT). By fluorescence-activated cell sorting (FACS) analysis, we identified that PROM1 positive cells are enriched in PDGFRα+Sca1+ AP cells from SAT. Interestingly, Prom1 knockout stromal vascular fractions showed reduced PDGFRα expression, suggesting a role of PROM1 in beige adipogenic potential. Indeed, we found that Prom1-deficient AP cells from SAT showed reduced potential for beige adipogenesis. Furthermore, AP cell-specific depletion of Prom1, but not adipocyte-specific depletion of Prom1, displayed defects in adaptive thermogenesis as evidenced by resistance to cold-induced browning of SAT and dampened energy expenditure in mice.
    CONCLUSION: We found that PROM1 positive AP cells are essential for the adaptive thermogenesis by ensuing stress-induced beige adipogenesis. Identification of PROM1 ligand might be useful in the activation of thermogenesis that could be potentially beneficial in combating obesity.
    Keywords:  Adaptive thermogenesis; Adipogenic progenitor cells; Beige adipogenesis; PROM1
    DOI:  https://doi.org/10.1016/j.metabol.2023.155536
  3. Elife. 2023 Mar 23. pii: e84415. [Epub ahead of print]12
    Resting mitochondrial complex I from Drosophila melanogaster adopts a helix-locked state.
    Abhilash Padavannil, Anjaneyulu Murari, Shauna-Kay Rhooms, Edward Owusu-Ansah, James A Letts.
      Respiratory complex I is a proton-pumping oxidoreductase key to bioenergetic metabolism. Biochemical studies have found a divide in the behavior of complex I in metazoans that aligns with the evolutionary split between Protostomia and Deuterostomia. Complex I from Deuterostomia including mammals can adopt a biochemically defined off-pathway 'deactive' state, whereas complex I from Protostomia cannot. The presence of off-pathway states complicates the interpretation of structural results and has led to considerable mechanistic debate. Here, we report the structure of mitochondrial complex I from the thoracic muscles of the model protostome Drosophila melanogaster. We show that although D. melanogaster complex I (Dm-CI) does not have a NEM-sensitive deactive state, it does show slow activation kinetics indicative of an off-pathway resting state. The resting-state structure of Dm-CI from the thoracic muscle reveals multiple conformations. We identify a helix-locked state in which an N-terminal α-helix on the NDUFS4 subunit wedges between the peripheral and membrane arms. Comparison of the Dm-CI structure and conformational states to those observed in bacteria, yeast, and mammals provides insight into the roles of subunits across organisms, explains why the Dm-CI off-pathway resting state is NEM insensitive, and raises questions regarding current mechanistic models of complex I turnover.
    Keywords:  complex I; drosophila melanogaster; electron transport chain; mitochondria; molecular biophysics; respiration; single particle cryoEM; structural biology
    DOI:  https://doi.org/10.7554/eLife.84415
  4. Cell Rep Methods. 2023 Feb 27. 3(2): 100394
    A FRET sensor for the real-time detection of long chain acyl-CoAs and synthetic ABHD5 ligands.
    Emilio P Mottillo, Ljiljana Mladenovic-Lucas, Huamei Zhang, Li Zhou, Christopher V Kelly, Pablo A Ortiz, James G Granneman.
      Intracellular long-chain acyl-coenzyme As (LC-acyl-CoAs) are thought to be under tight spatial and temporal controls, yet the ability to image LC-acyl-CoAs in live cells is lacking. Here, we developed a fluorescence resonance energy transfer (FRET) sensor for LC-acyl-CoAs based on the allosterically regulated interaction between α/β hydrolase domain-containing 5 (ABHD5) and Perilipin 5. The genetically encoded sensor rapidly detects intracellular LC-acyl-CoAs generated from exogenous and endogenous fatty acids (FAs), as well as synthetic ABHD5 ligands. Stimulation of lipolysis in brown adipocytes elevated intracellular LC-acyl-CoAs in a cyclic fashion, which was eliminated by inhibiting PNPLA2 (ATGL), the major triglyceride lipase. Interestingly, inhibition of LC-acyl-CoA transport into mitochondria elevated intracellular LC-acyl-CoAs and dampened their cycling. Together, these observations reveal an intimate feedback control between LC-acyl-CoA generation from lipolysis and utilization in mitochondria. We anticipate that this sensor will be an important tool to dissect intracellular LC-acyl-CoA dynamics as well to discover novel synthetic ABHD5 ligands.
    Keywords:  CGI-58; Perilipin; adipose triglyceride lipase; fatty acids; genetically encoded FRET sensor; lipid droplet; long-chain acyl-CoAs; mitochondria; real-time monitoring; α/β hydrolase domain-containing 5
    DOI:  https://doi.org/10.1016/j.crmeth.2023.100394
  5. Proc Natl Acad Sci U S A. 2023 Mar 28. 120(13): e2214949120
    Structure of mycobacterial respiratory complex I.
    Yingke Liang, Alicia Plourde, Stephanie A Bueler, Jun Liu, Peter Brzezinski, Siavash Vahidi, John L Rubinstein.
      Oxidative phosphorylation, the combined activity of the electron transport chain (ETC) and adenosine triphosphate synthase, has emerged as a valuable target for the treatment of infection by Mycobacterium tuberculosis and other mycobacteria. The mycobacterial ETC is highly branched with multiple dehydrogenases transferring electrons to a membrane-bound pool of menaquinone and multiple oxidases transferring electrons from the pool. The proton-pumping type I nicotinamide adenine dinucleotide (NADH) dehydrogenase (Complex I) is found in low abundance in the plasma membranes of mycobacteria in typical in vitro culture conditions and is often considered dispensable. We found that growth of Mycobacterium smegmatis in carbon-limited conditions greatly increased the abundance of Complex I and allowed isolation of a rotenone-sensitive preparation of the enzyme. Determination of the structure of the complex by cryoEM revealed the "orphan" two-component response regulator protein MSMEG_2064 as a subunit of the assembly. MSMEG_2064 in the complex occupies a site similar to the proposed redox-sensing subunit NDUFA9 in eukaryotic Complex I. An apparent purine nucleoside triphosphate within the NuoG subunit resembles the GTP-derived molybdenum cofactor in homologous formate dehydrogenase enzymes. The membrane region of the complex binds acyl phosphatidylinositol dimannoside, a characteristic three-tailed lipid from the mycobacterial membrane. The structure also shows menaquinone, which is preferentially used over ubiquinone by gram-positive bacteria, in two different positions along the quinone channel, comparable to ubiquinone in other structures and suggesting a conserved quinone binding mechanism.
    Keywords:  complex I; membrane protein; mycobacteria; respiration; structure
    DOI:  https://doi.org/10.1073/pnas.2214949120
  6. Annu Rev Microbiol. 2023 Mar 21.
    TonB-Dependent Transport Across the Bacterial Outer Membrane.
    Augustinas Silale, Bert van den Berg.
      TonB-dependent transporters (TBDTs) are present in all gram-negative bacteria and mediate energy-dependent uptake of molecules that are too scarce or large to be taken up efficiently by outer membrane (OM) diffusion channels. This process requires energy that is derived from the proton motive force and delivered to TBDTs by the TonB-ExbBD motor complex in the inner membrane. Together with the need to preserve the OM permeability barrier, this has led to an extremely complex and fascinating transport mechanism for which the fundamentals, despite decades of research, are still unclear. In this review, we describe our current understanding of the transport mechanism of TBDTs, their potential role in the delivery of novel antibiotics, and the important contributions made by TBDT-associated (lipo)proteins. Expected final online publication date for the Annual Review of Microbiology, Volume 77 is September 2023. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    DOI:  https://doi.org/10.1146/annurev-micro-032421-111116
  7. J Exp Biol. 2023 Mar 20. pii: jeb.245439. [Epub ahead of print]
    Balanced mitochondrial function at low temperature is linked to cold adaptation in Drosophila species.
    Lisa Bjerregaard Jørgensen, Andrea Milena Hansen, Quentin Willot, Johannes Overgaard.
      The ability of ectothermic animals to live in different thermal environments is closely associated with their capacity to maintain physiological homeostasis across diurnal and seasonal temperature fluctuations. For chill-susceptible insects, such as Drosophila, cold tolerance is tightly linked to ion and water homeostasis obtained through a regulated balance of active and passive transport. Active transport at low temperature requires a constant delivery of ATP and we therefore hypothesize that cold-adapted Drosophila are characterized by superior mitochondrial capacity at low temperature relative to cold-sensitive species. To address this, we investigated how experimental temperatures from 1 to 19 °C affected mitochondrial substrate oxidation in flight muscle of seven Drosophila species and compared it to a measure of species cold tolerance (CTmin, the temperature inducing cold coma). Mitochondrial oxygen consumption rates measured using a substrate-uncoupler-inhibitor-titration (SUIT) protocol showed that cooling generally reduced oxygen consumption of the electron transport system across species, as was expected due to thermodynamic effects. Complex I is the primary consumer of oxygen at non-stressful temperatures, but low temperature decreases complex I respiration to a much greater extent in cold-sensitive species than in cold-adapted species. Accordingly, cold-induced reduction of complex I correlates strongly with CTmin. The relative contribution of other substrates (proline, succinate and glycerol-3-phosphate) increased as temperature decreased, particularly in the cold-sensitive species. At present, it is unclear whether the oxidation of alternative substrates can be used to offset the effects of the temperature-sensitive complex I, and the potential functional consequences of such a substrate switch are discussed.
    Keywords:  CTmin; Cold tolerance; Complex I; Mitochondrial flexibility; OXPHOS; Thermal sensitivity
    DOI:  https://doi.org/10.1242/jeb.245439
  8. J Gen Physiol. 2023 May 01. pii: e202213226. [Epub ahead of print]155(5):
    A cooperative knock-on mechanism underpins Ca2+-selective cation permeation in TRPV channels.
    Callum M Ives, Neil J Thomson, Ulrich Zachariae.
      The selective exchange of ions across cellular membranes is a vital biological process. Ca2+-mediated signaling is implicated in a broad array of physiological processes in cells, while elevated intracellular concentrations of Ca2+ are cytotoxic. Due to the significance of this cation, strict Ca2+ concentration gradients are maintained across the plasma and organelle membranes. Therefore, Ca2+ signaling relies on permeation through selective ion channels that control the flux of Ca2+ ions. A key family of Ca2+-permeable membrane channels is the polymodal signal-detecting transient receptor potential (TRP) ion channels. TRP channels are activated by a wide variety of cues including temperature, small molecules, transmembrane voltage, and mechanical stimuli. While most members of this family permeate a broad range of cations non-selectively, TRPV5 and TRPV6 are unique due to their strong Ca2+ selectivity. Here, we address the question of how some members of the TRPV subfamily show a high degree of Ca2+ selectivity while others conduct a wider spectrum of cations. We present results from all-atom molecular dynamics simulations of ion permeation through two Ca2+-selective and two non-selective TRPV channels. Using a new method to quantify permeation cooperativity based on mutual information, we show that Ca2+-selective TRPV channel permeation occurs by a three-binding site knock-on mechanism, whereas a two-binding site knock-on mechanism is observed in non-selective TRPV channels. Each of the ion binding sites involved displayed greater affinity for Ca2+ over Na+. As such, our results suggest that coupling to an extra binding site in the Ca2+-selective TRPV channels underpins their increased selectivity for Ca2+ over Na+ ions. Furthermore, analysis of all available TRPV channel structures shows that the selectivity filter entrance region is wider for the non-selective TRPV channels, slightly destabilizing ion binding at this site, which is likely to underlie mechanistic decoupling.
    DOI:  https://doi.org/10.1085/jgp.202213226
  9. J Biol Chem. 2023 Mar 22. pii: S0021-9258(23)00277-6. [Epub ahead of print] 104635
    Inhibition of nucleotide biosynthesis disrupts lipid accumulation and adipogenesis.
    Abhijit B Shinde, Elizabeth R Nunn, Genesis A Wilson, Mathew T Chvasta, Julia A Pinette, Jacob W Myers, Sun H Peck, Jessica B Spinelli, Elma Zaganjor.
      Energy balance and nutrient availability are key determinants of cellular decisions to remain quiescent, proliferate or differentiate into a mature cell. After assessing its environmental state, the cell must rewire its metabolism to support distinct cellular outcomes. Mechanistically, how metabolites regulate cell fate decisions is poorly understood. We used adipogenesis as our model system to ascertain the role of metabolism in differentiation. We isolated adipose tissue stromal vascular fraction (SVF) cells and profiled metabolites before and after adipogenic differentiation to identify metabolic signatures associated with these distinct cellular states. We found that differentiation alters nucleotide accumulation. Furthermore, inhibition of nucleotide biosynthesis prevented lipid storage within adipocytes and downregulated the expression of lipogenic factors. In contrast to proliferating cells, in which mTORC1 is activated by purine accumulation, mTORC1 signaling was unaffected by purine levels in differentiating adipocytes. Rather, our data indicated that purines regulate transcriptional activators of adipogenesis, PPARγ and C/EBPα to promote differentiation. Although de novo nucleotide biosynthesis has mainly been studied in proliferation, our study points to its requirement in adipocyte differentiation.
    Keywords:  adipocytes; adipogenesis; lipid droplets; metabolism; nucleotides; purine; pyrimidine
    DOI:  https://doi.org/10.1016/j.jbc.2023.104635
  10. bioRxiv. 2023 Mar 12. pii: 2023.03.11.532186. [Epub ahead of print]
    Pharmacologic Activation of an Integrated Stress Response Kinase Promotes Mitochondrial Remodeling.
    Valerie Perea, Kelsey R Baron, Vivian Dolina, Giovanni Aviles, Jessica D Rosarda, Xiaoyan Guo, Martin Kampmann, R Luke Wiseman.
      The integrated stress response (ISR) is a network of eIF2 α kinases, comprising PERK, GCN2, HRI, and PKR, that induce translational and transcriptional signaling in response to diverse insults. The PERK ISR kinase regulates mitochondria in response to endoplasmic reticulum (ER) stress. Deficiencies in PERK signaling lead to mitochondrial dysfunction and contribute to the pathogenesis of numerous diseases. We define the potential for pharmacologic activators of other ISR kinases to rescue ISR signaling and promote mitochondrial adaptation in cells lacking PERK. We show that the HRI activator BtdCPU and the GCN2 activator halofuginone activate ISR signaling and restore ER stress sensitivity in Perk- deficient cells. However, these compounds differentially impact mitochondria. BtdCPU induces mitochondrial depolarization, leading to mitochondrial fragmentation and ISR activation through the OMA1-DELE1-HRI signaling axis. In contrast, halofuginone promotes mitochondrial elongation and altered mitochondrial respiration, mimicking the regulation induced by PERK. This shows halofuginone can compensate for deficiencies in PERK activity and promote adaptive mitochondrial remodeling, highlighting the potential for pharmacologic ISR activation to mitigate mitochondrial dysfunction and motivating the pursuit of highly-selective ISR activators.
    DOI:  https://doi.org/10.1101/2023.03.11.532186
  11. Redox Biol. 2023 Mar 15. pii: S2213-2317(23)00071-X. [Epub ahead of print]62 102670
    Hydrogen peroxide production by epidermal dual oxidase 1 regulates nociceptive sensory signals.
    Anna Pató, Kata Bölcskei, Ágnes Donkó, Diána Kaszás, Melinda Boros, Lilla Bodrogi, György Várady, Veronika F S Pape, Benoit T Roux, Balázs Enyedi, Zsuzsanna Helyes, Fiona M Watt, Gábor Sirokmány, Miklós Geiszt.
      Keratinocytes of the mammalian skin provide not only mechanical protection for the tissues, but also transmit mechanical, chemical, and thermal stimuli from the external environment to the sensory nerve terminals. Sensory nerve fibers penetrate the epidermal basement membrane and function in the tight intercellular space among keratinocytes. Here we show that epidermal keratinocytes produce hydrogen peroxide upon the activation of the NADPH oxidase dual oxidase 1 (DUOX1). This enzyme can be activated by increasing cytosolic calcium levels. Using DUOX1 knockout animals as a model system we found an increased sensitivity towards certain noxious stimuli in DUOX1-deficient animals, which is not due to structural changes in the skin as evidenced by detailed immunohistochemical and electron-microscopic analysis of epidermal tissue. We show that DUOX1 is expressed in keratinocytes but not in the neural sensory pathway. The release of hydrogen peroxide by activated DUOX1 alters both the activity of neuronal TRPA1 and redox-sensitive potassium channels expressed in dorsal root ganglia primary sensory neurons. We describe hydrogen peroxide, produced by DUOX1 as a paracrine mediator of nociceptive signal transmission. Our results indicate that a novel, hitherto unknown redox mechanism modulates noxious sensory signals.
    Keywords:  DUOX1; Dual oxidase 1; Hydrogen peroxide; NADPH oxidase; Nociception; Skin
    DOI:  https://doi.org/10.1016/j.redox.2023.102670
  12. J Biol Chem. 2023 Mar 22. pii: S0021-9258(23)00270-3. [Epub ahead of print] 104628
    The yeast Gdt1 protein mediates the exchange of H+ for Ca2+ and Mn2+ influencing the Golgi pH.
    Antoine Deschamps, Louise Thines, Anne-Sophie Colinet, Jiri Stribny, Pierre Morsomme.
      The GDT1 family is broadly spread and highly conserved among living organisms. GDT1 members have functions in key processes like glycosylation in humans and yeasts, and photosynthesis in plants. These functions are mediated by their ability to transport ions. While transport of Ca2+ or Mn2+ is well established for several GDT1 members, their transport mechanism is poorly understood. Here, we demonstrate that H+ ions are transported in exchange for Ca2+ and Mn2+ cations by the Golgi-localized yeast Gdt1 protein. We performed direct transport measurement across a biological membrane by expressing Gdt1p in Lactococcus lactis bacterial cells and by recording either the extracellular pH or the intracellular pH during the application of Ca2+, Mn2+ or H+ gradients. Besides, in vivo cytosolic and Golgi pH measurements were performed in Saccharomyces cerevisiae with genetically encoded pH probes targeted to those subcellular compartments. These data point out that the flow of H+ ions carried by Gdt1p could be reversed according to the physiological conditions. Together, our experiments unravel the influence of the relative concentration gradients for Gdt1p-mediated H+ transport and pave the way to decipher the regulatory mechanisms driving the activity of GDT1 orthologs in various biological contexts.
    Keywords:  GDT1; Golgi; Saccharomyces cerevisiae; UPF0016; exchanger; organellar pH homeostasis; proton transport
    DOI:  https://doi.org/10.1016/j.jbc.2023.104628
  13. Biophys J. 2023 Mar 20. pii: S0006-3495(23)00199-6. [Epub ahead of print]
    Influence of Electronic Polarization on the Binding of Anions to a Chloride-Pumping Rhodopsin.
    Linda X Phan, Victor Cruces Chamorro, Hector Martinez-Seara, Jason Crain, Mark S P Sansom, Stephen J Tucker.
      The functional properties of some biological ion channels and membrane transport proteins are proposed to exploit anion-hydrophobic interactions. Here, we investigate a chloride-pumping rhodopsin (ClR) as an example of a membrane protein known to contain a defined anion binding site composed predominantly of hydrophobic residues. Using molecular dynamics simulations, we explore Cl- binding to this hydrophobic site and compare the dynamics arising when electronic polarization is neglected (CHARMM36 (c36) fixed-charge force field), included implicitly (via the prosECCo force field), or included explicitly (through the polarizable force field, AMOEBA). Free energy landscapes of Cl- moving out of the binding site and into bulk solution demonstrate that the inclusion of polarization results in stronger ion binding and a second metastable binding site in ClR. Simulations focused on this hydrophobic binding site also indicate longer binding durations and closer ion proximity when polarization is included. Furthermore, simulations reveal that Cl- within this binding site interacts with an adjacent loop to facilitate rebinding events that are not observed when polarization is neglected. These results demonstrate how the inclusion of polarization can influence the behavior of anions within protein binding sites and can yield results comparable to more accurate and computationally demanding methods.
    DOI:  https://doi.org/10.1016/j.bpj.2023.03.026
  14. EMBO Rep. 2023 Mar 20. e55760
    A quantitative fluorescence-based approach to study mitochondrial protein import.
    Naintara Jain, Ridhima Gomkale, Olaf Bernhard, Peter Rehling, Luis Daniel Cruz-Zaragoza.
      Mitochondria play central roles in cellular energy production and metabolism. Most proteins required to carry out these functions are synthesized in the cytosol and imported into mitochondria. A growing number of metabolic disorders arising from mitochondrial dysfunction can be traced to errors in mitochondrial protein import. The mechanisms underlying the import of precursor proteins are commonly studied using radioactively labeled precursor proteins imported into purified mitochondria. Here, we establish a fluorescence-based import assay to analyze protein import into mitochondria. We show that fluorescently labeled precursors enable import analysis with similar sensitivity to those using radioactive precursors, yet they provide the advantage of quantifying import with picomole resolution. We adapted the import assay to a 96-well plate format allowing for fast analysis in a screening-compatible format. Moreover, we show that fluorescently labeled precursors can be used to monitor the assembly of the F1 F0 ATP synthase in purified mitochondria. Thus, we provide a sensitive fluorescence-based import assay that enables quantitative and fast import analysis.
    Keywords:  fluorescent precursor; in vitro import; mitochondria; presequence pathway; protein import
    DOI:  https://doi.org/10.15252/embr.202255760
  15. Elife. 2023 Mar 23. pii: e85289. [Epub ahead of print]12
    Lipid hydroperoxides promote sarcopenia through carbonyl stress.
    Hiroaki Eshima, Justin L Shahtout, Piyarat Siripoksup, MacKenzie J Pearson, Ziad S Mahmassani, Patrick J Ferrara, Alexis W Lyons, John Alan Maschek, Alek D Peterlin, Anthony R P Verkerke, Jordan M Johnson, Anahy Salcedo, Jonathan J Petrocelli, Edwin R Miranda, Ethan J Anderson, Sihem Boudina, Qitao Ran, James E Cox, Micah J Drummond, Katsuhiko Funai.
      Reactive oxygen species (ROS) accumulation is a cardinal feature of skeletal muscle atrophy. ROS refers to a collection of radical molecules whose cellular signals are vast, and it is unclear which downstream consequences of ROS are responsible for the loss of muscle mass and strength. Here we show that lipid hydroperoxides (LOOH) are increased with age and disuse, and the accumulation of LOOH by deletion of glutathione peroxidase 4 (GPx4) is sufficient to augment muscle atrophy. LOOH promoted atrophy in a lysosomal-dependent, proteasomal-independent manner. In young and old mice, genetic and pharmacologic neutralization of LOOH or their secondary reactive lipid aldehydes robustly prevented muscle atrophy and weakness, indicating that LOOH-derived carbonyl stress mediates age- and disuse-induced muscle dysfunction. Our findings provide novel insights for the role of LOOH in sarcopenia including a therapeutic implication by pharmacologic suppression.
    Keywords:  cell biology; mouse
    DOI:  https://doi.org/10.7554/eLife.85289
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