14 Result(s)
within
Thomas L. James
Biological and Medical Physics, Biophysics
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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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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
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
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
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...
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Chapter
NMR Methods in Studies of Brain Ischemia
In vivo NMR spectroscopy has gained world-wide attention since the publication of the use of surface coils to noninvasively observe metabolic changes in whole animals (Ackerman et al., 1980)...
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Chapter
Structure Determination via Complete Relaxation Matrix Analysis (CORMA) of Two-Dimensional Nuclear Overhauser Effect Spectra
Methods for the complete high-resolution determination of molecular structure in solution have been a goal of scientists since the development of X-ray diffraction techniques in the early part of this century....
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Chapter
Structure and Dynamics Studied Via Two-Dimensional NMR. Illustrations with DNA Fragments
A major objective of scientists for many years has been the determination of molecular structures in non-crystalline environments. In general, researchers were forced to accept limited structural information i...
