Search results for: Arthur Pardi

Items from 1 to 20 out of 36 results

article

Flexibility in the Periplasmic Domain of BamA Is Important for Function

Lisa R. Warner, Petia Z. Gatzeva-Topalova, Pamela A. Doerner, Arthur Pardi, more

Structure > 2017 > 25 > 1 > 94-106

The β-barrel assembly machine (BAM) mediates the biogenesis of outer membrane proteins (OMPs) in Gram-negative bacteria. BamA, the central BAM subunit composed of a transmembrane β-barrel domain linked to five polypeptide transport-associated (POTRA) periplasmic domains, is thought to bind nascent OMPs and undergo conformational cycling to catalyze OMP folding and insertion. One model is that conformational...

article

Efficient Detection of Hydrogen Bonds in Dynamic Regions of RNA by Sensitivity‐Optimized NMR Pulse Sequences

Andre Dallmann, Bernd Simon, Malgorzata M. Duszczyk, Hamed Kooshapur, more

Angewandte Chemie > 125 > 40 > 10681 - 10684

Verbesserte Empfindlichkeit: Mit effizienten NMR‐Experimenten, die auf der J‐Kopplung entlang von Wasserstoffbrücken basieren, wird die Sekundärstruktur von großen und dynamischen RNA‐Molekülen bestimmt (siehe Bild). Die Experimente liefern eine bis zu 8fach verbesserte Empfindlichkeit und ermöglichen so die Detektion von Basenpaaren in den dynamischen Bereichen großer RNA‐Moleküle.

article

Efficient Detection of Hydrogen Bonds in Dynamic Regions of RNA by Sensitivity‐Optimized NMR Pulse Sequences

Andre Dallmann, Bernd Simon, Malgorzata M. Duszczyk, Hamed Kooshapur, more

Angewandte Chemie International Edition > 52 > 40 > 10487 - 10490

Improved Sensitivity: Efficient NMR experiments are presented for determining the secondary structure in large and dynamic RNAs using J‐couplings across hydrogen bonds (see picture). The experiments provide up to eight‐fold improved sensitivity and thus enable detection of base pairs in dynamic regions even in large RNAs.

article

Structure of the BamC Two-Domain Protein Obtained by Rosetta with a Limited NMR Data Set

Lisa R. Warner, Krisztina Varga, Oliver F. Lange, Susan L. Baker, more

Journal of Molecular Biology > 2011 > 411 > 1 > 83-95

The CS-RDC-NOE Rosetta program was used to generate the solution structure of a 27-kDa fragment of the Escherichia coli BamC protein from a limited set of NMR data. The BamC protein is a component of the essential five-protein β-barrel assembly machine in E. coli. The first 100 residues in BamC were disordered in solution. The Rosetta calculations showed that BamC _101–344 forms two well-defined...

article

Structure and Flexibility of the Complete Periplasmic Domain of BamA: The Protein Insertion Machine of the Outer Membrane

Petia Zvezdanova Gatzeva-Topalova, Lisa Rosa Warner, Arthur Pardi, Marcelo Carlos Sousa

Structure > 2010 > 18 > 11 > 1492-1501

Folding and insertion of β-barrel outer membrane proteins (OMPs) is essential for Gram-negative bacteria. This process is mediated by the multiprotein complex BAM, composed of the essential β-barrel OMP BamA and four lipoproteins (BamBCDE). The periplasmic domain of BamA is key for its function and contains five “polypeptide transport-associated” (POTRA) repeats. Here, we report the crystal structure...

article

Ultrafast Dynamics Show That the Theophylline and 3-Methylxanthine Aptamers Employ a Conformational Capture Mechanism for Binding Their Ligands

Sang Won Lee, Liang Zhao, Arthur Pardi, Tianbing Xia

Biochemistry > 2010 > 49 > 13 > 2943 - 2951

article

Chemical Shift Anisotropy of Imino ¹⁵ N Nuclei in Watson−Crick Base Pairs from Magic Angle Spinning Liquid Crystal NMR and Nuclear Spin Relaxation

Alexander Grishaev, Lishan Yao, Jinfa Ying, Arthur Pardi, more

Journal of the American Chemical Society > 2009 > 131 > 27 > 9490 - 9491

article

Longitudinal-Relaxation-Enhanced NMR Experiments for the Study of Nucleic Acids in Solution

Jonathan Farjon, Jérôme Boisbouvier, Paul Schanda, Arthur Pardi, more

Journal of the American Chemical Society > 2009 > 131 > 24 > 8571 - 8577

article

NMR Chemical Exchange as a Probe for Ligand-Binding Kinetics in a Theophylline-Binding RNA Aptamer

Michael P. Latham, Grant R. Zimmermann, Arthur Pardi

Journal of the American Chemical Society > 2009 > 131 > 14 > 5052 - 5053

article

Measurement of imino ¹H–¹H residual dipolar couplings in RNA

Michael P. Latham, Arthur Pardi

Journal of Biomolecular NMR > 2009 > 43 > 2 > 121-129

Imino ¹H–¹⁵N residual dipolar couplings (RDCs) provide additional structural information that complements standard ¹H–¹H NOEs leading to improvements in both the local and global structure of RNAs. Here, we report measurement of imino ¹H–¹H RDCs for the Iron Responsive Element (IRE) RNA and native E. coli tRNA^Val using a BEST-Jcomp-HMQC2 experiment. ¹H–¹H RDCs are observed between the imino protons...

article

Imino proton exchange rates imply an induced-fit binding mechanism for the VEGF165-targeting aptamer, Macugen

Joon-Hwa Lee, Fiona Jucker, Arthur Pardi

FEBS Letters > 2008 > 582 > 13 > 1835-1839

The 2′-fluoro/2′-O-methyl modified RNA aptamer Macugen is a potent inhibitor of the angiogenic regulatory protein, VEGF ₁₆₅ . Macugen binds with high affinity to the heparin-binding domain (HBD) of VEGF ₁₆₅ . Hydrogen exchange rates of the imino protons were measured for free Macugen and Macugen bound to the HBD or full-length VEGF to better understand the mechanism for high affinity...

article

Comparison of alignment tensors generated for native tRNA^Val using magnetic fields and liquid crystalline media

Michael P. Latham, Paul Hanson, Darin J. Brown, Arthur Pardi

Journal of Biomolecular NMR > 2008 > 40 > 2 > 83-94

Residual dipolar couplings (RDCs) complement standard NOE distance and J-coupling torsion angle data to improve the local and global structure of biomolecules in solution. One powerful application of RDCs is for domain orientation studies, which are especially valuable for structural studies of nucleic acids, where the local structure of a double helix is readily modeled and the orientations of the...

article

Solution structure of tRNA^Val from refinement of homology model against residual dipolar coupling and SAXS data

Alexander Grishaev, Jinfa Ying, Marella D. Canny, Arthur Pardi, more

Journal of Biomolecular NMR > 2008 > 42 > 2 > 99-109

A procedure is presented for refinement of a homology model of E. coli tRNA^Val, originally based on the X-ray structure of yeast tRNA^Phe, using experimental residual dipolar coupling (RDC) and small angle X-ray scattering (SAXS) data. A spherical sampling algorithm is described for refinement against SAXS data that does not require a globbic approximation, which is particularly important for nucleic...

article

High-resolution pyrimidine- and ribose-specific 4D HCCH-COSY spectra of RNA using the filter diagonalization method

Justin T. Douglas, Michael P. Latham, Geoffrey S. Armstrong, Brad Bendiak, more

Journal of Biomolecular NMR > 2008 > 41 > 4 > 209-219

The NMR spectra of nucleic acids suffer from severe peak overlap, which complicates resonance assignments. 4D NMR experiments can overcome much of the degeneracy in 2D and 3D spectra; however, the linear increase in acquisition time with each new dimension makes it impractical to acquire high-resolution 4D spectra using standard Fourier transform (FT) techniques. The filter diagonalization method...

article

Influence of Hydrostatic Pressure and Cosolutes on RNA Tertiary Structure

Christopher D. Downey, Ryan L. Crisman, Theodore W. Randolph, Arthur Pardi

Journal of the American Chemical Society > 2007 > 129 > 30 > 9290 - 9291

article

Efficient Ligation of the Schistosoma Hammerhead Ribozyme ^†

Marella D. Canny, Fiona M. Jucker, Arthur Pardi

Biochemistry > 2007 > 46 > 12 > 3826 - 3834

article

Magnetic field induced residual dipolar couplings of imino groups in nucleic acids from measurements at a single magnetic field

Jinfa Ying, Alexander Grishaev, Michael P. Latham, Arthur Pardi, more

Journal of Biomolecular NMR > 2007 > 39 > 2 > 91-96

For base-paired nucleic acids, variations in ¹ J _NH and the imino ¹H chemical shift are both dominated by hydrogen bond length. In the absence of molecular alignment, the ¹ J _NH coupling for the imino proton then can be approximated by ¹ J _NH = (1.21Hz/ppm)δ_H − 103.5 ± 0.6 Hz, where δ_H represents the chemical shift of the imino proton in ppm. This relation permits imino residual dipolar couplings...

article

Metal Ion Dependence, Thermodynamics, and Kinetics for Intramolecular Docking of a GAAA Tetraloop and Receptor Connected by a Flexible Linker ^†

Christopher D. Downey, Julie L. Fiore, Colby D. Stoddard, Jose H. Hodak, more

Biochemistry > 2006 > 45 > 11 > 3664 - 3673

article

Comparison of the Global Structure and Dynamics of Native and Unmodified tRNA ^val ^†

Annaleen Vermeulen, Scott A. McCallum, Arthur Pardi

Biochemistry > 2005 > 44 > 16 > 6024 - 6033

article

Resolution-Enhanced Base-Type-Edited HCN Experiment for RNA

Hélène Van Melckebeke, Arthur Pardi, Jérôme Boisbouvier, Jean-Pierre Simorre, more

Journal of Biomolecular NMR > 2005 > 32 > 4 > 263-271

New base-type-edited transverse-relaxation optimized CT-HCN(C) experiments are presented that yield intra-base and sugar-to-base correlations for ¹³C−¹⁵N labeled RNA. High spectral resolution in the ¹³C and ¹⁵N dimensions is achieved by constant time (CT) frequency editing. A spectral editing filter applied during the CT ¹⁵N labeling period separates the correlation peaks arising from G/U and A/C...

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Search results for: Arthur Pardi

Flexibility in the Periplasmic Domain of BamA Is Important for Function

Efficient Detection of Hydrogen Bonds in Dynamic Regions of RNA by Sensitivity‐Optimized NMR Pulse Sequences

Efficient Detection of Hydrogen Bonds in Dynamic Regions of RNA by Sensitivity‐Optimized NMR Pulse Sequences

Structure of the BamC Two-Domain Protein Obtained by Rosetta with a Limited NMR Data Set

Structure and Flexibility of the Complete Periplasmic Domain of BamA: The Protein Insertion Machine of the Outer Membrane

Ultrafast Dynamics Show That the Theophylline and 3-Methylxanthine Aptamers Employ a Conformational Capture Mechanism for Binding Their Ligands

Chemical Shift Anisotropy of Imino ¹⁵ N Nuclei in Watson−Crick Base Pairs from Magic Angle Spinning Liquid Crystal NMR and Nuclear Spin Relaxation

Longitudinal-Relaxation-Enhanced NMR Experiments for the Study of Nucleic Acids in Solution

NMR Chemical Exchange as a Probe for Ligand-Binding Kinetics in a Theophylline-Binding RNA Aptamer

Measurement of imino ¹H–¹H residual dipolar couplings in RNA

Imino proton exchange rates imply an induced-fit binding mechanism for the VEGF165-targeting aptamer, Macugen

Comparison of alignment tensors generated for native tRNA^Val using magnetic fields and liquid crystalline media

Solution structure of tRNA^Val from refinement of homology model against residual dipolar coupling and SAXS data

High-resolution pyrimidine- and ribose-specific 4D HCCH-COSY spectra of RNA using the filter diagonalization method

Influence of Hydrostatic Pressure and Cosolutes on RNA Tertiary Structure

Efficient Ligation of the Schistosoma Hammerhead Ribozyme ^†

Magnetic field induced residual dipolar couplings of imino groups in nucleic acids from measurements at a single magnetic field

Metal Ion Dependence, Thermodynamics, and Kinetics for Intramolecular Docking of a GAAA Tetraloop and Receptor Connected by a Flexible Linker ^†

Comparison of the Global Structure and Dynamics of Native and Unmodified tRNA ^val ^†

Resolution-Enhanced Base-Type-Edited HCN Experiment for RNA

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