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Proceedings of the National Academy of... Mar 2022SignificanceThe use of biological enzyme catalysts could have huge ramifications for chemical industries. However, these enzymes are often inactive in nonbiological...
SignificanceThe use of biological enzyme catalysts could have huge ramifications for chemical industries. However, these enzymes are often inactive in nonbiological conditions, such as high temperatures, present in industrial settings. Here, we show that the enzyme PETase (polyethylene terephthalate [PET]), with potential application in plastic recycling, is stabilized at elevated temperature through complexation with random copolymers. We demonstrate this through simulations and experiments on different types of substrates. Our simulations also provide strategies for designing more enzymatically active complexes by altering polymer composition and enzyme charge distribution.
Topics: Hydrolases; Multienzyme Complexes; Plastics; Polyethylene Terephthalates; Polymers; Recycling
PubMed: 35312375
DOI: 10.1073/pnas.2119509119 -
PLoS Biology Dec 2019Peptide-based intercellular communication is a ubiquitous and ancient process that predates evolution of the nervous system. Cilia are essential signaling centers that...
Peptide-based intercellular communication is a ubiquitous and ancient process that predates evolution of the nervous system. Cilia are essential signaling centers that both receive information from the environment and secrete bioactive extracellular vesicles (ectosomes). However, the nature of these secreted signals and their biological functions remain poorly understood. Here, we report the developmentally regulated release of the peptide amidating enzyme, peptidylglycine α-amidating monooxygenase (PAM), and the presence of peptidergic signaling machinery (including propeptide precursors, subtilisin-like prohormone convertases, amidated products, and receptors) in ciliary ectosomes from the green alga Chlamydomonas. One identified amidated PAM product serves as a chemoattractant for mating-type minus gametes but repels plus gametes. Thus, cilia provide a previously unappreciated route for the secretion of amidated signaling peptides. Our study in Chlamydomonas and the presence of PAM in mammalian cilia suggest that ciliary ectosome-mediated peptidergic signaling dates to the early eukaryotes and plays key roles in metazoan physiology.
Topics: Cell Communication; Cell-Derived Microparticles; Chlamydomonas; Chlorophyta; Cilia; Mixed Function Oxygenases; Multienzyme Complexes; Peptides; Signal Transduction
PubMed: 31809498
DOI: 10.1371/journal.pbio.3000566 -
Nature Nov 2022The SEA complex (SEAC) is a growth regulator that acts as a GTPase-activating protein (GAP) towards Gtr1, a Rag GTPase that relays nutrient status to the Target of...
The SEA complex (SEAC) is a growth regulator that acts as a GTPase-activating protein (GAP) towards Gtr1, a Rag GTPase that relays nutrient status to the Target of Rapamycin Complex 1 (TORC1) in yeast. Functionally, the SEAC has been divided into two subcomplexes: SEACIT, which has GAP activity and inhibits TORC1, and SEACAT, which regulates SEACIT. This system is conserved in mammals: the GATOR complex, consisting of GATOR1 (SEACIT) and GATOR2 (SEACAT), transmits amino acid and glucose signals to mTORC1. Despite its importance, the structure of SEAC/GATOR, and thus molecular understanding of its function, is lacking. Here, we solve the cryo-EM structure of the native eight-subunit SEAC. The SEAC has a modular structure in which a COPII-like cage corresponding to SEACAT binds two flexible wings, which correspond to SEACIT. The wings are tethered to the core via Sea3, which forms part of both modules. The GAP mechanism of GATOR1 is conserved in SEACIT, and GAP activity is unaffected by SEACAT in vitro. In vivo, the wings are essential for recruitment of the SEAC to the vacuole, primarily via the EGO complex. Our results indicate that rather than being a direct inhibitor of SEACIT, SEACAT acts as a scaffold for the binding of TORC1 regulators.
Topics: Animals; Cryoelectron Microscopy; GTP Phosphohydrolases; GTPase-Activating Proteins; Mammals; Mechanistic Target of Rapamycin Complex 1; Multienzyme Complexes; Saccharomyces cerevisiae; Saccharomyces cerevisiae Proteins; Protein Subunits; Amino Acids; Glucose; COP-Coated Vesicles
PubMed: 36289347
DOI: 10.1038/s41586-022-05370-0 -
Biochimica Et Biophysica Acta. Gene... Feb 2021Gcn5 serves as the defining member of the Gcn5-related N-acetyltransferase (GNAT) superfamily of proteins that display a common structural fold and catalytic mechanism... (Review)
Review
Gcn5 serves as the defining member of the Gcn5-related N-acetyltransferase (GNAT) superfamily of proteins that display a common structural fold and catalytic mechanism involving the transfer of the acyl-group, primarily acetyl-, from CoA to an acceptor nucleophile. In the case of Gcn5, the target is the ε-amino group of lysine primarily on histones. Over the years, studies on Gcn5 structure-function have often formed the basis by which we understand the complex activities and regulation of the entire protein acetyltransferase family. It is now appreciated that protein acetylation occurs on thousands of proteins and can reversibly regulate the function of many cellular processes. In this review, we provide an overview of our fundamental understanding of catalysis, regulation of activity and substrate selection, and inhibitor development for this archetypal acetyltransferase.
Topics: Acetyl Coenzyme A; Acetylation; Biocatalysis; Crystallography; Drug Development; Enzyme Inhibitors; Epigenesis, Genetic; Gene Expression Regulation, Developmental; Histone Acetyltransferases; Histones; Lysine; Models, Molecular; Multienzyme Complexes; Protein Domains; Recombinant Proteins; Saccharomyces cerevisiae Proteins; Structure-Activity Relationship; Substrate Specificity; Transcriptional Activation; p300-CBP Transcription Factors
PubMed: 32841743
DOI: 10.1016/j.bbagrm.2020.194627 -
Molecular Cell Sep 2021With the elucidation of myriad anabolic and catabolic enzyme-catalyzed cellular pathways crisscrossing each other, an obvious question arose: how could these networks... (Review)
Review
With the elucidation of myriad anabolic and catabolic enzyme-catalyzed cellular pathways crisscrossing each other, an obvious question arose: how could these networks operate with maximal catalytic efficiency and minimal interference? A logical answer was the postulate of metabolic channeling, which in its simplest embodiment assumes that the product generated by one enzyme passes directly to a second without diffusion into the surrounding medium. This tight coupling of activities might increase a pathway's metabolic flux and/or serve to sequester unstable/toxic/reactive intermediates as well as prevent their access to other networks. Here, we present evidence for this concept, commencing with enzymes that feature a physical molecular tunnel, to multi-enzyme complexes that retain pathway substrates through electrostatics or enclosures, and finally to metabolons that feature collections of enzymes assembled into clusters with variable stoichiometric composition. Lastly, we discuss the advantages of reversibly assembled metabolons in the context of the purinosome, the purine biosynthesis metabolon.
Topics: Animals; Humans; Metabolic Networks and Pathways; Metabolism; Metabolome; Multienzyme Complexes; Protein Interaction Maps; Purines
PubMed: 34547238
DOI: 10.1016/j.molcel.2021.08.030 -
Photosynthesis Research May 2020Photosynthesis is regulated by a dynamic interplay between proteins, enzymes, pigments, lipids, and cofactors that takes place on a large spatio-temporal scale.... (Review)
Review
Photosynthesis is regulated by a dynamic interplay between proteins, enzymes, pigments, lipids, and cofactors that takes place on a large spatio-temporal scale. Molecular dynamics (MD) simulations provide a powerful toolkit to investigate dynamical processes in (bio)molecular ensembles from the (sub)picosecond to the (sub)millisecond regime and from the Å to hundreds of nm length scale. Therefore, MD is well suited to address a variety of questions arising in the field of photosynthesis research. In this review, we provide an introduction to the basic concepts of MD simulations, at atomistic and coarse-grained level of resolution. Furthermore, we discuss applications of MD simulations to model photosynthetic systems of different sizes and complexity and their connection to experimental observables. Finally, we provide a brief glance on which methods provide opportunities to capture phenomena beyond the applicability of classical MD.
Topics: Light-Harvesting Protein Complexes; Molecular Dynamics Simulation; Photosynthesis; Photosystem II Protein Complex; Quantum Theory; Thylakoids; Workflow
PubMed: 32297102
DOI: 10.1007/s11120-020-00741-y -
Proceedings of the National Academy of... Jan 2022
Topics: Bacteria; Biological Evolution; Multienzyme Complexes
PubMed: 34996854
DOI: 10.1073/pnas.2120286118 -
Nature Communications Apr 2021Regulation of mRNA translation elongation impacts nascent protein synthesis and integrity and plays a critical role in disease establishment. Here, we investigate...
Regulation of mRNA translation elongation impacts nascent protein synthesis and integrity and plays a critical role in disease establishment. Here, we investigate features linking regulation of codon-dependent translation elongation to protein expression and homeostasis. Using knockdown models of enzymes that catalyze the mcms wobble uridine tRNA modification (U-enzymes), we show that gene codon content is necessary but not sufficient to predict protein fate. While translation defects upon perturbation of U-enzymes are strictly dependent on codon content, the consequences on protein output are determined by other features. Specific hydrophilic motifs cause protein aggregation and degradation upon codon-dependent translation elongation defects. Accordingly, the combination of codon content and the presence of hydrophilic motifs define the proteome whose maintenance relies on U-tRNA modification. Together, these results uncover the mechanism linking wobble tRNA modification to mRNA translation and aggregation to maintain proteome homeostasis.
Topics: Amino Acids; Cell Line, Tumor; Codon Usage; Gene Knockdown Techniques; Humans; Hydrophobic and Hydrophilic Interactions; Multienzyme Complexes; Peptide Chain Elongation, Translational; Protein Aggregates; Proteolysis; Proteomics; RNA Processing, Post-Transcriptional; RNA, Messenger; RNA, Transfer; Uridine
PubMed: 33859181
DOI: 10.1038/s41467-021-22254-5 -
Nature Communications Nov 2021AGPATs (1-acylglycerol-3-phosphate O-acyltransferases) catalyze the acylation of lysophosphatidic acid to form phosphatidic acid (PA), a key step in the...
AGPATs (1-acylglycerol-3-phosphate O-acyltransferases) catalyze the acylation of lysophosphatidic acid to form phosphatidic acid (PA), a key step in the glycerol-3-phosphate pathway for the synthesis of phospholipids and triacylglycerols. AGPAT2 is the only AGPAT isoform whose loss-of-function mutations cause a severe form of human congenital generalized lipodystrophy. Paradoxically, AGPAT2 deficiency is known to dramatically increase the level of its product, PA. Here, we find that AGPAT2 deficiency impairs the biogenesis and growth of lipid droplets. We show that AGPAT2 deficiency compromises the stability of CDP-diacylglycerol (DAG) synthases (CDSs) and decreases CDS activity in both cell lines and mouse liver. Moreover, AGPAT2 and CDS1/2 can directly interact and form functional complexes, which promote the metabolism of PA along the CDP-DAG pathway of phospholipid synthesis. Our results provide key insights into the regulation of metabolic flux during lipid synthesis and suggest substrate channelling at a major branch point of the glycerol-3-phosphate pathway.
Topics: Acyltransferases; Animals; Biosynthetic Pathways; Cell Line; Cytidine Diphosphate Diglycerides; Diacylglycerol Cholinephosphotransferase; Fatty Acids; Humans; Lipid Droplets; Lipogenesis; Liver; Mice; Multienzyme Complexes; Oleic Acid; Phosphatidic Acids
PubMed: 34824276
DOI: 10.1038/s41467-021-27279-4 -
Current Opinion in Structural Biology Apr 2021The RNA exosome is a conserved complex of proteins that mediates 3'-5' RNA processing and decay. Its functions range from processing of non-coding RNAs such as ribosomal... (Review)
Review
The RNA exosome is a conserved complex of proteins that mediates 3'-5' RNA processing and decay. Its functions range from processing of non-coding RNAs such as ribosomal RNAs and decay of aberrant transcripts in the nucleus to cytoplasmic mRNA turnover and quality control. Ski2-like RNA helicases translocate substrates to exosome-associated ribonucleases and interact with the RNA exosome either directly or as part of multi-subunit helicase-containing complexes that identify and target RNA substrates for decay. Recent structures of these helicases with their RNA-binding partners or the RNA exosome have advanced our understanding of a system of modular and mutually exclusive contacts between the exosome and exosome-associated helicase complexes that shape the transcriptome by orchestrating exosome-dependent 3'-5' decay.
Topics: Exosome Multienzyme Ribonuclease Complex; Exosomes; Humans; RNA; RNA Helicases; RNA Stability; Saccharomyces cerevisiae Proteins
PubMed: 33147539
DOI: 10.1016/j.sbi.2020.09.010