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Lakdawala, Ami S.; Wang, Minmin; Nevins, Neysa; Liotta, Dennis; Rusinska-Roszak, Danuta; Lozynski, Marek; Snyder, James P.

doi:10.1186/1472-6769-1-2

Cited by 25 publications

(23 citation statements)

References 16 publications

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“…c Calculated using the complete relaxation matrix (CORMA) method. as pointed out earlier, [25,29] and evidenced in this work from the differences observed between the two force-field methods. Thus, given a number of conformers, the ensemble of all sets of conformers' relative contributions should be considered and assessed for matching theoretical data to the experimental data.…”

Section: Conformational Equilibriumsupporting

confidence: 50%

“…In this work, the MM2 * energies seem to underestimate the relative stability of conformer I (population ∼50%) as opposed to MMFF which overestimates it (population ∼100%). These discrepancies have been pointed out previously [25,29] in the conformational analysis of small molecules, thus criticizing the calculation of the relative conformational stability on the basis of force-field energies. A more accurate approach to this problem could be the consideration of all conformers irrespective of their relative energies identifying the relative population ratio that could explain the experimental data better.…”

Section: Discussionmentioning

confidence: 93%

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Conformational properties of the macrocyclic trichothecene mycotoxin verrucarin A in solution

Fragaki¹,

Stefanaki²,

Dais³

et al. 2008

Magnetic Reson in Chemistry

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Phase-sensitive nuclear Overhauser enhancement spectroscopy (NOESY) experiments, (3)J couplings and computational molecular modeling (MM2* and MMFF force fields) were employed to examine the conformational properties of verrucarin A in chloroform solutions. The MMFF force field calculations resulted in a family of 12 low-energy structures along with their populations, the latter being determined by the NMR analysis of molecular flexibility in solution(NAMFIS) deconvolution analysis. The concluded model was capable of reproducing successfully the experimental NOESY cross-peak volumes and the proton-coupling constants. Among the 12 conformers, the one which was similar to the structure of verrucarin A in the solid state was the predominant accounting for 75% of the total relative population, although other low-energy conformations contributed to a lesser degree in order to explain the experimental data.

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Section: Conformational Equilibriumsupporting

confidence: 50%

Section: Discussionmentioning

confidence: 93%

Conformational properties of the macrocyclic trichothecene mycotoxin verrucarin A in solution

Fragaki¹,

Stefanaki²,

Dais³

et al. 2008

Magnetic Reson in Chemistry

View full text Add to dashboard Cite

show abstract

“…One advantage of the NAMFIS approach is that it does not rely on the calculated energies of the conformers, which have proven to provide unreliable values at least with highly polar molecules like PTX [65] . Instead, NAMFIS uses all reasonable conformational minima proposals regardless of their energies and selects them on the basis of their fitting to the experimental NMR data.…”

Section: Namfis Deconvolution Analysismentioning

confidence: 99%

The Tubulin Binding Mode of MT Stabilizing and Destabilizing Agents Studied by NMR

Sánchez-Pedregal

Griesinger

2008

Topics in Current Chemistry

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Tubulin is a fascinating molecule that forms the cytoskeleton of the cells and plays an important role in cell division and trafficking of molecules. It polymerizes and depolymerizes in order to fulfill this biological function. This function can be modulated by small molecules that interfere with the polymerization or the depolymerization. In this article, the structural basis of this behavior is reviewed with special attention to the contribution of NMR spectroscopy. Complex structures of small molecules that bind to tubulin and microtubules will be discussed. Many of them have been determined using NMR spectroscopy, which proves to be an important method in tubulin research.

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“…26 The purpose here was simply to give a penalty to those conformer proportions very far from the calculated energies.…”

Section: Resultsmentioning

confidence: 99%

A quantitative application of the J‐based configuration analysis method to a flexible small molecule

Sharman

2007

Magnetic Reson in Chemistry

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An example of the use of the J-based configuration analysis method to determine relative stereochemistry of a small molecule related to reboxetine is described. This study was complicated by the fact that the molecule did not exhibit J-couplings and NOEs consistent with a single conformation, but rather an ensemble average. A quantitative fitting procedure using predicted couplings and NOEs from all possible conformers was used. This gave a clear indication of the stereochemistry, and the populations of the conformers involved.

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Untitled

Cited by 25 publications

References 16 publications

Conformational properties of the macrocyclic trichothecene mycotoxin verrucarin A in solution

Conformational properties of the macrocyclic trichothecene mycotoxin verrucarin A in solution

The Tubulin Binding Mode of MT Stabilizing and Destabilizing Agents Studied by NMR

A quantitative application of the J‐based configuration analysis method to a flexible small molecule

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