Importance of potassium ions for ribosome structure and function revealed by long-wavelength X-ray diffraction

[1]  P. Auffinger,et al.  Nucleobase carbonyl groups are poor Mg2+ inner-sphere binders but excellent monovalent ion binders—a critical PDB survey , 2019, RNA.

[2]  I. Ivanov,et al.  Roles of polyamines in translation , 2018, The Journal of Biological Chemistry.

[3]  Alan Brown,et al.  Ribosomes and cryo-EM: a duet. , 2018, Current opinion in structural biology.

[4]  E. Westhof,et al.  Tautomeric G•U pairs within the molecular ribosomal grip and fidelity of decoding in bacteria , 2018, Nucleic acids research.

[5]  W. Minor,et al.  Characterizing metal-binding sites in proteins with X-ray crystallography , 2018, Nature Protocols.

[6]  M. Ehrenberg,et al.  2′-O-methylation in mRNA disrupts tRNA decoding during translation elongation , 2018, Nature Structural & Molecular Biology.

[7]  N. Elad,et al.  Detection of isolated protein-bound metal ions by single-particle cryo-STEM , 2017, Proceedings of the National Academy of Sciences.

[8]  P. Auffinger,et al.  Mg2+ ions: do they bind to nucleobase nitrogens? , 2016, Nucleic acids research.

[9]  E. Westhof,et al.  New Structural Insights into Translational Miscoding. , 2016, Trends in biochemical sciences.

[10]  E. Westhof,et al.  The ribosome prohibits the G•U wobble geometry at the first position of the codon–anticodon helix , 2016, Nucleic acids research.

[11]  Keith Henderson,et al.  In-vacuum long-wavelength macromolecular crystallography , 2016, Acta crystallographica. Section D, Structural biology.

[12]  E. Westhof,et al.  Novel base-pairing interactions at the tRNA wobble position crucial for accurate reading of the genetic code , 2016, Nature Communications.

[13]  M. Ehrenberg,et al.  N6-methyladenosine in mRNA disrupts tRNA selection and translation elongation dynamics , 2016, Nature Structural &Molecular Biology.

[14]  P. Auffinger,et al.  Sodium and Potassium Interactions with Nucleic Acids. , 2016, Metal ions in life sciences.

[15]  Eric Westhof,et al.  Structural insights into the translational infidelity mechanism , 2015, Nature Communications.

[16]  M. Yusupov,et al.  Ribosome biochemistry in crystal structure determination , 2015, RNA.

[17]  B. Wiedenheft,et al.  Mechanism of foreign DNA recognition by a CRISPR RNA-guided surveillance complex from Pseudomonas aeruginosa , 2015, Nucleic acids research.

[18]  K. Nierhaus Mg2+, K+, and the Ribosome , 2014, Journal of bacteriology.

[19]  T. Steitz,et al.  A proton wire to couple aminoacyl-tRNA accommodation and peptide bond formation on the ribosome , 2014, Nature Structural &Molecular Biology.

[20]  Nicholas J. Pace,et al.  Zinc-Binding Cysteines: Diverse Functions and Structural Motifs , 2014, Biomolecules.

[21]  Li Tian,et al.  Copper active sites in biology. , 2014, Chemical reviews.

[22]  M. Yusupov,et al.  One core, two shells: bacterial and eukaryotic ribosomes , 2012, Nature Structural &Molecular Biology.

[23]  E. Westhof,et al.  A new understanding of the decoding principle on the ribosome , 2012, Nature.

[24]  Gang Wu,et al.  NMR studies of alkali metal ions in organic and biological solids. , 2012, Progress in nuclear magnetic resonance spectroscopy.

[25]  G. Sheldrick,et al.  ANODE: anomalous and heavy-atom density calculation , 2011, Journal of applied crystallography.

[26]  A. Bashan,et al.  Crystal structure of the synergistic antibiotic pair, lankamycin and lankacidin, in complex with the large ribosomal subunit , 2011, Proceedings of the National Academy of Sciences.

[27]  H. Sigel,et al.  Structural and catalytic roles of metal ions in RNA. , 2011, Metal ions in life sciences.

[28]  F. Murphy,et al.  Modification of 16S ribosomal RNA by the KsgA methyltransferase restructures the 30S subunit to optimize ribosome function. , 2010, RNA.

[29]  M. Yusupov,et al.  Structural rearrangements of the ribosome at the tRNA proofreading step , 2010, Nature Structural &Molecular Biology.

[30]  M. Yusupov,et al.  Structural aspects of messenger RNA reading frame maintenance by the ribosome , 2010, Nature Structural &Molecular Biology.

[31]  P. Emsley,et al.  Features and development of Coot , 2010, Acta crystallographica. Section D, Biological crystallography.

[32]  W. Kabsch XDS , 2010, Acta crystallographica. Section D, Biological crystallography.

[33]  Randy J. Read,et al.  Acta Crystallographica Section D Biological , 2003 .

[34]  D. Draper,et al.  The influence of monovalent cation size on the stability of RNA tertiary structures. , 2009, Journal of molecular biology.

[35]  R. Strange,et al.  Biological X-ray absorption spectroscopy and metalloproteomics. , 2009, Journal of synchrotron radiation.

[36]  David E Draper,et al.  Ion-RNA interactions thermodynamic analysis of the effects of mono- and divalent ions on RNA conformational equilibria. , 2009, Methods in enzymology.

[37]  Takeshi Wada,et al.  Modified Uridines with C5-methylene Substituents at the First Position of the tRNA Anticodon Stabilize U·G Wobble Pairing during Decoding* , 2008, Journal of Biological Chemistry.

[38]  G. Hannon,et al.  The Piwi-piRNA Pathway Provides an Adaptive Defense in the Transposon Arms Race , 2007, Science.

[39]  M. Murphy,et al.  Type-2 copper-containing enzymes , 2007, Cellular and Molecular Life Sciences.

[40]  M. Yusupov,et al.  Messenger RNA conformations in the ribosomal E site revealed by X‐ray crystallography , 2007, EMBO reports.

[41]  Franck A. P. Vendeix,et al.  Mechanism of expanding the decoding capacity of tRNAs by modification of uridines , 2007, Nature Structural &Molecular Biology.

[42]  Bernard Rees,et al.  Structural basis for messenger RNA movement on the ribosome , 2006, Nature.

[43]  M. Selmer,et al.  Structure of the 70S Ribosome Complexed with mRNA and tRNA , 2006, Science.

[44]  M. Weiss,et al.  Softer and soft X-rays in macromolecular crystallography. , 2005, Journal of synchrotron radiation.

[45]  Conrad C. Huang,et al.  UCSF Chimera—A visualization system for exploratory research and analysis , 2004, J. Comput. Chem..

[46]  T. Steitz,et al.  The contribution of metal ions to the structural stability of the large ribosomal subunit. , 2004, RNA.

[47]  H. Noll,et al.  Structural dynamics of bacterial ribosomes , 1973, Molecular and General Genetics MGG.

[48]  P. Farabaugh,et al.  Transfer RNA modifications that alter +1 frameshifting in general fail to affect -1 frameshifting. , 2003, RNA.

[49]  E. Westhof,et al.  The Mg2+ binding sites of the 5S rRNA loop E motif as investigated by molecular dynamics simulations. , 2003, Chemistry & biology.

[50]  W. Epstein,et al.  The roles and regulation of potassium in bacteria. , 2003, Progress in nucleic acid research and molecular biology.

[51]  J. Strominger,et al.  A pH-sensitive histidine residue as control element for ligand release from HLA-DR molecules , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[52]  V. Ramakrishnan,et al.  Selection of tRNA by the Ribosome Requires a Transition from an Open to a Closed Form , 2002, Cell.

[53]  A. Pyle,et al.  Metal ions in the structure and function of RNA , 2002, JBIC Journal of Biological Inorganic Chemistry.

[54]  Stephen Neidle,et al.  Crystal structure of the potassium form of an Oxytricha nova G-quadruplex. , 2002, Journal of molecular biology.

[55]  Eaton E Lattman,et al.  A compact RNA tertiary structure contains a buried backbone-K+ complex. , 2002, Journal of molecular biology.

[56]  D. Draper,et al.  The linkage between magnesium binding and RNA folding. , 2002, Journal of molecular biology.

[57]  Eric Westhof,et al.  Effects of magnesium ions on the stabilization of RNA oligomers of defined structures. , 2002, RNA.

[58]  R. Sleator,et al.  Bacterial osmoadaptation: the role of osmolytes in bacterial stress and virulence. , 2001, FEMS microbiology reviews.

[59]  G. Björk,et al.  Improvement of reading frame maintenance is a common function for several tRNA modifications , 2001, The EMBO journal.

[60]  Harry F. Noller,et al.  The Path of Messenger RNA through the Ribosome , 2001, Cell.

[61]  V. Ramakrishnan,et al.  Recognition of Cognate Transfer RNA by the 30S Ribosomal Subunit , 2001, Science.

[62]  T. Earnest,et al.  Crystal Structure of the Ribosome at 5.5 Å Resolution , 2001, Science.

[63]  C. Fierke,et al.  Function and mechanism of zinc metalloenzymes. , 2000, The Journal of nutrition.

[64]  J. Frank,et al.  Solution Structure of the E. coli 70S Ribosome at 11.5 Å Resolution , 2000, Cell.

[65]  Khan,et al.  Arachidonic acid metabolites alter G protein-mediated signal transduction in heart. Effects on muscarinic K+ channels , 1990, The Journal of general physiology.

[66]  C. Chothia,et al.  The Packing Density in Proteins: Standard Radii and Volumes , 1999 .

[67]  P. Kollman,et al.  A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat. , 1999, Journal of biomolecular structure & dynamics.

[68]  D. Draper,et al.  On the role of magnesium ions in RNA stability , 1998, Biopolymers.

[69]  Edward I. Solomon,et al.  Structural and Functional Aspects of Metal Sites in Biology. , 1996, Chemical reviews.

[70]  J. Frank,et al.  A model of the translational apparatus based on a three-dimensional reconstruction of the Escherichia coli ribosome. , 1995, Biochemistry and cell biology = Biochimie et biologie cellulaire.

[71]  A. Rich,et al.  Crystal structure of four-stranded Oxytricha telomeric DNA , 1992, Nature.

[72]  T. Cech,et al.  Visualizing the higher order folding of a catalytic RNA molecule. , 1991, Science.

[73]  B. Roe,et al.  Presence of the hypermodified nucleotide N6-(delta 2-isopentenyl)-2-methylthioadenosine prevents codon misreading by Escherichia coli phenylalanyl-transfer RNA. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[74]  K. Nierhaus,et al.  Mg2+/NH4+/polyamine system for polyuridine-dependent polyphenylalanine synthesis with near in vivo characteristics. , 1988, Methods in enzymology.

[75]  H. Rheinberger,et al.  The ribosomal E site at low Mg2+: coordinate inactivation of ribosomal functions at Mg2+ concentrations below 10 mM and its prevention by polyamines. , 1987, Journal of biomolecular structure & dynamics.

[76]  J. Potter,et al.  A structural role for the Ca2+-Mg2+ sites on troponin C in the regulation of muscle contraction. Preparation and properties of troponin C depleted myofibrils. , 1982, The Journal of biological chemistry.

[77]  C. Kurland,et al.  Nucleoside triphosphate regeneration decreases the frequency of translation errors. , 1979, Proceedings of the National Academy of Sciences of the United States of America.

[78]  G. Kramer,et al.  Polyamines are necessary for maximum in vitro synthesis of globin peptides and play a role in chain initiation. , 1975, Archives of biochemistry and biophysics.

[79]  K. Igarashi,et al.  Effect of polyamines of polyphenylalanine synthesis by Escherichia coli and rat-liver ribosomes. , 1974, European journal of biochemistry.

[80]  K. Hikami,et al.  Effect of polyamines on polypeptide synthesis in rat liver cell-free system. , 1973, Biochimica et biophysica acta.

[81]  D. Morris,et al.  Cations and ribosome structure. 3. Effects on the 30S and 50S subunits of replacing bound Mg 2+ by inorganic cations. , 1973, Biochemistry.

[82]  D. Morris,et al.  Cations and ribosome structure. I. Effects on the 30S subunit of substituting polyamines for magnesium ion. , 1973, Biochemistry.

[83]  D. Morris,et al.  Cations and ribosome structure. II. Effects on the 50S subunit of substituting polyamines for magnesium ion. , 1973, Biochemistry.

[84]  R. Zitomer,et al.  Magnesium dependence and equilibrium of the Escherichia coli ribosomal subunit association. , 1972, Journal of molecular biology.

[85]  Robert C. Weast,et al.  Handbook of chemistry and physics : a readyreference book of chemical and physical data , 1972 .

[86]  A. Spirin,et al.  Dependence of dissociation—association of uncharged ribosomes of Escherichia coli on the Mg2+ concentration, ionic strength, pH and temperature , 1971, FEBS letters.

[87]  P. Näslund,et al.  Effects of potassium deficiency on mammalian ribosomes. , 1970, Biochimica et biophysica acta.

[88]  M. Tal Metal ions and ribosomal conformation. , 1969, Biochimica et biophysica acta.

[89]  Y. Takeda Polyamines and protein synthesis. I. The effect of polyamines on cell free polyphenylalanine synthesis in Escherichia coli. , 1969, Journal of biochemistry.

[90]  J. Gordon,et al.  Role of divalent ions in poly U-directed phenylalanine polymerization* , 1967 .

[91]  R. Gesteland,et al.  Unfolding of Escherichia coli ribosomes by removal of magnesium. , 1966, Journal of molecular biology.

[92]  A. Spirin,et al.  Studies on the structure of ribosomes. 3. Stepwise unfolding of the 50 s particles without loss of ribosomal protein. , 1966, Journal of molecular biology.

[93]  B. Ames,et al.  THE EFFECT OF POLYAMINES AND OF POLY U SIZE ON PHENYLALANINE INCORPORATION. , 1962, Proceedings of the National Academy of Sciences of the United States of America.

[94]  B. Mccarthy The effects of magnesium starvation on the ribosome content of Escherichia coli , 1962 .

[95]  A. Hershko,et al.  Effect of polyamines and divalent metals on in vitro incorporation of amino acids into ribonucleoprotein particles. , 1961, Biochemical and biophysical research communications.

[96]  D. Nathans,et al.  Amino acid transfer from aminoacyl-ribonucleic acids to protein on ribosomes of Escherichia coli. , 1961, Proceedings of the National Academy of Sciences of the United States of America.

[97]  S. Cohen,et al.  Polyamines and ribosome structure. , 1960, The Journal of biological chemistry.

[98]  Joseph John Thomson,et al.  Determination , 2014, ATZ worldwide.