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Zafar H, Hassan AH, Demo G. Translation machinery captured in motion. Wiley Interdiscip Rev RNA 2023; 14:e1792. [PMID: 37132456 DOI: 10.1002/wrna.1792] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 03/14/2023] [Accepted: 04/17/2023] [Indexed: 05/04/2023]
Abstract
Translation accuracy is one of the most critical factors for protein synthesis. It is regulated by the ribosome and its dynamic behavior, along with translation factors that direct ribosome rearrangements to make translation a uniform process. Earlier structural studies of the ribosome complex with arrested translation factors laid the foundation for an understanding of ribosome dynamics and the translation process as such. Recent technological advances in time-resolved and ensemble cryo-EM have made it possible to study translation in real time at high resolution. These methods provided a detailed view of translation in bacteria for all three phases: initiation, elongation, and termination. In this review, we focus on translation factors (in some cases GTP activation) and their ability to monitor and respond to ribosome organization to enable efficient and accurate translation. This article is categorized under: Translation > Ribosome Structure/Function Translation > Mechanisms.
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Affiliation(s)
- Hassan Zafar
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Ahmed H Hassan
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Gabriel Demo
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
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2
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Jouravleva K, Golovenko D, Demo G, Dutcher RC, Hall TMT, Zamore PD, Korostelev AA. Structural basis of microRNA biogenesis by Dicer-1 and its partner protein Loqs-PB. Mol Cell 2022; 82:4049-4063.e6. [PMID: 36182693 PMCID: PMC9637774 DOI: 10.1016/j.molcel.2022.09.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 06/24/2022] [Accepted: 08/31/2022] [Indexed: 12/22/2022]
Abstract
In animals and plants, Dicer enzymes collaborate with double-stranded RNA-binding domain (dsRBD) proteins to convert precursor-microRNAs (pre-miRNAs) into miRNA duplexes. We report six cryo-EM structures of Drosophila Dicer-1 that show how Dicer-1 and its partner Loqs‑PB cooperate (1) before binding pre-miRNA, (2) after binding and in a catalytically competent state, (3) after nicking one arm of the pre-miRNA, and (4) following complete dicing and initial product release. Our reconstructions suggest that pre-miRNA binds a rare, open conformation of the Dicer‑1⋅Loqs‑PB heterodimer. The Dicer-1 dsRBD and three Loqs‑PB dsRBDs form a tight belt around the pre-miRNA, distorting the RNA helix to place the scissile phosphodiester bonds in the RNase III active sites. Pre-miRNA cleavage shifts the dsRBDs and partially closes Dicer-1, which may promote product release. Our data suggest a model for how the Dicer‑1⋅Loqs‑PB complex affects a complete cycle of pre-miRNA recognition, stepwise endonuclease cleavage, and product release.
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Affiliation(s)
- Karina Jouravleva
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Dmitrij Golovenko
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Gabriel Demo
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, MA 01605, USA; Central European Institute of Technology, Masaryk University, Kamenice 5, Brno 62500, Czech Republic
| | - Robert C Dutcher
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, 111 T.W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Traci M Tanaka Hall
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, 111 T.W. Alexander Drive, Research Triangle Park, NC 27709, USA.
| | - Phillip D Zamore
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, MA 01605, USA; Howard Hughes Medical Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, MA 01605, USA.
| | - Andrei A Korostelev
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, MA 01605, USA.
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Loveland AB, Svidritskiy E, Susorov D, Lee S, Park A, Zvornicanin S, Demo G, Gao FB, Korostelev AA. Ribosome inhibition by C9ORF72-ALS/FTD-associated poly-PR and poly-GR proteins revealed by cryo-EM. Nat Commun 2022; 13:2776. [PMID: 35589706 PMCID: PMC9120013 DOI: 10.1038/s41467-022-30418-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 04/29/2022] [Indexed: 12/15/2022] Open
Abstract
Toxic dipeptide-repeat (DPR) proteins are produced from expanded G4C2 repeats in the C9ORF72 gene, the most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Two DPR proteins, poly-PR and poly-GR, repress cellular translation but the molecular mechanism remains unknown. Here we show that poly-PR and poly-GR of ≥20 repeats inhibit the ribosome's peptidyl-transferase activity at nanomolar concentrations, comparable to specific translation inhibitors. High-resolution cryogenic electron microscopy (cryo-EM) reveals that poly-PR and poly-GR block the polypeptide tunnel of the ribosome, extending into the peptidyl-transferase center (PTC). Consistent with these findings, the macrolide erythromycin, which binds in the tunnel, competes with poly-PR and restores peptidyl-transferase activity. Our results demonstrate that strong and specific binding of poly-PR and poly-GR in the ribosomal tunnel blocks translation, revealing the structural basis of their toxicity in C9ORF72-ALS/FTD.
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Affiliation(s)
- Anna B Loveland
- RNA Therapeutics Institute, UMass Chan Medical School, 368 Plantation Street, Worcester, MA, 01605, USA
| | - Egor Svidritskiy
- RNA Therapeutics Institute, UMass Chan Medical School, 368 Plantation Street, Worcester, MA, 01605, USA
| | - Denis Susorov
- RNA Therapeutics Institute, UMass Chan Medical School, 368 Plantation Street, Worcester, MA, 01605, USA
| | - Soojin Lee
- Department of Neurology, UMass Chan Medical School, 368 Plantation Street, Worcester, MA, 01605, USA
| | - Alexander Park
- RNA Therapeutics Institute, UMass Chan Medical School, 368 Plantation Street, Worcester, MA, 01605, USA
| | - Sarah Zvornicanin
- RNA Therapeutics Institute, UMass Chan Medical School, 368 Plantation Street, Worcester, MA, 01605, USA
| | - Gabriel Demo
- RNA Therapeutics Institute, UMass Chan Medical School, 368 Plantation Street, Worcester, MA, 01605, USA
- Central European Institute of Technology, Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic
| | - Fen-Biao Gao
- Department of Neurology, UMass Chan Medical School, 368 Plantation Street, Worcester, MA, 01605, USA.
| | - Andrei A Korostelev
- RNA Therapeutics Institute, UMass Chan Medical School, 368 Plantation Street, Worcester, MA, 01605, USA.
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Gaubitz C, Liu X, Pajak J, Stone NP, Hayes JA, Demo G, Kelch BA. Cryo-EM structures reveal high-resolution mechanism of a DNA polymerase sliding clamp loader. eLife 2022; 11:74175. [PMID: 35179493 PMCID: PMC8893722 DOI: 10.7554/elife.74175] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 02/01/2022] [Indexed: 11/13/2022] Open
Abstract
Sliding clamps are ring-shaped protein complexes that are integral to the DNA replication machinery of all life. Sliding clamps are opened and installed onto DNA by clamp loader AAA+ ATPase complexes. However, how a clamp loader opens and closes the sliding clamp around DNA is still unknown. Here, we describe structures of the Saccharomyces cerevisiae clamp loader Replication Factor C (RFC) bound to its cognate sliding clamp Proliferating Cell Nuclear Antigen (PCNA) en route to successful loading. RFC first binds to PCNA in a dynamic, closed conformation that blocks both ATPase activity and DNA binding. RFC then opens the PCNA ring through a large-scale ‘crab-claw’ expansion of both RFC and PCNA that explains how RFC prefers initial binding of PCNA over DNA. Next, the open RFC:PCNA complex binds DNA and interrogates the primer-template junction using a surprising base-flipping mechanism. Our structures indicate that initial PCNA opening and subsequent closure around DNA do not require ATP hydrolysis, but are driven by binding energy. ATP hydrolysis, which is necessary for RFC release, is triggered by interactions with both PCNA and DNA, explaining RFC’s switch-like ATPase activity. Our work reveals how a AAA+ machine undergoes dramatic conformational changes for achieving binding preference and substrate remodeling.
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Affiliation(s)
- Christl Gaubitz
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
| | - Xingchen Liu
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
| | - Joshua Pajak
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
| | - Nicholas P Stone
- Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
| | - Janelle A Hayes
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
| | - Gabriel Demo
- Central European Institute of Technology - Masaryk University, Brno, Czech Republic
| | - Brian A Kelch
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
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Carbone CE, Loveland AB, Gamper HB, Hou YM, Demo G, Korostelev AA. Time-resolved cryo-EM visualizes ribosomal translocation with EF-G and GTP. Nat Commun 2021; 12:7236. [PMID: 34903725 PMCID: PMC8668904 DOI: 10.1038/s41467-021-27415-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 11/12/2021] [Indexed: 11/18/2022] Open
Abstract
During translation, a conserved GTPase elongation factor-EF-G in bacteria or eEF2 in eukaryotes-translocates tRNA and mRNA through the ribosome. EF-G has been proposed to act as a flexible motor that propels tRNA and mRNA movement, as a rigid pawl that biases unidirectional translocation resulting from ribosome rearrangements, or by various combinations of motor- and pawl-like mechanisms. Using time-resolved cryo-EM, we visualized GTP-catalyzed translocation without inhibitors, capturing elusive structures of ribosome•EF-G intermediates at near-atomic resolution. Prior to translocation, EF-G binds near peptidyl-tRNA, while the rotated 30S subunit stabilizes the EF-G GTPase center. Reverse 30S rotation releases Pi and translocates peptidyl-tRNA and EF-G by ~20 Å. An additional 4-Å translocation initiates EF-G dissociation from a transient ribosome state with highly swiveled 30S head. The structures visualize how nearly rigid EF-G rectifies inherent and spontaneous ribosomal dynamics into tRNA-mRNA translocation, whereas GTP hydrolysis and Pi release drive EF-G dissociation.
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Affiliation(s)
| | - Anna B Loveland
- RNA Therapeutics Institute, UMass Chan Medical School, Worcester, MA, USA
| | - Howard B Gamper
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Ya-Ming Hou
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Gabriel Demo
- RNA Therapeutics Institute, UMass Chan Medical School, Worcester, MA, USA.
- Central European Institute of Technology, Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic.
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Demo G, Gamper HB, Loveland AB, Masuda I, Carbone CE, Svidritskiy E, Hou YM, Korostelev AA. Structural basis for +1 ribosomal frameshifting during EF-G-catalyzed translocation. Nat Commun 2021; 12:4644. [PMID: 34330903 PMCID: PMC8324841 DOI: 10.1038/s41467-021-24911-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 07/12/2021] [Indexed: 12/25/2022] Open
Abstract
Frameshifting of mRNA during translation provides a strategy to expand the coding repertoire of cells and viruses. How and where in the elongation cycle +1-frameshifting occurs remains poorly understood. We describe seven ~3.5-Å-resolution cryo-EM structures of 70S ribosome complexes, allowing visualization of elongation and translocation by the GTPase elongation factor G (EF-G). Four structures with a + 1-frameshifting-prone mRNA reveal that frameshifting takes place during translocation of tRNA and mRNA. Prior to EF-G binding, the pre-translocation complex features an in-frame tRNA-mRNA pairing in the A site. In the partially translocated structure with EF-G•GDPCP, the tRNA shifts to the +1-frame near the P site, rendering the freed mRNA base to bulge between the P and E sites and to stack on the 16S rRNA nucleotide G926. The ribosome remains frameshifted in the nearly post-translocation state. Our findings demonstrate that the ribosome and EF-G cooperate to induce +1 frameshifting during tRNA-mRNA translocation.
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MESH Headings
- Biocatalysis
- Cryoelectron Microscopy
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Escherichia coli Proteins/chemistry
- Escherichia coli Proteins/genetics
- Escherichia coli Proteins/metabolism
- Frameshifting, Ribosomal/genetics
- Models, Molecular
- Nucleic Acid Conformation
- Peptide Chain Elongation, Translational/genetics
- Peptide Elongation Factor G/chemistry
- Peptide Elongation Factor G/genetics
- Peptide Elongation Factor G/metabolism
- Protein Conformation
- RNA, Messenger/chemistry
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 16S/metabolism
- RNA, Transfer/chemistry
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
- Ribosomes/genetics
- Ribosomes/metabolism
- Ribosomes/ultrastructure
- tRNA Methyltransferases/genetics
- tRNA Methyltransferases/metabolism
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Affiliation(s)
- Gabriel Demo
- RNA Therapeutics Institute, Department of Biochemistry and Molecular Pharmacology, UMass Medical School, Worcester, MA, USA
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Howard B Gamper
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Anna B Loveland
- RNA Therapeutics Institute, Department of Biochemistry and Molecular Pharmacology, UMass Medical School, Worcester, MA, USA
| | - Isao Masuda
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Christine E Carbone
- RNA Therapeutics Institute, Department of Biochemistry and Molecular Pharmacology, UMass Medical School, Worcester, MA, USA
| | - Egor Svidritskiy
- RNA Therapeutics Institute, Department of Biochemistry and Molecular Pharmacology, UMass Medical School, Worcester, MA, USA
| | - Ya-Ming Hou
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA.
| | - Andrei A Korostelev
- RNA Therapeutics Institute, Department of Biochemistry and Molecular Pharmacology, UMass Medical School, Worcester, MA, USA.
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Abstract
Ribosomes stalled during translation must be rescued to replenish the pool of translation-competent ribosomal subunits. Bacterial alternative rescue factor B (ArfB) releases nascent peptides from ribosomes stalled on mRNAs truncated at the A site, allowing ribosome recycling. Prior structural work revealed that ArfB recognizes such ribosomes by inserting its C-terminal α-helix into the vacant mRNA tunnel. In this work, we report that ArfB can efficiently recognize a wider range of mRNA substrates, including longer mRNAs that extend beyond the A-site codon. Single-particle cryo-EM unveils that ArfB employs two modes of function depending on the mRNA length. ArfB acts as a monomer to accommodate a shorter mRNA in the ribosomal A site. By contrast, longer mRNAs are displaced from the mRNA tunnel by more than 20 Å and are stabilized in the intersubunit space by dimeric ArfB. Uncovering distinct modes of ArfB function resolves conflicting biochemical and structural studies, and may lead to re-examination of other ribosome rescue pathways, whose functions depend on mRNA lengths.
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Affiliation(s)
- Christine E Carbone
- RNA Therapeutics Institute, Department of Biochemistry and Molecular Pharmacology, UMass Medical School, Worcester, Massachusetts, 01605, United States
| | - Gabriel Demo
- RNA Therapeutics Institute, Department of Biochemistry and Molecular Pharmacology, UMass Medical School, Worcester, Massachusetts, 01605, United States
- Central European Institute of Technology, Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic
| | - Rohini Madireddy
- RNA Therapeutics Institute, Department of Biochemistry and Molecular Pharmacology, UMass Medical School, Worcester, Massachusetts, 01605, United States
- Medicago Inc., 7 Triangle drive, Durham, NC, 27713, USA
| | - Egor Svidritskiy
- RNA Therapeutics Institute, Department of Biochemistry and Molecular Pharmacology, UMass Medical School, Worcester, Massachusetts, 01605, United States.
- Sanofi, 49 New York Ave, Suite 3660, Framingham, MA, 01701, USA.
| | - Andrei A Korostelev
- RNA Therapeutics Institute, Department of Biochemistry and Molecular Pharmacology, UMass Medical School, Worcester, Massachusetts, 01605, United States.
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Loveland AB, Demo G, Korostelev AA. Cryo-EM of elongating ribosome with EF-Tu•GTP elucidates tRNA proofreading. Nature 2020; 584:640-645. [PMID: 32612237 PMCID: PMC7483604 DOI: 10.1038/s41586-020-2447-x] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 04/10/2020] [Indexed: 11/13/2022]
Abstract
Ribosomes accurately decode mRNA by proofreading each aminoacyl-tRNA delivered by elongation factor EF-Tu1. Understanding the molecular mechanism of proofreading requires visualizing GTP-catalyzed elongation, which has remained a challenge2–4. Here, time-resolved cryo-EM revealed 33 states following aminoacyl-tRNA delivery by EF-Tu•GTP. Instead of locking cognate tRNA upon initial recognition, the ribosomal decoding center (DC) dynamically monitors codon-anticodon interactions before and after GTP hydrolysis. GTP hydrolysis allows EF-Tu’s GTPase domain to extend away, releasing EF-Tu from tRNA. Then, the 30S subunit locks cognate tRNA in the DC, and rotates, enabling the tRNA to bypass 50S protrusions during accommodation into the peptidyl transferase center. By contrast, the DC fails to lock near-cognate tRNA, allowing dissociation of near-cognate tRNA during both initial selection (before GTP hydrolysis) and proofreading (after GTP hydrolysis). These findings reveal structural similarity between initial selection5,6 and the previously unseen proofreading, which together govern efficient rejection of incorrect tRNA.
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Affiliation(s)
- Anna B Loveland
- RNA Therapeutics Institute, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Gabriel Demo
- RNA Therapeutics Institute, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA.,Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Andrei A Korostelev
- RNA Therapeutics Institute, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA.
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Sýkorová P, Novotná J, Demo G, Pompidor G, Dubská E, Komárek J, Fujdiarová E, Houser J, Hároníková L, Varrot A, Shilova N, Imberty A, Bovin N, Pokorná M, Wimmerová M. Characterization of novel lectins from Burkholderia pseudomallei and Chromobacterium violaceum with seven-bladed β-propeller fold. Int J Biol Macromol 2020; 152:1113-1124. [DOI: 10.1016/j.ijbiomac.2019.10.200] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 10/22/2019] [Accepted: 10/23/2019] [Indexed: 01/08/2023]
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Svidritskiy E, Demo G, Loveland AB, Xu C, Korostelev AA. Extensive ribosome and RF2 rearrangements during translation termination. eLife 2019; 8:46850. [PMID: 31513010 PMCID: PMC6742477 DOI: 10.7554/elife.46850] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 08/28/2019] [Indexed: 12/31/2022] Open
Abstract
Protein synthesis ends when a ribosome reaches an mRNA stop codon. Release factors (RFs) decode the stop codon, hydrolyze peptidyl-tRNA to release the nascent protein, and then dissociate to allow ribosome recycling. To visualize termination by RF2, we resolved a cryo-EM ensemble of E. coli 70S•RF2 structures at up to 3.3 Å in a single sample. Five structures suggest a highly dynamic termination pathway. Upon peptidyl-tRNA hydrolysis, the CCA end of deacyl-tRNA departs from the peptidyl transferase center. The catalytic GGQ loop of RF2 is rearranged into a long β-hairpin that plugs the peptide tunnel, biasing a nascent protein toward the ribosome exit. Ribosomal intersubunit rotation destabilizes the catalytic RF2 domain on the 50S subunit and disassembles the central intersubunit bridge B2a, resulting in RF2 departure. Our structures visualize how local rearrangements and spontaneous inter-subunit rotation poise the newly-made protein and RF2 to dissociate in preparation for ribosome recycling.
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Affiliation(s)
- Egor Svidritskiy
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, United States
| | - Gabriel Demo
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, United States
| | - Anna B Loveland
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, United States
| | - Chen Xu
- Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
| | - Andrei A Korostelev
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, United States.,Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
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11
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Abstract
Accurate translation termination by release factors (RFs) is critical for the integrity of cellular proteomes. Premature termination on sense codons, for example, results in truncated proteins, whose accumulation could be detrimental to the cell. Nevertheless, some sense codons are prone to triggering premature termination, but the structural basis for this is unclear. To investigate premature termination, we determined a cryo-EM structure of the Escherichia coli 70S ribosome bound with RF1 in response to a UAU (Tyr) sense codon. The structure reveals that RF1 recognizes a UAU codon similarly to a UAG stop codon, suggesting that sense codons induce premature termination because they structurally mimic a stop codon. Hydrophobic interaction between the nucleobase of U3 (the third position of the UAU codon) and conserved Ile-196 in RF1 is important for misreading the UAU codon. Analyses of RNA binding in ribonucleoprotein complexes or by amino acids reveal that Ile-U packing is a frequent protein-RNA-binding motif with key functional implications. We discuss parallels with eukaryotic translation termination by the release factor eRF1.
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Affiliation(s)
- Egor Svidritskiy
- From the RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - Gabriel Demo
- From the RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - Andrei A Korostelev
- From the RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts 01605
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12
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Komárek J, Ivanov Kavková E, Houser J, Horáčková A, Ždánská J, Demo G, Wimmerová M. Structure and properties of AB21, a novelAgaricus bisporusprotein with structural relation to bacterial pore-forming toxins. Proteins 2018; 86:897-911. [DOI: 10.1002/prot.25522] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 04/23/2018] [Accepted: 04/26/2018] [Indexed: 12/13/2022]
Affiliation(s)
- Jan Komárek
- Central European Institute of Technology, Masaryk University, Kamenice 5; Brno 62500 Czech Republic
- National Centre for Biomolecular Research; Faculty of Science, Masaryk University, Kotlarska 2; Brno 61137 Czech Republic
| | - Eva Ivanov Kavková
- Department of Biochemistry; Faculty of Science, Masaryk University, Kotlarska 2; Brno 61137 Czech Republic
| | - Josef Houser
- Central European Institute of Technology, Masaryk University, Kamenice 5; Brno 62500 Czech Republic
- National Centre for Biomolecular Research; Faculty of Science, Masaryk University, Kotlarska 2; Brno 61137 Czech Republic
| | - Aneta Horáčková
- Department of Biochemistry; Faculty of Science, Masaryk University, Kotlarska 2; Brno 61137 Czech Republic
| | - Jitka Ždánská
- Central European Institute of Technology, Masaryk University, Kamenice 5; Brno 62500 Czech Republic
| | - Gabriel Demo
- Central European Institute of Technology, Masaryk University, Kamenice 5; Brno 62500 Czech Republic
- National Centre for Biomolecular Research; Faculty of Science, Masaryk University, Kotlarska 2; Brno 61137 Czech Republic
| | - Michaela Wimmerová
- Central European Institute of Technology, Masaryk University, Kamenice 5; Brno 62500 Czech Republic
- National Centre for Biomolecular Research; Faculty of Science, Masaryk University, Kotlarska 2; Brno 61137 Czech Republic
- Department of Biochemistry; Faculty of Science, Masaryk University, Kotlarska 2; Brno 61137 Czech Republic
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13
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Demo G, Rasouly A, Vasilyev N, Svetlov V, Loveland AB, Diaz-Avalos R, Grigorieff N, Nudler E, Korostelev AA. Structure of RNA polymerase bound to ribosomal 30S subunit. eLife 2017; 6:28560. [PMID: 29027901 PMCID: PMC5655137 DOI: 10.7554/elife.28560] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 10/11/2017] [Indexed: 11/29/2022] Open
Abstract
In bacteria, mRNA transcription and translation are coupled to coordinate optimal gene expression and maintain genome stability. Coupling is thought to involve direct interactions between RNA polymerase (RNAP) and the translational machinery. We present cryo-EM structures of E. coli RNAP core bound to the small ribosomal 30S subunit. The complex is stable under cell-like ionic conditions, consistent with functional interaction between RNAP and the 30S subunit. The RNA exit tunnel of RNAP aligns with the Shine-Dalgarno-binding site of the 30S subunit. Ribosomal protein S1 forms a wall of the tunnel between RNAP and the 30S subunit, consistent with its role in directing mRNAs onto the ribosome. The nucleic-acid-binding cleft of RNAP samples distinct conformations, suggesting different functional states during transcription-translation coupling. The architecture of the 30S•RNAP complex provides a structural basis for co-localization of the transcriptional and translational machineries, and inform future mechanistic studies of coupled transcription and translation.
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Affiliation(s)
- Gabriel Demo
- RNA Therapeutics Institute, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
| | - Aviram Rasouly
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, United States.,Howard Hughes Medical Institute, New York University School of Medicine, New York, United States
| | - Nikita Vasilyev
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, United States
| | - Vladimir Svetlov
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, United States
| | - Anna B Loveland
- RNA Therapeutics Institute, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
| | - Ruben Diaz-Avalos
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Nikolaus Grigorieff
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Evgeny Nudler
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, United States.,Howard Hughes Medical Institute, New York University School of Medicine, New York, United States
| | - Andrei A Korostelev
- RNA Therapeutics Institute, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
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14
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Otrusinová O, Demo G, Padrta P, Jaseňáková Z, Pekárová B, Gelová Z, Szmitkowska A, Kadeřávek P, Jansen S, Zachrdla M, Klumpler T, Marek J, Hritz J, Janda L, Iwaï H, Wimmerová M, Hejátko J, Žídek L. Conformational dynamics are a key factor in signaling mediated by the receiver domain of a sensor histidine kinase from Arabidopsis thaliana. J Biol Chem 2017; 292:17525-17540. [PMID: 28860196 DOI: 10.1074/jbc.m117.790212] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 08/28/2017] [Indexed: 11/06/2022] Open
Abstract
Multistep phosphorelay (MSP) cascades mediate responses to a wide spectrum of stimuli, including plant hormonal signaling, but several aspects of MSP await elucidation. Here, we provide first insight into the key step of MSP-mediated phosphotransfer in a eukaryotic system, the phosphorylation of the receiver domain of the histidine kinase CYTOKININ-INDEPENDENT 1 (CKI1RD) from Arabidopsis thaliana We observed that the crystal structures of free, Mg2+-bound, and beryllofluoridated CKI1RD (a stable analogue of the labile phosphorylated form) were identical and similar to the active state of receiver domains of bacterial response regulators. However, the three CKI1RD variants exhibited different conformational dynamics in solution. NMR studies revealed that Mg2+ binding and beryllofluoridation alter the conformational equilibrium of the β3-α3 loop close to the phosphorylation site. Mutations that perturbed the conformational behavior of the β3-α3 loop while keeping the active-site aspartate intact resulted in suppression of CKI1 function. Mechanistically, homology modeling indicated that the β3-α3 loop directly interacts with the ATP-binding site of the CKI1 histidine kinase domain. The functional relevance of the conformational dynamics observed in the β3-α3 loop of CKI1RD was supported by a comparison with another A. thaliana histidine kinase, ETR1. In contrast to the highly dynamic β3-α3 loop of CKI1RD, the corresponding loop of the ETR1 receiver domain (ETR1RD) exhibited little conformational exchange and adopted a different orientation in crystals. Biochemical data indicated that ETR1RD is involved in phosphorylation-independent signaling, implying a direct link between conformational behavior and the ability of eukaryotic receiver domains to participate in MSP.
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Affiliation(s)
- Olga Otrusinová
- From the Central European Institute of Technology and.,Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic and
| | - Gabriel Demo
- From the Central European Institute of Technology and
| | - Petr Padrta
- From the Central European Institute of Technology and.,Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic and
| | - Zuzana Jaseňáková
- From the Central European Institute of Technology and.,Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic and
| | - Blanka Pekárová
- From the Central European Institute of Technology and.,Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic and
| | - Zuzana Gelová
- From the Central European Institute of Technology and.,Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic and
| | - Agnieszka Szmitkowska
- From the Central European Institute of Technology and.,Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic and
| | - Pavel Kadeřávek
- From the Central European Institute of Technology and.,Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic and
| | - Séverine Jansen
- From the Central European Institute of Technology and.,Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic and
| | - Milan Zachrdla
- From the Central European Institute of Technology and.,Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic and
| | | | - Jaromír Marek
- From the Central European Institute of Technology and
| | - Jozef Hritz
- From the Central European Institute of Technology and
| | - Lubomír Janda
- From the Central European Institute of Technology and.,Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic and
| | - Hideo Iwaï
- the Institute of Biotechnology, University of Helsinki, Viikinkaari 1 (P. O. Box 65), 00014 Helsinki, Finland
| | - Michaela Wimmerová
- From the Central European Institute of Technology and.,Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic and
| | - Jan Hejátko
- From the Central European Institute of Technology and.,Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic and
| | - Lukáš Žídek
- From the Central European Institute of Technology and .,Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic and
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15
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Jančaříková G, Houser J, Dobeš P, Demo G, Hyršl P, Wimmerová M. Characterization of novel bangle lectin from Photorhabdus asymbiotica with dual sugar-binding specificity and its effect on host immunity. PLoS Pathog 2017; 13:e1006564. [PMID: 28806750 PMCID: PMC5584973 DOI: 10.1371/journal.ppat.1006564] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 09/05/2017] [Accepted: 07/31/2017] [Indexed: 01/08/2023] Open
Abstract
Photorhabdus asymbiotica is one of the three recognized species of the Photorhabdus genus, which consists of gram-negative bioluminescent bacteria belonging to the family Morganellaceae. These bacteria live in a symbiotic relationship with nematodes from the genus Heterorhabditis, together forming a complex that is highly pathogenic for insects. Unlike other Photorhabdus species, which are strictly entomopathogenic, P. asymbiotica is unique in its ability to act as an emerging human pathogen. Analysis of the P. asymbiotica genome identified a novel fucose-binding lectin designated PHL with a strong sequence similarity to the recently described P. luminescens lectin PLL. Recombinant PHL exhibited high affinity for fucosylated carbohydrates and the unusual disaccharide 3,6-O-Me2-Glcβ1-4(2,3-O-Me2)Rhaα-O-(p-C6H4)-OCH2CH2NH2 from Mycobacterium leprae. Based on its crystal structure, PHL forms a seven-bladed β-propeller assembling into a homo-dimer with an inter-subunit disulfide bridge. Investigating complexes with different ligands revealed the existence of two sets of binding sites per monomer-the first type prefers l-fucose and its derivatives, whereas the second type can bind d-galactose. Based on the sequence analysis, PHL could contain up to twelve binding sites per monomer. PHL was shown to interact with all types of red blood cells and insect haemocytes. Interestingly, PHL inhibited the production of reactive oxygen species induced by zymosan A in human blood and antimicrobial activity both in human blood, serum and insect haemolymph. Concurrently, PHL increased the constitutive level of oxidants in the blood and induced melanisation in haemolymph. Our results suggest that PHL might play a crucial role in the interaction of P. asymbiotica with both human and insect hosts.
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Affiliation(s)
- Gita Jančaříková
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Josef Houser
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Pavel Dobeš
- Department of Animal Physiology and Immunology, Institute of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Gabriel Demo
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Pavel Hyršl
- Department of Animal Physiology and Immunology, Institute of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Michaela Wimmerová
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
- * E-mail:
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16
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Abstract
Gene translation depends on accurate decoding of mRNA, the structural mechanism of which remains poorly understood. Ribosomes decode mRNA codons by selecting cognate aminoacyl-tRNAs delivered by elongation factor Tu (EF-Tu). Here we present high-resolution structural ensembles of ribosomes with cognate or near-cognate aminoacyl-tRNAs delivered by EF-Tu. Both cognate and near-cognate tRNA anticodons explore the aminoacyl-tRNA-binding site (A site) of an open 30S subunit, while inactive EF-Tu is separated from the 50S subunit. A transient conformation of decoding-centre nucleotide G530 stabilizes the cognate codon-anticodon helix, initiating step-wise 'latching' of the decoding centre. The resulting closure of the 30S subunit docks EF-Tu at the sarcin-ricin loop of the 50S subunit, activating EF-Tu for GTP hydrolysis and enabling accommodation of the aminoacyl-tRNA. By contrast, near-cognate complexes fail to induce the G530 latch, thus favouring open 30S pre-accommodation intermediates with inactive EF-Tu. This work reveals long-sought structural differences between the pre-accommodation of cognate and near-cognate tRNAs that elucidate the mechanism of accurate decoding.
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MESH Headings
- Anticodon/chemistry
- Anticodon/genetics
- Anticodon/ultrastructure
- Codon/chemistry
- Codon/genetics
- Codon/ultrastructure
- Cryoelectron Microscopy
- Escherichia coli/chemistry
- Escherichia coli/genetics
- Escherichia coli/ultrastructure
- GTP Phosphohydrolases/metabolism
- GTP Phosphohydrolases/ultrastructure
- Guanosine Triphosphate/metabolism
- Hydrolysis
- Models, Molecular
- Peptide Elongation Factor Tu/metabolism
- Peptide Elongation Factor Tu/ultrastructure
- Protein Biosynthesis
- Protein Domains
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 16S/metabolism
- RNA, Ribosomal, 16S/ultrastructure
- RNA, Transfer, Amino Acyl/genetics
- RNA, Transfer, Amino Acyl/metabolism
- RNA, Transfer, Amino Acyl/ultrastructure
- Ribosome Subunits/chemistry
- Ribosome Subunits/metabolism
- Ribosome Subunits/ultrastructure
- Ribosomes/chemistry
- Ribosomes/metabolism
- Ribosomes/ultrastructure
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Affiliation(s)
- Anna B. Loveland
- RNA Therapeutics Institute, Department of Biochemistry and Molecular Pharmacology. University of Massachusetts Medical School, 368 Plantation St., Worcester, MA 01605, USA
| | - Gabriel Demo
- RNA Therapeutics Institute, Department of Biochemistry and Molecular Pharmacology. University of Massachusetts Medical School, 368 Plantation St., Worcester, MA 01605, USA
| | - Nikolaus Grigorieff
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA 20147, USA
| | - Andrei A. Korostelev
- RNA Therapeutics Institute, Department of Biochemistry and Molecular Pharmacology. University of Massachusetts Medical School, 368 Plantation St., Worcester, MA 01605, USA
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17
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Demo G, Svidritskiy E, Madireddy R, Diaz-Avalos R, Grant T, Grigorieff N, Sousa D, Korostelev AA. Mechanism of ribosome rescue by ArfA and RF2. eLife 2017; 6. [PMID: 28300532 PMCID: PMC5378476 DOI: 10.7554/elife.23687] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2016] [Accepted: 03/14/2017] [Indexed: 11/13/2022] Open
Abstract
ArfA rescues ribosomes stalled on truncated mRNAs by recruiting release factor RF2, which normally binds stop codons to catalyze peptide release. We report two 3.2 Å resolution cryo-EM structures – determined from a single sample – of the 70S ribosome with ArfA•RF2 in the A site. In both states, the ArfA C-terminus occupies the mRNA tunnel downstream of the A site. One state contains a compact inactive RF2 conformation. Ordering of the ArfA N-terminus in the second state rearranges RF2 into an extended conformation that docks the catalytic GGQ motif into the peptidyl-transferase center. Our work thus reveals the structural dynamics of ribosome rescue. The structures demonstrate how ArfA ‘senses’ the vacant mRNA tunnel and activates RF2 to mediate peptide release without a stop codon, allowing stalled ribosomes to be recycled. DOI:http://dx.doi.org/10.7554/eLife.23687.001
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Affiliation(s)
- Gabriel Demo
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, United States
| | - Egor Svidritskiy
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, United States
| | - Rohini Madireddy
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
| | - Ruben Diaz-Avalos
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Timothy Grant
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Nikolaus Grigorieff
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Duncan Sousa
- Department of Biological Science, Florida State University, Tallahassee, United States
| | - Andrei A Korostelev
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, United States.,Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
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18
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Kumar A, Sýkorová P, Demo G, Dobeš P, Hyršl P, Wimmerová M. A Novel Fucose-binding Lectin from Photorhabdus luminescens (PLL) with an Unusual Heptabladed β-Propeller Tetrameric Structure. J Biol Chem 2016; 291:25032-25049. [PMID: 27758853 DOI: 10.1074/jbc.m115.693473] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2015] [Revised: 09/18/2016] [Indexed: 01/08/2023] Open
Abstract
Photorhabdus luminescens is known for its symbiosis with the entomopathogenic nematode Heterorhabditis bacteriophora and its pathogenicity toward insect larvae. A hypothetical protein from P. luminescens was identified, purified from the native source, and characterized as an l-fucose-binding lectin, named P. luminescens lectin (PLL). Glycan array and biochemical characterization data revealed PLL to be specific toward l-fucose and the disaccharide glycan 3,6-O-Me2-Glcβ1-4(2,3-O-Me2)Rhaα-O-(p-C6H4)-OCH2CH2NH2 PLL was discovered to be a homotetramer with an intersubunit disulfide bridge. The crystal structures of native and recombinant PLL revealed a seven-bladed β-propeller fold creating seven putative fucose-binding sites per monomer. The crystal structure of the recombinant PLL·l-fucose complex confirmed that at least three sites were fucose-binding. Moreover, the crystal structures indicated that some of the other sites are masked either by the tetrameric nature of the lectin or by incorporation of the C terminus of the lectin into one of these sites. PLL exhibited an ability to bind to insect hemocytes and the cuticular surface of a nematode, H. bacteriophora.
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Affiliation(s)
- Atul Kumar
- From the Central European Institute of Technology (CEITEC)
| | - Petra Sýkorová
- From the Central European Institute of Technology (CEITEC).,the Department of Biochemistry, Faculty of Science
| | - Gabriel Demo
- From the Central European Institute of Technology (CEITEC).,the National Centre for Biomolecular Research, Faculty of Science, and
| | - Pavel Dobeš
- the Department of Animal Physiology and Immunology, Institute of Experimental Biology, Masaryk University, Brno 625 00, Czech Republic
| | - Pavel Hyršl
- the Department of Animal Physiology and Immunology, Institute of Experimental Biology, Masaryk University, Brno 625 00, Czech Republic
| | - Michaela Wimmerová
- From the Central European Institute of Technology (CEITEC), .,the Department of Biochemistry, Faculty of Science.,the National Centre for Biomolecular Research, Faculty of Science, and
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19
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Vícha J, Babinský M, Demo G, Otrusinová O, Jansen S, Pekárová B, Žídek L, Munzarová ML. The influence of Mg2+ coordination on 13C and 15N chemical shifts in CKI1RD protein domain from experiment and molecular dynamics/density functional theory calculations. Proteins 2016; 84:686-99. [PMID: 26879585 DOI: 10.1002/prot.25019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Revised: 01/29/2016] [Accepted: 02/10/2016] [Indexed: 11/09/2022]
Abstract
Sequence dependence of (13) C and (15) N chemical shifts in the receiver domain of CKI1 protein from Arabidopsis thaliana, CKI1RD , and its complexed form, CKI1RD •Mg(2+), was studied by means of MD/DFT calculations. MD simulations of a 20-ns production run length were performed. Nine explicitly hydrated structures of increasing complexity were explored, up to a 40-amino-acid structure. The size of the model necessary depended on the type of nucleus, the type of amino acid and its sequence neighbors, other spatially close amino acids, and the orientation of amino acid NH groups and their surface/interior position. Using models covering a 10 and a 15 Å environment of Mg(2+), a semi-quantitative agreement has been obtained between experiment and theory for the V67-I73 sequence. The influence of Mg(2+) binding was described better by the 15 Å as compared to the 10 Å model. Thirteen chemical shifts were analyzed in terms of the effect of Mg(2+) insertion and geometry preparation. The effect of geometry was significant and opposite in sign to the effect of Mg(2+) binding. The strongest individual effects were found for (15) N of D70, S74, and V68, where the electrostatics dominated; for (13) Cβ of D69 and (15) N of K76, where the influences were equal, and for (13) Cα of F72 and (13) Cβ of K76, where the geometry adjustment dominated. A partial correlation between dominant geometry influence and torsion angle shifts upon the coordination has been observed.
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Affiliation(s)
- Jan Vícha
- Central European Institute of Technology, Masaryk University, Kamenice 5, Brno, 62500, Czech Republic
| | - Martin Babinský
- Central European Institute of Technology, Masaryk University, Kamenice 5, Brno, 62500, Czech Republic
| | - Gabriel Demo
- Central European Institute of Technology, Masaryk University, Kamenice 5, Brno, 62500, Czech Republic
| | - Olga Otrusinová
- Central European Institute of Technology, Masaryk University, Kamenice 5, Brno, 62500, Czech Republic.,Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, Brno, 62500, Czech Republic
| | - Séverine Jansen
- Central European Institute of Technology, Masaryk University, Kamenice 5, Brno, 62500, Czech Republic
| | - Blanka Pekárová
- Central European Institute of Technology, Masaryk University, Kamenice 5, Brno, 62500, Czech Republic
| | - Lukáš Žídek
- Central European Institute of Technology, Masaryk University, Kamenice 5, Brno, 62500, Czech Republic.,Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, Brno, 62500, Czech Republic
| | - Markéta L Munzarová
- Faculty of Science, Department of Chemistry, Masaryk University, Kotlářská 2, Brno, 61137, Czech Republic
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20
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Frömmel J, Šebela M, Demo G, Lenobel R, Pospíšil T, Soural M, Kopečný D. N-acyl-ω-aminoaldehydes are efficient substrates of plant aminoaldehyde dehydrogenases. Amino Acids 2015; 47:175-87. [PMID: 25344796 DOI: 10.1007/s00726-014-1853-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 10/07/2014] [Indexed: 11/29/2022]
Abstract
Plant aminoaldehyde dehydrogenases (AMADHs, EC 1.2.1.19) belong to the family 10 of aldehyde dehydrogenases and participate in the metabolism of compounds related to amino acids such as polyamines or osmoprotectants. Their broad specificity covers ω-aminoaldehydes, aliphatic and aromatic aldehydes as well as nitrogen-containing heterocyclic aldehydes. The substrate preference of plant AMADHs is determined by the presence of aspartic acid and aromatic residues in the substrate channel. In this work, 15 new N-acyl derivates of 3-aminopropanal (APAL) and 4-aminobutanal (ABAL) were synthesized and confirmed as substrates of two pea AMADH isoenzymes (PsAMADH 1 and 2). The compounds were designed considering the previously demonstrated conversion of N-acetyl derivatives as well as substrate channel dimensions (5-8 Å × 14 Å). The acyl chain length and its branching were found less significant for substrate properties than the length of the initial natural substrate. In general, APAL derivatives were found more efficient than the corresponding ABAL derivatives because of the prevailing higher conversion rates and lower K m values. Differences in enzymatic performance between the two isoenzymes corresponded in part to their preferences to APAL to ABAL. The higher PsAMADH2 affinity to substrates correlated with more frequent occurrence of an excess substrate inhibition. Molecular docking indicated the possible auxiliary role of Tyr163, Ser295 and Gln451 in binding of the new substrates. The only derivative carrying a free carboxyl group (N-adipoyl APAL) was surprisingly better substrate than ABAL in PsAMADH2 reaction indicating that also negatively charged aldehydes might be good substrates for ALDH10 family.
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Affiliation(s)
- Jan Frömmel
- Department of Protein Biochemistry and Proteomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 11, 783 71, Olomouc, Czech Republic
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21
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Jeremias L, Demo G, Kubát V, Trávníček Z, Novosad J. Synthesis and X-Ray Structures of Zinc(II) and Cadmium(II) Heteroleptic Complexes Involving 1,1-Dithiolate and N-Donor Ligands. PHOSPHORUS SULFUR 2014. [DOI: 10.1080/10426507.2014.902825] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Lukáš Jeremias
- Department of Chemistry, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Gabriel Demo
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
- Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Václav Kubát
- Department of Chemistry, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Zdeněk Trávníček
- Department of Inorganic Chemistry, Faculty of Science, Palacký University, 17. listopadu 12, 771 46 Olomouc, Czech Republic
| | - Josef Novosad
- Department of Chemistry, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
- Department of Inorganic Chemistry, Faculty of Science, Palacký University, 17. listopadu 12, 771 46 Olomouc, Czech Republic
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22
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Demo G, Horská V, Fliedrová B, Stěpán J, Koča J, Weignerová L, Křen V, Wimmerová M. Protein engineering study of β-mannosidase to set up a potential chemically efficient biocatalyst. Glycobiology 2014; 24:1301-11. [PMID: 25049237 DOI: 10.1093/glycob/cwu074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
This study is focused on the analysis and mutagenesis of β-mannosidase from Bacteroides thetaiotaomicron with the aim of broadening its substrate specificity to 2-acetamido-2-deoxy-β-d-mannopyranosyl (β-ManNAc) derivatives. Various conformations ((4)C1, (4)H5 and (1)S5) of native and modified ligands were docked to the binding site of the protein to determine the most suitable conformation of sugars for further hydrolysis. Key amino acid residues were mutated in silico focusing on stabilizing the acetamido group of β-ManNAc as well as forming the oxazoline intermediate needed for hydrolysis. The results of large set of 5 ns molecular dynamic simulations showed that the majority of the active site residues are involved in substrate interaction and do not exhibit a higher flexibility except for Asn178. Mutations of Asn178 to alanine and Asp199 to serine could lead to a stabilization of the acetamido group in the binding site. So far, in vitro mutagenesis and the screen of a large variety of biological sources were unable to extend β-mannosidase's activity to include β-ManNAc derivatives.
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Affiliation(s)
- Gabriel Demo
- National Centre for Biomolecular Research, Faculty of Science Central European Institute of Technology, Masaryk University, Kamenice 5/A4, Brno 62500, Czech Republic
| | - Veronika Horská
- National Centre for Biomolecular Research, Faculty of Science
| | - Barbora Fliedrová
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, Prague 142 20, Czech Republic
| | - Jakub Stěpán
- National Centre for Biomolecular Research, Faculty of Science Central European Institute of Technology, Masaryk University, Kamenice 5/A4, Brno 62500, Czech Republic
| | - Jaroslav Koča
- National Centre for Biomolecular Research, Faculty of Science Central European Institute of Technology, Masaryk University, Kamenice 5/A4, Brno 62500, Czech Republic
| | - Lenka Weignerová
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, Prague 142 20, Czech Republic
| | - Vladimír Křen
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, Prague 142 20, Czech Republic
| | - Michaela Wimmerová
- National Centre for Biomolecular Research, Faculty of Science Central European Institute of Technology, Masaryk University, Kamenice 5/A4, Brno 62500, Czech Republic Department of Biochemistry, Faculty of Science, Masaryk University, Kamenice 5/A5, Brno 62500, Czech Republic
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23
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Jeremias L, Demo G, Babiak M, Vícha J, Trávníček Z, Novosad J. X-ray structures of heteroleptic zinc(II) complexes involving combinations of O,O′-dialkyldithiophosphato and bidentate N-donor ligands. Z KRIST-CRYST MATER 2014. [DOI: 10.1515/zkri-2014-1736] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
The detailed X-ray structural elucidation of reaction products of a zinc(II) salt with O,O′-dialkyldithiophosphate and nitrogen-containing heterocycles (N–N=1,10-phenanthroline (phen) or 2,2′-bipyridine (bpy)) has been performed. Surprisingly, together with [Zn(S2 P(OR)2)2(N–N)] compounds, also ionic-type complexes having the formula of [Zn(N–N)3](S2 P(OR)2)2 have been obtained using the same molar ratios of the reactants. The prepared complexes have been characterized by elemental analysis and single-crystal X-ray analysis. The crystallographic analysis showed that the bond lengths and bite angles of the prepared complexes are in good agreement with those of similar compounds. The crystal packing of described complexes is formed via π–π stacking interactions and/or C–H···S non-covalent contacts.
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Affiliation(s)
- Lukáš Jeremias
- Faculty of Science, Department of Chemistry, Masaryk University, Kotlářska 2, 611 37 Brno, Czech Republic
| | | | | | | | - Zdeněk Trávníček
- Faculty of Science, Department of Inorganic Chemistry, Palacký University, 17. listopadu 12, 771 46 Olomouc, Czech Republic
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Kubat V, Demo G, Jeremias L, Novosad J. Synthesis and structure of tris(dimethyldithiocarbamato)(1,10-phenanthroline)lanthanide complexes. Z KRIST-CRYST MATER 2013. [DOI: 10.1524/zkri.2013.1625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Demo G, Fliedrová B, Weignerová L, Wimmerová M. Crystallization and preliminary X-ray crystallographic analysis of recombinant β-mannosidase from Aspergillus niger. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:288-91. [PMID: 23519806 PMCID: PMC3606576 DOI: 10.1107/s1744309113002522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Accepted: 01/24/2013] [Indexed: 11/10/2022]
Abstract
β-Mannosidase (EC 3.2.1.25) is an important exoglycosidase specific for the hydrolysis of terminal β-linked mannoside in various oligomeric saccharide structures. β-Mannosidase from Aspergillus niger was expressed in Pichia pastoris and purified to clear homogeneity. β-Mannosidase was crystallized in the presence of D-mannose and the crystal diffracted to 2.41 Å resolution. The crystal belonged to space group P1, with unit-cell parameters a=62.37, b=69.73, c=69.90 Å, α=108.20, β=101.51, γ=103.20°. The parameters derived from the data collection indicate the presence of one molecule in the asymmetric unit.
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Affiliation(s)
- Gabriel Demo
- Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Barbora Fliedrová
- Laboratory of Biotransformation, Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, 142 20 Prague, Czech Republic
- Department of Biochemistry, Faculty of Science, Charles University in Prague, Hlavova 2030, 128 40 Prague, Czech Republic
| | - Lenka Weignerová
- Laboratory of Biotransformation, Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, 142 20 Prague, Czech Republic
| | - Michaela Wimmerová
- Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
- Department of Biochemistry, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
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Frömmel J, Soural M, Tylichová M, Kopečný D, Demo G, Wimmerová M, Sebela M. Plant aminoaldehyde dehydrogenases oxidize a wide range of nitrogenous heterocyclic aldehydes. Amino Acids 2012; 43:1189-202. [PMID: 22160258 DOI: 10.1007/s00726-011-1174-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Accepted: 11/21/2011] [Indexed: 11/29/2022]
Abstract
The metabolic degradation of aldehydes is catalyzed by oxidoreductases from which aldehyde dehydrogenases (EC 1.2.1) comprise nonspecific or substrate-specific enzymes. The latter subset is represented, e.g., by NAD(+)-dependent aminoaldehyde dehydrogenases (AMADHs; EC 1.2.1.19) oxidizing a group of naturally occurring ω-aminoaldehydes including polyamine oxidation products. Recombinant isoenzymes from pea (PsAMADH1 and 2) and tomato (LeAMADH1 and 2) were subjected to kinetic measurements with synthetic aldehydes containing a nitrogenous heterocycle such as pyridinecarbaldehydes and their halogenated derivatives, (pyridinylmethylamino)-aldehydes, pyridinyl propanals and aldehydes derived from purine, 7-deazapurine and pyrimidine to characterize their substrate specificity and significance of the resulting data for in vivo reactions. The enzymatic production of the corresponding carboxylic acids was analyzed by liquid chromatography coupled to electrospray ionization mass spectrometry. Although the studied AMADHs are largely homologous and supposed to have a very similar active site architecture, significant differences were observed. LeAMADH1 displayed the broadest specificity oxidizing almost all compounds followed by PsAMADH2 and 1. In contrast, LeAMADH2 accepted only a few compounds as substrates. Pyridinyl propanals were converted by all isoenzymes, usually better than pyridinecarbaldehydes and aldehydes with fused rings. The K (m) values for the best substrates were in the range of 10(-5)-10(-4) M. Nevertheless, the catalytic efficiency values (V (max)/K (m)) reached only a very small fraction of that with 3-aminopropanal (except for LeAMADH1 activity with two pyridine-derived compounds). Docking experiments using the crystal structure of PsAMADH2 were involved to discuss differences in results with position isomers or alkyl chain homologs.
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Affiliation(s)
- Jan Frömmel
- Department of Protein Biochemistry and Proteomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 11, Olomouc, Czech Republic
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Vícha J, Demo G, Marek R. Platinum-Modified Adenines: Unprecedented Protonation Behavior Revealed by NMR Spectroscopy and Relativistic Density-Functional Theory Calculations. Inorg Chem 2012; 51:1371-9. [DOI: 10.1021/ic201595e] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Affiliation(s)
- Jan Vícha
- National Center for Biomolecular Research, Faculty
of Science and Central European Institute of Technology-CEITEC, Masaryk University, Kamenice 5/A4, CZ-62500 Brno, Czech
Republic
| | - Gabriel Demo
- National Center for Biomolecular Research, Faculty
of Science and Central European Institute of Technology-CEITEC, Masaryk University, Kamenice 5/A4, CZ-62500 Brno, Czech
Republic
| | - Radek Marek
- National Center for Biomolecular Research, Faculty
of Science and Central European Institute of Technology-CEITEC, Masaryk University, Kamenice 5/A4, CZ-62500 Brno, Czech
Republic
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Dastych D, Rotter P, Demo G, Dastychová L. Di-μ-chlorido-bis-[diacetonitrile-chlorido-oxidovanadium(IV)]. Acta Crystallogr Sect E Struct Rep Online 2011; 67:m1398. [PMID: 22058702 PMCID: PMC3201240 DOI: 10.1107/s1600536811037184] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2011] [Accepted: 09/13/2011] [Indexed: 11/18/2022]
Abstract
The title compound, [V2Cl4O2(CH3CN)4], is a centrosymmetric dinuclear VIV complex associated with four molecules of acetonitrile. The coordination around both VIV atoms is essentially square-planar, involving three Cl atoms and one O atom [maximum deviation = 0.017 (3) Å for the O atom]. The augmented octahedral coordination of the metal atom is completed by the N atoms of acetonitrile ligands. The VIV atoms are linked by two Cl atoms, acting as bridging atoms. The crystal studied was a non-merohedral twin with a ratio of the two twin components of 0.8200 (3):0.1800 (3). Although Cl and O atoms are present as potential acceptors in the title compound, no hydrogen bonds were observed in the crystal structure.
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