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feenstra's spectroscopy [8 articles]

 
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A novel energy partition for gaining new insight into aromaticity and conjugation

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Journal of Physical Chemistry A, Vol. 104, No. 8. (2000), pp. 1736-1747
by Z. H. Yu, Z. Q. Xuan, T. X. Wang, H. M. Yu
posted to bibtex-anton crystal-structures delocalization heterocycles microwave molecular-structure motion neutron-diffraction spectra spectroscopy structure substitution temperature-dependence thermal by feenstra on 2005-12-02 14:30:59 **
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Abstract

To gain new insight into the nature of aromaticity and conjugation, we have developed a novel procedure for constructing a localized fragment molecular orbital basis set. It is a three-step procedure: (i) obtainment of each subcanonical FMO (fragment molecular orbital) basis set from aspecific double bond fragment and its fragment molecule; (ii) the localization of the canonical FMOs; (iii) the superposition of all sublocalized FMO basis sets. On the basis of our procedure, Morokuma's energy partition provides, in the framework of ...
 

The solution conformations of amino acids from molecular dynamics simulations of Gly-X-Gly peptides: comparison with NMR parameters

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Biochemistry and Cell Biology-Biochimie Et Biologie Cellulaire, Vol. 76, No. 2-3. (1998), pp. 164-170
by D. van der Spoel
posted to angles backbone bibtex-anton chemical chemical-shifts coil conformations continuous coupling-constants dihedral distribution dynamics ggxgg j-coupling magnetic md measurements molecular nmr nuclear pancreatic probability probability-distribution random relaxation resonance secondary series shift spectroscopy structure torsion trypsin-inhibitor by feenstra on 2005-12-02 14:30:57 **
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Abstract

The conformations that amino acids can adopt in the random coil state are of fundamental interest in the context of protein folding research and studies of protein-peptide interactions. To date, no detailed quantitative data from experimental studies have been reported; only nuclear magnetic resonance parameters such as chemical shifts and J coupling constants have been reported. These experimental nuclear magnetic resonance data represent averages over multiple conformations, and hence they do not provide unique structural information. I have performed relatively long ...
 

General framework for studying the dynamics of folded and nonfolded proteins by NMR relaxation spectroscopy and MD simulation

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Journal of the American Chemical Society, Vol. 124, No. 16. (2002), pp. 4522-4534
by J. J. Prompers, R. Bruschweiler
posted to approach backbone bibtex-anton coupling drosophila-melanogaster dynamics homeodomain human magnetic-resonance main-chain model-free molecular-dynamics nuclease smoluchowski spectroscopy staphylococcal ubiquitin vndnk-2 by feenstra on 2005-12-02 14:30:55 **
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Abstract

A general framework is presented for the interpretation of NMR relaxation data of proteins. The method, termed isotropic reorientational eigenmode dynamics (iRED), relies on a principal component analysis of the isotropically averaged covariance matrix of the lattice functions of the spin interactions responsible for spin relaxation. The covariance matrix, which is evaluated using a molecular dynamics (MD) simulation, is diagonalized yielding reorientational eigenmodes and amplitudes that reveal detailed information about correlated protein dynamics. The eigenvalue distribution allows one to quantitatively assess ...
 

Qualitative EH-FMO interpretation of the Pt-195 NMR shifts in heterobimetallic complexes containing the Pt-Pd-Y core: an inverse halogen dependence

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Inorganica Chimica Acta, Vol. 264, No. 1-2. (1997), pp. 109-116
by F. Pichierri, E. Chiarparin, E. Zangrando, L. Randaccio, D. Holthenrich, B. Lippert
posted to analysis bibtex-anton bonds chemical-shifts complexes crystal heterobimetallic ligands molecular nucleobase orbital platinum spectroscopy structures by feenstra on 2005-12-02 14:30:54 **
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Abstract

The Pt-195 chemical shift in complexes of type trans-[a(2)Pt(mecyt)(2)PdY](n+) (mecyt = 1-methylcytosinato, a = NH3 or NH2Me, Y = neutral or monoanionic ligand) covers a range of 500 ppm, depending on the variation of the Y ligand bound trans to the Pt atom. These chemical shifts were correlated with energy differences between MOs, obtained from extended Huckel-fragment molecular orbital (EH-FMO) calcu lations. An inverse halogen dependence of the Pt-195 chemical shift versus orbital energy differences is obtained, with a correlation coefficient ...
 

The catalytic mechanism of cytochrome P450 BM3 involves a 6 A movement of the bound substrate on reduction

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Nat Struct Biol, Vol. 3, No. 5. (1996), pp. 414-7
by S. Modi, M. J. Sutcliffe, W. U. Primrose, L. Y. Lian, G. C. Roberts
posted to bacillus bibtex-anton camphor comparative computer cytochrome enzyme function hydroxylation laurateschemistrymetabolism magnetic megateriumenzymology mixed models molecular movement oxidation-reduction oxygenaseschemistrymetabolism p-450 resonance simulation spectroscopy study systemchemistrymetabolism by feenstra on 2005-12-02 14:30:54 **
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A model for human cytochrome P450 2D6 based on homology modeling and NMR studies of substrate binding

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Biochemistry, Vol. 35, No. 14. (1996), pp. 4540-50
by S. Modi, M. J. Paine, M. J. Sutcliffe, et al.L. Y. Lian, W. U. Primrose, C. R. Wolf, G. C. Roberts
posted to acid amino animal baculoviridaegenetics base bibtex-anton binding cell complementarygenetics cyp2d6 cytochrome data dna enzyme function govt hemechemistry homology human in line magnetic mixed models molecular non-us oxygenaseschemistrygeneticsmetabolism p-450 primersgenetics proteinschemistrygeneticsmetabolism recombinant resonance sequence sites specificity spectrophotometry spectroscopy spodoptera structure substrate support systemchemistrygeneticsmetabolism vitro by feenstra on 2005-12-02 14:30:54 **
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Abstract

The cytochrome P450 responsible for the debrisoquine/sparteine polymorphism (P450 2D6) has been produced in large quantities by expression of a modified cDNA in baculovirus. A polyhistidine extension was incorporated at the C-terminus of the expressed protein, which, after purification of the protein on a nickel-agarose column, could be removed proteolytically by treatment with thrombin. Purified yields of P450 2D6 were 2.4 mg from 700 mL of cell culture. The protein had a greater than 90% heme content and was fully active, ...
 

Prediction of Regiospecific Hydroxylation of Camphor Analogs by Cytochrome-P450(Cam)

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Journal of the American Chemical Society, Vol. 117, No. 10. (1995), pp. 2738-2746
by D. Harris, G. Loew
posted to bibtex-anton characterization compound- crystal-structure domain exafs hemoprotein i metabolism molecular-dynamics norcamphor spectroscopy stereochemistry structural thiocamphor by feenstra on 2005-12-02 14:30:51 **
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Abstract

The regiospecificities of the hydroxylations of d-camphor, d- camphane, d-thiocamphor, and d- and l-norcamphor have been predicted by employing geometric criteria obtained from molecular dynamic simulations of enzyme-substrate interactions in conjunction with the thermodynamic criteria of relative radical energetics derived from nb initio and semiempirical quantum mechanics. Molecular dynamic simulations were performed using the Amber 4.0 suite of programs with modified Lennard- Jones 6-12 parameters and explicit inclusion of all atoms within a 16 Angstrom ”belly” region surrounding the reactive ferryl ...
 

Relative stability of protein structures determined by X-ray crystallography or NMR spectroscopy: A molecular dynamics simulation study

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Proteins-Structure Function and Genetics, Vol. 53, No. 1. (2003), pp. 111-120
by H. Fan, A. E. Mark
posted to bibtex-anton crystal-structure crystallography dna-binding domain dynamic molecular nmr nuclear-magnetic-resonance protein quality refinement repressor resolution sh3 simulation single-crystals solution spectroscopy structure structures terminal x-ray by feenstra on 2005-12-02 14:30:49 **
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Abstract

The relative stability of protein structures determined by either X-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy has been investigated by using molecular dynamics simulation techniques. Published structures of 34 proteins containing between 50 and 100 residues have been evaluated. The proteins selected represent a mixture of secondary structure types including all alpha, all beta, and alpha/beta. The proteins selected do not contain cysteine-eysteine bridges. In addition, any crystallographic waters, metal ions, cofactors, or bound ligands were removed before the systems ...
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