Auffinger P, Ennifar E, D'Ascenzo L
Deflating the RNA Mg 2+ bubble. Stereochemistry to the rescue! Article de journal
Dans: RNA, vol. 27, no. 3, p. 243-252, 2020.
Résumé | Liens | BibTeX | Étiquettes: cryo-EM, ENNIFAR, ionic atmosphere, solvent, Unité ARN, validation, X-Ray
@article{P.2020,
title = {Deflating the RNA Mg 2+ bubble. Stereochemistry to the rescue! },
author = {P Auffinger and E Ennifar and L D'Ascenzo},
url = {https://doi.org/10.1261/rna.076067.120},
doi = {10.1261/rna.076067.120 },
year = {2020},
date = {2020-12-02},
journal = {RNA},
volume = {27},
number = {3},
pages = {243-252},
abstract = {Proper evaluation of the ionic structure of biomolecular systems remains challenging in X ray and cryo-EM techniques but is essential for advancing our understanding of complex structure/activity/solvent relationships. However, numerous studies overestimate the number of MgProper evaluation of the ionic structure of biomolecular systems remains challenging in X ray and cryo-EM techniques but is essential for advancing our understanding of complex structure/activity/solvent relationships. However, numerous studies overestimate the number of Mg2+ in the deposited structures and underrate the importance of stereochemical rules to correctly assign these ions. Herein, we re-evaluate the PDBid 6QNR and 6SJ6 models of the ribosome ionic structure and establish that stereochemical principles need consideration when evaluating ion binding features, even when K+ anomalous signals are available as it is the case for 6QNR. Assignment errors can result in misleading conceptions of the solvent structure of ribosomes and other RNA systems and should therefore be avoided. Our analysis resulted in a significant decrease of the number of bound Mg2+ in the 6QNR structure, suggesting that K+ and not Mg2+ is the prevalent ion in the ribosome 1st solvation shell. We stress that the use of proper stereochemical guidelines is critical for deflating the current Mg2+ bubble witnessed in many ribosome and other RNA structures. Herewith, we would like to draw the attention of the researchers interested in the ionic structure of biomolecular systems on the importance and complementarity of stereochemistry and other ion identification techniques such as those pertaining to the detection of anomalous signals of transition metals and K+ We also stress that for the identification of lighter ions such as Mg2+, Na+, , stereochemistry coupled with high resolution structures remain the best currently available option. in the deposited structures and underrate the importance of stereochemical rules to correctly assign these ions. Herein, we re-evaluate the PDBid 6QNR and 6SJ6 models of the ribosome ionic structure and establish that stereochemical principles need consideration when evaluating ion binding features, even when K+ anomalous signals are available as it is the case for 6QNR. Assignment errors can result in misleading conceptions of the solvent structure of ribosomes and other RNA systems and should therefore be avoided. Our analysis resulted in a significant decrease of the number of bound Mg2+ in the 6QNR structure, suggesting that K+ and not Mg2+ is the prevalent ion in the ribosome 1st solvation shell. We stress that the use of proper stereochemical guidelines is critical for deflating the current Mg2+ bubble witnessed in many ribosome and other RNA structures. Herewith, we would like to draw the attention of the researchers interested in the ionic structure of biomolecular systems on the importance and complementarity of stereochemistry and other ion identification techniques such as those pertaining to the detection of anomalous signals of transition metals and K+ We also stress that for the identification of lighter ions such as Mg2+, Na+, , stereochemistry coupled with high resolution structures remain the best currently available option. },
keywords = {cryo-EM, ENNIFAR, ionic atmosphere, solvent, Unité ARN, validation, X-Ray},
pubstate = {published},
tppubtype = {article}
}
Coste Franck, Kemp Cordula, Bobezeau Vanessa, Hetru Charles, Kellenberger Christine, Imler Jean-Luc, Roussel Alain
Crystal structure of Diedel, a marker of the immune response of Drosophila melanogaster Article de journal
Dans: PloS One, vol. 7, no. 3, p. e33416, 2012, ISSN: 1932-6203.
Résumé | Liens | BibTeX | Étiquettes: Animals, Aphids, Crystallography, imler, Janus Kinases, M3i, Protein Folding, Protein Structure, Signal Transduction, STAT Transcription Factors, Tertiary, Transcription Factors, X-Ray
@article{coste_crystal_2012,
title = {Crystal structure of Diedel, a marker of the immune response of Drosophila melanogaster},
author = {Franck Coste and Cordula Kemp and Vanessa Bobezeau and Charles Hetru and Christine Kellenberger and Jean-Luc Imler and Alain Roussel},
doi = {10.1371/journal.pone.0033416},
issn = {1932-6203},
year = {2012},
date = {2012-01-01},
journal = {PloS One},
volume = {7},
number = {3},
pages = {e33416},
abstract = {BACKGROUND: The Drosophila melanogaster gene CG11501 is up regulated after a septic injury and was proposed to act as a negative regulator of the JAK/STAT signaling pathway. Diedel, the CG11501 gene product, is a small protein of 115 residues with 10 cysteines. METHODOLOGY/PRINCIPAL FINDINGS: We have produced Diedel in Drosophila S2 cells as an extra cellular protein thanks to its own signal peptide and solved its crystal structure at 1.15 Å resolution by SIRAS using an iodo derivative. Diedel is composed of two sub domains SD1 and SD2. SD1 is made of an antiparallel β-sheet covered by an α-helix and displays a ferredoxin-like fold. SD2 reveals a new protein fold made of loops connected by four disulfide bridges. Further structural analysis identified conserved hydrophobic residues on the surface of Diedel that may constitute a potential binding site. The existence of two conformations, cis and trans, for the proline 52 may be of interest as prolyl peptidyl isomerisation has been shown to play a role in several physiological mechanisms. The genome of D. melanogaster contains two other genes coding for proteins homologous to Diedel, namely CG43228 and CG34329. Strikingly, apart from Drosophila and the pea aphid Acyrthosiphon pisum, Diedel-related sequences were exclusively identified in a few insect DNA viruses of the Baculoviridae and Ascoviridae families. CONCLUSION/SIGNIFICANCE: Diedel, a marker of the Drosophila antimicrobial/antiviral response, is a member of a small family of proteins present in drosophilids, aphids and DNA viruses infecting lepidopterans. Diedel is an extracellular protein composed of two sub-domains. Two special structural features (hydrophobic surface patch and cis/trans conformation for proline 52) may indicate a putative interaction site, and support an extra cellular signaling function for Diedel, which is in accordance with its proposed role as negative regulator of the JAK/STAT signaling pathway.},
keywords = {Animals, Aphids, Crystallography, imler, Janus Kinases, M3i, Protein Folding, Protein Structure, Signal Transduction, STAT Transcription Factors, Tertiary, Transcription Factors, X-Ray},
pubstate = {published},
tppubtype = {article}
}
Mishima Yumiko, Quintin Jessica, Aimanianda Vishukumar, Kellenberger Christine, Coste Franck, Clavaud Cecile, Hetru Charles, Hoffmann Jules A, Latgé Jean-Paul, Ferrandon Dominique, Roussel Alain
The N-terminal domain of Drosophila Gram-negative binding protein 3 (GNBP3) defines a novel family of fungal pattern recognition receptors Article de journal
Dans: J. Biol. Chem., vol. 284, no. 42, p. 28687–28697, 2009, ISSN: 1083-351X.
Résumé | Liens | BibTeX | Étiquettes: Animals, beta-Glucans, Bombyx, Carrier Proteins, Crystallography, ferrandon, Fungal Proteins, Hemolymph, hoffmann, ligands, M3i, Molecular Conformation, Mutagenesis, Polysaccharides, Protein Structure, Secondary, Tertiary, X-Ray
@article{mishima_n-terminal_2009,
title = {The N-terminal domain of Drosophila Gram-negative binding protein 3 (GNBP3) defines a novel family of fungal pattern recognition receptors},
author = {Yumiko Mishima and Jessica Quintin and Vishukumar Aimanianda and Christine Kellenberger and Franck Coste and Cecile Clavaud and Charles Hetru and Jules A Hoffmann and Jean-Paul Latgé and Dominique Ferrandon and Alain Roussel},
doi = {10.1074/jbc.M109.034587},
issn = {1083-351X},
year = {2009},
date = {2009-10-01},
journal = {J. Biol. Chem.},
volume = {284},
number = {42},
pages = {28687--28697},
abstract = {Gram-negative binding protein 3 (GNBP3), a pattern recognition receptor that circulates in the hemolymph of Drosophila, is responsible for sensing fungal infection and triggering Toll pathway activation. Here, we report that GNBP3 N-terminal domain binds to fungi upon identifying long chains of beta-1,3-glucans in the fungal cell wall as a major ligand. Interestingly, this domain fails to interact strongly with short oligosaccharides. The crystal structure of GNBP3-Nter reveals an immunoglobulin-like fold in which the glucan binding site is masked by a loop that is highly conserved among glucan-binding proteins identified in several insect orders. Structure-based mutagenesis experiments reveal an essential role for this occluding loop in discriminating between short and long polysaccharides. The displacement of the occluding loop is necessary for binding and could explain the specificity of the interaction with long chain structured polysaccharides. This represents a novel mechanism for beta-glucan recognition.},
keywords = {Animals, beta-Glucans, Bombyx, Carrier Proteins, Crystallography, ferrandon, Fungal Proteins, Hemolymph, hoffmann, ligands, M3i, Molecular Conformation, Mutagenesis, Polysaccharides, Protein Structure, Secondary, Tertiary, X-Ray},
pubstate = {published},
tppubtype = {article}
}
Kondo J.
[Exploring the "motion" = "function" of the ribosomal A-site molecular switch] Article de journal
Dans: Tanpakushitsu Kakusan Koso, vol. 54, no. 11, p. 1356-62, 2009, (0039-9450 (Print) 0039-9450 (Linking) Journal Article Review).
BibTeX | Étiquettes: *Binding, *RNA/genetics, Agents/adverse, Anti-Bacterial, Bacteria/drug, Biosynthesis/genetics, Crystallography, Disorders/genetics, effects, effects/pharmacology, Hearing, Humans, Mutation, Protein, Ribosomes/chemistry/*genetics/*physiology, RNA, Sites, Transfer, Untranslated, WESTHOF, X-Ray
@article{,
title = {[Exploring the "motion" = "function" of the ribosomal A-site molecular switch]},
author = { J. Kondo},
year = {2009},
date = {2009-01-01},
journal = {Tanpakushitsu Kakusan Koso},
volume = {54},
number = {11},
pages = {1356-62},
note = {0039-9450 (Print)
0039-9450 (Linking)
Journal Article
Review},
keywords = {*Binding, *RNA/genetics, Agents/adverse, Anti-Bacterial, Bacteria/drug, Biosynthesis/genetics, Crystallography, Disorders/genetics, effects, effects/pharmacology, Hearing, Humans, Mutation, Protein, Ribosomes/chemistry/*genetics/*physiology, RNA, Sites, Transfer, Untranslated, WESTHOF, X-Ray},
pubstate = {published},
tppubtype = {article}
}
Delarue M., Dumas P.
On the use of low-frequency normal modes to enforce collective movements in refining macromolecular structural models Article de journal
Dans: Proc Natl Acad Sci U S A, vol. 101, no. 18, p. 6957-62, 2004, (0027-8424 Journal Article).
Résumé | BibTeX | Étiquettes: *Models, Carrier, coli, Computer, Diffraction, DUMAS, Escherichia, Gov't, Molecular, Non-U.S., Proteins/*chemistry, Proteins/chemistry, Simulation, Support, X-Ray
@article{,
title = {On the use of low-frequency normal modes to enforce collective movements in refining macromolecular structural models},
author = { M. Delarue and P. Dumas},
year = {2004},
date = {2004-01-01},
journal = {Proc Natl Acad Sci U S A},
volume = {101},
number = {18},
pages = {6957-62},
abstract = {As more and more structures of macromolecular complexes get solved in different conditions, it has become apparent that flexibility is an inherent part of their biological function. Normal mode analysis using simplified models of proteins such as the elastic network model has proved very effective in showing that many of the structural transitions derived from a survey of the Protein Data Bank can be explained by just a few of the lowest-frequency normal modes. In this work, normal modes are used to carry out medium- or low-resolution structural refinement, enforcing collective and large-amplitude movements that are beyond the reach of existing methods. Refinement is carried out in reciprocal space with respect to the normal mode amplitudes, by using standard conjugate-gradient minimization. Several tests on synthetic diffraction data whose mode concentration follows the one of real movements observed in the Protein Data Bank have shown that the radius of convergence is larger than the one of rigid-body refinement. Tests with experimental diffraction data for the same protein in different environments also led to refined structural models showing drastic reduction of the rms deviation with the target model. Because the structural transition is described by very few parameters, over-fitting of real experimental data is easily detected by using a cross-validation test. The method has also been applied to the refinement of atomic models into molecular envelopes and could readily be used to fit large macromolecular complex rearrangements into cryo-electron microscopy-reconstructed images as well as small-angle x-ray scattering-derived envelopes.},
note = {0027-8424
Journal Article},
keywords = {*Models, Carrier, coli, Computer, Diffraction, DUMAS, Escherichia, Gov't, Molecular, Non-U.S., Proteins/*chemistry, Proteins/chemistry, Simulation, Support, X-Ray},
pubstate = {published},
tppubtype = {article}
}
Moine H., Mandel J. L.
Biomedicine. Do G quartets orchestrate fragile X pathology? Article de journal
Dans: Science, vol. 294, no. 5551, p. 2487-8, 2001, (0036-8075 Journal Article).
BibTeX | Étiquettes: Acid, Analysis, Animals, Array, Binding, Brain/metabolism, Conformation, Crystallography, Expression, Fragile, Gene, Genetic, Human, Messenger/*chemistry/genetics/*metabolism, Mice, Nerve, Nucleic, Oligonucleotide, Protein, Proteins/chemistry/genetics/*metabolism, Regions, Regulation, RNA, Sequence, Sites, structure, Synapses/physiology, Syndrome/genetics/*metabolism, Tertiary, Tissue, Translation, Untranslated, X, X-Ray
@article{,
title = {Biomedicine. Do G quartets orchestrate fragile X pathology?},
author = { H. Moine and J. L. Mandel},
year = {2001},
date = {2001-01-01},
journal = {Science},
volume = {294},
number = {5551},
pages = {2487-8},
note = {0036-8075
Journal Article},
keywords = {Acid, Analysis, Animals, Array, Binding, Brain/metabolism, Conformation, Crystallography, Expression, Fragile, Gene, Genetic, Human, Messenger/*chemistry/genetics/*metabolism, Mice, Nerve, Nucleic, Oligonucleotide, Protein, Proteins/chemistry/genetics/*metabolism, Regions, Regulation, RNA, Sequence, Sites, structure, Synapses/physiology, Syndrome/genetics/*metabolism, Tertiary, Tissue, Translation, Untranslated, X, X-Ray},
pubstate = {published},
tppubtype = {article}
}
Delagoutte B., Keith G., Moras D., Cavarelli J.
Crystallization and preliminary X-ray crystallographic analysis of yeast arginyl-tRNA synthetase-yeast tRNAArg complexes Article de journal
Dans: Acta Crystallogr D Biol Crystallogr, vol. 56, no. Pt 4, p. 492-4, 2000, (0907-4449 Journal Article).
Résumé | BibTeX | Étiquettes: &, Arg/*chemistry/isolation, Arginine-tRNA, cerevisiae/enzymology/genetics, Crystallization, Crystallography, Fungal/chemistry/isolation, Gov't, Ligase/*chemistry/isolation, Non-U.S., purification/*metabolism, purification/metabolism, RNA, Saccharomyces, Support, Transfer, X-Ray
@article{,
title = {Crystallization and preliminary X-ray crystallographic analysis of yeast arginyl-tRNA synthetase-yeast tRNAArg complexes},
author = { B. Delagoutte and G. Keith and D. Moras and J. Cavarelli},
year = {2000},
date = {2000-01-01},
journal = {Acta Crystallogr D Biol Crystallogr},
volume = {56},
number = {Pt 4},
pages = {492-4},
abstract = {Three different crystal forms of complexes between arginyl-tRNA synthetase from the yeast Saccharomyces cerevisae (yArgRS) and the yeast second major tRNA(Arg) (tRNA(Arg)(ICG)) isoacceptor have been crystallized by the hanging-drop vapour-diffusion method in the presence of ammonium sulfate. Crystal form II, which diffracts beyond 2.2 A resolution at the European Synchrotron Radiation Facility ID14-4 beamline, belongs to the orthorhombic space group P2(1)2(1)2, with unit-cell parameters a = 129.64},
note = {0907-4449
Journal Article},
keywords = {&, Arg/*chemistry/isolation, Arginine-tRNA, cerevisiae/enzymology/genetics, Crystallization, Crystallography, Fungal/chemistry/isolation, Gov't, Ligase/*chemistry/isolation, Non-U.S., purification/*metabolism, purification/metabolism, RNA, Saccharomyces, Support, Transfer, X-Ray},
pubstate = {published},
tppubtype = {article}
}
Bergdoll M., Eltis L. D., Cameron A. D., Dumas P., Bolin J. T.
All in the family: structural and evolutionary relationships among three modular proteins with diverse functions and variable assembly Article de journal
Dans: Protein Sci, vol. 7, no. 8, p. 1661-70, 1998, (0961-8368 Journal Article).
Résumé | BibTeX | Étiquettes: *Acetyltransferases, *Evolution, Acid, Amino, Bacterial, Burkholderia/*chemistry, Crystallography, Data, Genetic, Gov't, Homology, Human, Lactoylglutathione, Lyase/*chemistry, Models, Molecular, Non-U.S., Oxygenases/chemistry, P.H.S., Phylogeny, Protein, Proteins/*chemistry, Secondary, Sequence, structure, Support, U.S., X-Ray
@article{,
title = {All in the family: structural and evolutionary relationships among three modular proteins with diverse functions and variable assembly},
author = { M. Bergdoll and L. D. Eltis and A. D. Cameron and P. Dumas and J. T. Bolin},
year = {1998},
date = {1998-01-01},
journal = {Protein Sci},
volume = {7},
number = {8},
pages = {1661-70},
abstract = {The crystal structures of three proteins of diverse function and low sequence similarity were analyzed to evaluate structural and evolutionary relationships. The proteins include a bacterial bleomycin resistance protein, a bacterial extradiol dioxygenase, and human glyoxalase I. Structural comparisons, as well as phylogenetic analyses, strongly indicate that the modern family of proteins represented by these structures arose through a rich evolutionary history that includes multiple gene duplication and fusion events. These events appear to be historically shared in some cases, but parallel and historically independent in others. A significant early event is proposed to be the establishment of metal-binding in an oligomeric ancestor prior to the first gene fusion. Variations in the spatial arrangements of homologous modules are observed that are consistent with the structural principles of three-dimensional domain swapping, but in the unusual context of the formation of larger monomers from smaller dimers or tetramers. The comparisons support a general mechanism for metalloprotein evolution that exploits the symmetry of a homooligomeric protein to originate a metal binding site and relies upon the relaxation of symmetry, as enabled by gene duplication, to establish and refine specific functions.},
note = {0961-8368
Journal Article},
keywords = {*Acetyltransferases, *Evolution, Acid, Amino, Bacterial, Burkholderia/*chemistry, Crystallography, Data, Genetic, Gov't, Homology, Human, Lactoylglutathione, Lyase/*chemistry, Models, Molecular, Non-U.S., Oxygenases/chemistry, P.H.S., Phylogeny, Protein, Proteins/*chemistry, Secondary, Sequence, structure, Support, U.S., X-Ray},
pubstate = {published},
tppubtype = {article}
}
Dumas P., Bergdoll M., Cagnon C., Masson J. M.
Crystal structure and site-directed mutagenesis of a bleomycin resistance protein and their significance for drug sequestering Article de journal
Dans: EMBO J, vol. 13, no. 11, p. 2483-92, 1994, (0261-4189 Journal Article).
Résumé | BibTeX | Étiquettes: *Acetyltransferases, &, Acid, Amino, Bacterial, Bacterial/*genetics, Base, Binding, Bleomycin/*metabolism/pharmacology, Conformation, Crystallization, Crystallography, Data, Drug, Fusion, Genes, Gov't, Microbial/genetics, Models, Molecular, Mutagenesis, Non-U.S., Protein, Proteins/*chemistry/genetics/isolation, Proteins/isolation, purification, purification/metabolism, Recombinant, Relationship, Resistance, Secondary, Sequence, Site-Directed, Sites, Structural, structure, Structure-Activity, Support, X-Ray
@article{,
title = {Crystal structure and site-directed mutagenesis of a bleomycin resistance protein and their significance for drug sequestering},
author = { P. Dumas and M. Bergdoll and C. Cagnon and J. M. Masson},
year = {1994},
date = {1994-01-01},
journal = {EMBO J},
volume = {13},
number = {11},
pages = {2483-92},
abstract = {The antibiotic bleomycin, a strong DNA cutting agent, is naturally produced by actinomycetes which have developed a resistance mechanism against such a lethal compound. The crystal structure, at 2.3 A resolution, of a bleomycin resistance protein of 14 kDa reveals a structure in two halves with the same alpha/beta fold despite no sequence similarity. The crystal packing shows compact dimers with a hydrophobic interface and involved in mutual chain exchange. Two independent solution studies (analytical centrifugation and light scattering) showed that this dimeric form is not a packing artefact but is indeed the functional one. Furthermore, light scattering also showed that one dimer binds two antibiotic molecules as expected. A crevice located at the dimer interface, as well as the results of a site-directed mutagenesis study, led to a model wherein two bleomycin molecules are completely sequestered by one dimer. This provides a novel insight into antibiotic resistance due to drug sequestering, and probably also into drug transport and excretion.},
note = {0261-4189
Journal Article},
keywords = {*Acetyltransferases, &, Acid, Amino, Bacterial, Bacterial/*genetics, Base, Binding, Bleomycin/*metabolism/pharmacology, Conformation, Crystallization, Crystallography, Data, Drug, Fusion, Genes, Gov't, Microbial/genetics, Models, Molecular, Mutagenesis, Non-U.S., Protein, Proteins/*chemistry/genetics/isolation, Proteins/isolation, purification, purification/metabolism, Recombinant, Relationship, Resistance, Secondary, Sequence, Site-Directed, Sites, Structural, structure, Structure-Activity, Support, X-Ray},
pubstate = {published},
tppubtype = {article}
}