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Article
Open Access1H nuclear magnetic resonance brain metabolomics in neonatal mice after hypoxia–ischemia distinguished normothermic recovery from mild hypothermia recoveries
Mild brain hypothermia (31–34 °C) after neonatal hypoxia–ischemia (HI) improves neurodevelopmental outcomes in human and animal neonates. Using an asphyxia model with neonatal mice treated with mild hypothermi...
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Article
Perspectives on NMR in drug discovery: a technique comes of age
In the past decade, the ability of nuclear magnetic resonance (NMR) spectroscopy to provide information on intermolecular interactions that is valuable in drug discovery has been increasingly appreciated. Pell...
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Article
Resonance assignment of the first and second KH (hnRNP-K homology) domains of human poly(C)-binding protein-2 (PCBP2)
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Chapter
Refinement of Nucleic Acid Structures with Residual Dipolar Coupling Restraints in Cartesian Coordinate Space
During the past decade, measurement of residual dipolar constants (RDC) in weakly oriented molecules has been established as an invaluable source of structural information, and RDC data are now often used in s...
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Article
Using 31P NMR Spectroscopy at 14.1 Tesla to Investigate PARP-1 Associated Energy Failure and Metabolic Rescue in Cerebrocortical Slices
PARP-1 activation by H2O2 in an acute preparation of superfused, respiring, neonatal cerebrocortical slices was assessed from PAR-polymer formation detected with immunohistochemistry and Western blotting. 31P NMR...
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Article
High-resolution NMR structure of an AT-rich DNA sequence
We have determined, by proton NMR and complete relaxation matrix methods, the high-resolution structure of a DNA oligonucleotide in solution with nine contiguous AT base pairs. The stretch of AT pairs, TAATTAT...
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Chapter
Conformational Ensemble Calculations: Analysis of Protein and Nucleic Acid NMR Data
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Article
Identification of ligands for RNA targets via structure-based virtual screening: HIV-1 TAR
Binding of the Tat protein to TAR RNA is necessary for viral replication of HIV-1. We screened the Available Chemicals Directory (ACD) to identify ligands to bind to a TAR RNA structure using a four-step docki...
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Article
Determination of the populations and structures of multiple conformers in an ensemble from NMR data: Multiple-copy refinement of nucleic acid structures using floating weights
A new algorithm is presented for determination of structural conformers and their populations based on NMR data. Restrained Metropolis Monte Carlo simulations or restrained energy minimizations are performed f...
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Article
Structure of the most conserved internal loop in SRP RNA
The signal recognition particle (SRP) directs translating ribosomes to the protein translocation apparatus of endoplasmic reticulum (ER) membrane or the bacterial plasma membrane. The SRP is universally conser...
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Article
Contributory presentations/posters
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Article
Restrained molecular dynamics of solvated duplex DNA using the particle mesh Ewald method
Restrained and unrestrained aqueous solution molecular dynamics simulations applying the particle mesh Ewald (PME) method to DNA duplex structures previously determined via in vacuo restrained molecular dynami...
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Article
Structure of the dimer a initiation complex of HIV-1 genomic RNA
Retroviral genomes must dimerize to be fully infectious. Dimerization is directed by a unique RNA hairpin structure with a palindrome in its loop: hairpins of two strands first associate transiently through th...
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Article
Structure-based design of ligands for protein basic domains: Application to the HIV-1 Tat protein
A methodology has been developed for designing ligands to bind a flexible basic protein domain where the structure of the domain is essentially known. It is based on an empirical binding free energy function d...
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Article
The dynamic NMR structure of the TΨC-loop: Implications for the specificity of tRNA methylation
tRNA (m5U54)-methyltransferase (RUMT) catalyzes the S-adenosylmethionine-dependentmethylation of uridine-54 in the TΨC-loop of all transfer RNAs in E. coli to form the 54-ribosylthymine residue. However, in al...
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Chapter
Panel Discussion
Mildred Cohn - The subject of this panel discussion is NMR vis-à-vis Other Structural Methods. The way it is going to be run is that each panelist will give a presentation on his or her particular technique, whic...
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Chapter
Dynamic Structure of Nucleic Acid Duplexes
Sequence-dependent structural variations in nucleic acids are important for the protein-nucleic acid and RNA-DNA interactions essential for life. Furthermore, structural variations are important factors in the...
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Article
Interproton distance bounds from 2D NOE intensities: Effect of experimental noise and peak integration errors
The effect of experimental and integration errors on the calculations in interproton distances from NOE intensities is examined. It is shown that NOE intensity errors can have a large impact on the distances d...
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Chapter and Conference Paper
Determination of High-Resolution, Sequence-Dependent DNA Duplex Structures in Solution
There can be rather subtle structural variations in the DNA double helix which are sequence-dependent; but these subtle structural differences may direct protein, mutagen or drug recognition. These subtle vari...
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Article
Metropolis Monte Carlo calculations of DNA structure using internal coordinates and NMR distance restraints: An alternative method for generating a high-resolution solution structure
A new method, a restrained Monte Carlo (rMC) calculation, is demonstrated for generating high-resolution structures of DNA oligonucleotides in solution from interproton distance restraints and bounds derived f...
