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Biomedical subjects

J E Wampler

Publications and source records attributed to J E Wampler.

33 records · Page 2Linked to original sources
PubMed1976

Structural identification and synthesis of luciferin from the bioluminescent earthworm, Diplocardia longa.

For the first time, luciferin from a bioluminescent earthworm has been purified, identified, and synthesized. This luciferin from the North American species, Diplocardia longa, is a simple aldehyde compound, N-isovaleryl-3-aminopropanal, with an amide functional group. It is a clear, odorless oil at room temperature. It is nonvolatile and has no near-uv-visible absorption or fluorescence. Derivatives of this compound were made to facilitate its identification: the luciferin 2,4-dinitrophenylhydrazone (mp 174 degrees C), a yellow crystalline solid; and the luciferin alcohol, a clear oil. Synthesis of Diplocardia luciferin yielded an oil of identical spectroscopic (proton nuclear magnetic resonance (NMR), 13C NMR, mass, and ir), chemical (dinitrophenylhydrazone and alcohol derivatives, bioluminescence activity), and physical (thin-layer chromatography, volatility) properties to those of the purified native Diplocardia luciferin.

Animals↗
PubMed1975

Spectral characteristics of the bioluminescence induced in the marine fish, Porichthys notatus by Cypridina (ostracod) luciferin.

Specimens of Porichthys notatus, which are naturally luminous along the coast of California, are non-luminous in Puget Sound. However, luminescence capability may be induced in the adult Puget Sound Porichthys by the administration of purified Cypridina (ostracod) luciferin, synthetic Cypridina luciferin, or Cypridina organisms. The bioluminescence emission spectra produced by the Puget Sound fish following induction is similar, if not identical, to that of the naturally luminous Porichthys notatus from California waters (maxima: 485 and 507 nm).

Animals↗
PubMed1971

Mechanism of oxidative carbon dioxide production during Renilla reniformis bioluminescence.

The oxidation of luciferin catalyzed by sea pansy luciferase results in the emission of light. Molecular oxygen is required and carbon dioxide is produced. When the reaction occurs in the presence of H(2) (18)O, both of the oxygens of the carbon dioxide are labeled. One of the oxygens arises from the nonenzymic exchange of the ketone group of the substrate; the other oxygen is incorporated during the enzymic oxidation of the luciferin. When the reaction is carried out in the presence of (18)O(2), neither of the oxygens of the carbon dioxide is labeled. Thus the source of oxygen in the carbon dioxide is water. A mechanism for the oxidative reaction is proposed.

Carbon Dioxide↗
PubMedDate not supplied

Electrostatic potential derived charges for enzyme cofactors: methods, correlations, and scaling for organic cofactors.

The correlations between electrostatic potential (ESP) derived atomic charges for a wide range of different quantum mechanical approaches and basis sets have been investigated for both small and large organic structures including several enzyme cofactors. The previously observed linear correlation between ESP charges calculated by different approaches has been verified to extend to many different basis sets and procedures including effective core potential (ECP) basis sets, density functional theory (DFT) approaches, a hybrid Hartree-Fock (HF)/DFT approach, and inclusion of electron correlation corrections. Above a threshold level of complexity, most procedures and basis sets give results that correlate very well (linear correlation coefficients > 0.99), including several procedures that have reasonable computational costs for large molecules. These procedures have been used to calculate ESP charges for five different types and forms of enzyme cofactors: biotin, pyridoxal-5'-phosphate, pyridoxamine-5'-phosphate, and the flavin mononucleotide in two different oxidation states.

Biotin↗
PubMedDate not supplied

Distribution analysis of the variation of B-factors of X-ray crystal structures; temperature and structural variations in lysozyme.

The B-factor (isotropic temperature factor) data for X-ray structures of hen egg-white lysozyme from the study of Young et al. (Young, Dewan, Nave, and Tilton J. Appl. Cryst. 1993, 26, 309-319) potentially contain information about the relative contributions of static and dynamic variation to these factors. The six structures of the protein were obtained at two widely different temperatures (100 and 298 K), with two crystal forms (monoclinic and tetragonal) and other experimental differences. In addition, the monoclinic lysozyme crystals with two molecules per asymmetric unit allow direct examination of variation between structures determined under identical conditions at both temperatures. The B-factors from these structures all have complex distribution functions as might be expected considering all of the influences that these values must reflect. The empirical cumulative distribution functions (eCDF's) of these data show that they are representative of complex, multicomponent distributions. Distribution analysis using the DANFIP procedure (Wampler, Anal. Biochemistry 1990, 186, 209-218) of the data sets reveals that they can be modeled as four to six Gaussian subpopulations, that these subpopulations do not correlate with specific atom types, specific amino acid residues or fixed locations in the structure. While they do seem to correlate with localized groupings of atoms, these grouping vary from structure to structure even within the same crystal under the same conditions. Temperature seems to have a global effect in this case, but it is clear that other factors including experimental error influence the distribution of B-factors within a given structure. This analysis also helps explain the oft observed lack of atomic level correlation between experimental B-factors and calculated mean square displacements from molecular dynamics simulations.

Algorithms↗