17 Result(s)
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Article
Thomas L. James
English
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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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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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Resonance assignment of the first and second KH (hnRNP-K homology) domains of human poly(C)-binding protein-2 (PCBP2)
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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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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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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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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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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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Contributory presentations/posters
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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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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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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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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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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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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...
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Beneficial effects of verapamil during metabolic acidosis in isolated perfused rat hearts
Metabolic acidosis was produced in two groups of isolated, glucose-perfused beating rat hearts. The first group (control) was untreated whereas the second group was pretreated for 48 h by the addition of verap...
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Quantitative internuclear distancesvia two-dimensional nuclear magnetic resonance spectra: A test case and a DNA octamer duplex
Two-dimensional proton nuclear magnetic resonance nuclear Overhauser effect experiments have been performed at a series of mixing times on proflavine and on a DNA octamer duplex [d-(GGAATTCC)]2 in solution. Using...
