isomerism

Summary

Summary: The phenomenon whereby certain chemical compounds have structures that are different although the compounds possess the same elemental composition. (From McGraw-Hill Dictionary of Scientific and Technical Terms, 5th ed)

Top Publications

  1. ncbi Prolyl cis-trans isomerization as a molecular timer
    Kun Ping Lu
    Cancer Biology Program, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, 77 Avenue Louis Pasteur, NRB 1030, Boston, Massachusetts 02215, USA
    Nat Chem Biol 3:619-29. 2007
  2. ncbi Proline isomerization of histone H3 regulates lysine methylation and gene expression
    Christopher J Nelson
    Gurdon Institute and Department of Pathology, Tennis Court Road, Cambridge, CB2 1QR, UK
    Cell 126:905-16. 2006
  3. ncbi Ibuprofen binding to secondary sites allosterically modulates the spectroscopic and catalytic properties of human serum heme-albumin
    Alessandra di Masi
    Department of Biology, and Interdepartmental Laboratory of Electron Microscopy, University Roma Tre, Italy
    FEBS J 278:654-62. 2011
  4. ncbi Simultaneous racemization and isomerization at specific aspartic acid residues in alpha B-crystallin from the aged human lens
    N Fujii
    Discovery Research Division, Takeda Chemical Industries, Ltd, Ibaraki, Japan
    Biochim Biophys Acta 1204:157-63. 1994
  5. ncbi Identification of isomerization and racemization of aspartate in the Asp-Asp motifs of a therapeutic protein
    Jennifer Zhang
    Protein Analytical Chemistry, Genentech Inc, 1 DNA Way, South San Francisco, CA 94080, USA
    Anal Biochem 410:234-43. 2011
  6. ncbi Occurrence and detection of phosphopeptide isomers in large-scale phosphoproteomics experiments
    Mathieu Courcelles
    IRIC, Institute for Research in Immunology and Cancer, Universite de Montreal, P O Box 6128, Station Centre Ville, Montreal, Quebec, Canada H3C 3J7
    J Proteome Res 11:3753-65. 2012
  7. ncbi Chiral metallo-supramolecular complexes selectively induce human telomeric G-quadruplex formation under salt-deficient conditions
    Chuanqi Zhao
    Division of Biological Inorganic Chemistry, State Key Laboratory of Rare Earth Resource Utilization, Graduate School of the Chinese Academy of Sciences, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, PR China
    Chemistry 17:8209-15. 2011
  8. pmc The high mannose glycans from bovine ribonuclease B isomer characterization by ion trap MS
    Justin M Prien
    The Glycomics Center, Division of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire 03824, USA
    J Am Soc Mass Spectrom 20:539-56. 2009
  9. pmc Mass spectrometric analysis of asparagine deamidation and aspartate isomerization in polypeptides
    Hongqian Yang
    Division of Molecular Biometry, Department of Medicinal Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
    Electrophoresis 31:1764-72. 2010
  10. ncbi Photoactivation of the photoactive yellow protein: why photon absorption triggers a trans-to-cis Isomerization of the chromophore in the protein
    Gerrit Groenhof
    Department of Biophysical Chemistry, University of Groningen, Nijenborg 4, 9747 AG Groningen, The Netherlands
    J Am Chem Soc 126:4228-33. 2004

Research Grants

  1. Role of Pitx2 in Muscle Development and Regeneration
    Chrissa Kioussi; Fiscal Year: 2011
  2. Nitrogen Oxides and Heme
    GEORGE RICHTER ADDO; Fiscal Year: 2007
  3. OPTICAL PROPERTIES OF BIOLOGICAL MACROMOLECULES
    ROBERT WOODY; Fiscal Year: 2002
  4. OPTICAL PROPERTIES OF BIOLOGICAL MACROMOLECULES
    ROBERT WOODY; Fiscal Year: 2003
  5. EGF CFC GENES IN MAMMALIAN LEFT RIGHT AXIS DETERMINATION
    Michael Shen; Fiscal Year: 2004
  6. Synthesis of Macrolides, Steroids, Cyclopentanoids, etc.
    BARRY TROST; Fiscal Year: 2009
  7. ASSEMBLIES OF SELF COMPLEMENTARY STRUCTURES
    Julius Rebek; Fiscal Year: 2005
  8. STUDIES IN MOLECULAR RECOGNITION
    Julius Rebek; Fiscal Year: 2010
  9. Chemical Mechanism of Guanine Deamination
    Rainer Glaser; Fiscal Year: 2003
  10. Structural Studies of AIDS-Responsive Drugs
    Vivian Cody; Fiscal Year: 2010

Detail Information

Publications308 found, 100 shown here

  1. ncbi Prolyl cis-trans isomerization as a molecular timer
    Kun Ping Lu
    Cancer Biology Program, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, 77 Avenue Louis Pasteur, NRB 1030, Boston, Massachusetts 02215, USA
    Nat Chem Biol 3:619-29. 2007
    ....
  2. ncbi Proline isomerization of histone H3 regulates lysine methylation and gene expression
    Christopher J Nelson
    Gurdon Institute and Department of Pathology, Tennis Court Road, Cambridge, CB2 1QR, UK
    Cell 126:905-16. 2006
    ..These results identify proline isomerization as a novel noncovalent histone modification that regulates transcription and provides evidence for crosstalk between histone lysine methylation and proline isomerization...
  3. ncbi Ibuprofen binding to secondary sites allosterically modulates the spectroscopic and catalytic properties of human serum heme-albumin
    Alessandra di Masi
    Department of Biology, and Interdepartmental Laboratory of Electron Microscopy, University Roma Tre, Italy
    FEBS J 278:654-62. 2011
    ..Thus, tHSA is a valuable model with which to investigate the allosteric linkage between the heme cleft FA1 and the ligand-binding pockets FA2 and FA6, all located in domains I and II of (t)HSA...
  4. ncbi Simultaneous racemization and isomerization at specific aspartic acid residues in alpha B-crystallin from the aged human lens
    N Fujii
    Discovery Research Division, Takeda Chemical Industries, Ltd, Ibaraki, Japan
    Biochim Biophys Acta 1204:157-63. 1994
    ..We concluded that racemization, isomerization, and oxidation of alpha B-crystallin occur spontaneously in the aging process...
  5. ncbi Identification of isomerization and racemization of aspartate in the Asp-Asp motifs of a therapeutic protein
    Jennifer Zhang
    Protein Analytical Chemistry, Genentech Inc, 1 DNA Way, South San Francisco, CA 94080, USA
    Anal Biochem 410:234-43. 2011
    ..Another isomerization site was identified as Asp-24 in the heavy chain peptide H5 QAPGQGLEWMGWINTYTGETTYAD(24)DFK. No other isomerizations were detected in CDR peptides containing either Asp-Ser or Asp-Thr motifs...
  6. ncbi Occurrence and detection of phosphopeptide isomers in large-scale phosphoproteomics experiments
    Mathieu Courcelles
    IRIC, Institute for Research in Immunology and Cancer, Universite de Montreal, P O Box 6128, Station Centre Ville, Montreal, Quebec, Canada H3C 3J7
    J Proteome Res 11:3753-65. 2012
    ....
  7. ncbi Chiral metallo-supramolecular complexes selectively induce human telomeric G-quadruplex formation under salt-deficient conditions
    Chuanqi Zhao
    Division of Biological Inorganic Chemistry, State Key Laboratory of Rare Earth Resource Utilization, Graduate School of the Chinese Academy of Sciences, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, PR China
    Chemistry 17:8209-15. 2011
    ..P-enantiomer induced G-quadruplex formation is fast and does not require a large excess of P enantiomer. More importantly, this chiral compound induces loop sequence-dependent G-quadruplex formation...
  8. pmc The high mannose glycans from bovine ribonuclease B isomer characterization by ion trap MS
    Justin M Prien
    The Glycomics Center, Division of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire 03824, USA
    J Am Soc Mass Spectrom 20:539-56. 2009
    ..Duplication of these and results from comparable standards could bring an important analytical focus to carbohydrate sequencing that is greatly lacking...
  9. pmc Mass spectrometric analysis of asparagine deamidation and aspartate isomerization in polypeptides
    Hongqian Yang
    Division of Molecular Biometry, Department of Medicinal Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
    Electrophoresis 31:1764-72. 2010
    ..This review highlights the issues associated with these steps and discusses the prospects of high-throughput iso-Asp analysis...
  10. ncbi Photoactivation of the photoactive yellow protein: why photon absorption triggers a trans-to-cis Isomerization of the chromophore in the protein
    Gerrit Groenhof
    Department of Biophysical Chemistry, University of Groningen, Nijenborg 4, 9747 AG Groningen, The Netherlands
    J Am Chem Soc 126:4228-33. 2004
    ..It is this proton transfer that initiates the conformational changes within the protein, which are believed to lead to signaling...
  11. pmc Structural evolution of the chromophore in the primary stages of trans/cis isomerization in photoactive yellow protein
    Karsten Heyne
    Max Born Institut fur Nichtlineare Optik und Kurzzeitspektroskopie, Max Born Strasse 2A, D 12489 Berlin, Germany
    J Am Chem Soc 127:18100-6. 2005
    ....
  12. pmc Separation of peptide isomers with variant modified sites by high-resolution differential ion mobility spectrometry
    Alexandre A Shvartsburg
    Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, P O Box 999, Richland, Washington 99352, USA
    Anal Chem 82:8327-34. 2010
    ..Bisphosphorylated isomers that differ in only one modification site were separated to the same extent. We anticipate FAIMS capabilities for such separations to extend to other PTMs...
  13. pmc Comparison of biophysical and biologic properties of alpha-helical enantiomeric antimicrobial peptides
    Yuxin Chen
    Department of Biochemistry and Molecular Genetics, University of Colorado at Denver, Aurora, CO 80045, USA
    Chem Biol Drug Des 67:162-73. 2006
    ..The excellent stability of D-enantiomers to trypsin digestion (no proteolysis by trypsin) compared with the rapid breakdown of the L-enantiomers highlights the advantage of the D-enantiomers and their potential as clinical therapeutics...
  14. ncbi Synthesis, structure, spectroscopic properties, and antiproliferative activity in vitro of novel osmium(III) complexes with azole heterocycles
    Iryna N Stepanenko
    University of Vienna, Institute of Inorganic Chemistry, Wahringerstr 42, A 1090 Vienna, Austria
    Inorg Chem 47:7338-47. 2008
    ....
  15. ncbi Protein dynamics and enzymatic catalysis: investigating the peptidyl-prolyl cis-trans isomerization activity of cyclophilin A
    Pratul K Agarwal
    Computational Biology Institute and Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
    Biochemistry 43:10605-18. 2004
    ....
  16. pmc Catalytic site-selective thiocarbonylations and deoxygenations of vancomycin reveal hydroxyl-dependent conformational effects
    Brandon S Fowler
    Department of Chemistry, Yale University, P O Box 208107, New Haven, Connecticut 06520 8107, USA
    J Am Chem Soc 134:9755-61. 2012
    ..These effects were mirrored in the biological activities of the new analogues and support a structural role for certain hydroxyls in the native structure...
  17. pmc Au(I)-catalyzed ring expanding cycloisomerizations: total synthesis of ventricosene
    Steven G Sethofer
    Department of Chemistry, University of California, Berkeley, Berkeley, California 94720 1460, USA
    Org Lett 10:4315-8. 2008
    ..The utility of this methodology for the rapid assembly of polycyclic ring systems is illustrated by the total synthesis of the angular triquinane ventricosene...
  18. ncbi Mechanisms of photoisomerization of polyenes in confined media: from organic glasses to protein binding cavities
    Robert S H Liu
    Department of Chemistry, University of Hawaii, Honolulu, HI, USA
    Photochem Photobiol 83:2-10. 2007
    ..e. torsional relaxation) or bicycle-pedal or an extended HT process in photoisomerization...
  19. ncbi Positional isomerism markedly affects the growth inhibition of colon cancer cells by nitric oxide-donating aspirin in vitro and in vivo
    Khosrow Kashfi
    Division of Cancer Prevention, Department of Medicine, SUNY at Stony Brook, Stony Brook, NY 11794 8160, USA
    J Pharmacol Exp Ther 312:978-88. 2005
    ..isomers of NO-ASA with respect to the -CH(2)ONO(2) group (ortho, meta, and para) and examined whether this isomerism affects the biological activity of NO-ASA on HT-29 human colon cancer cells...
  20. ncbi Amide linkage isomerism as an activity switch for organometallic osmium and ruthenium anticancer complexes
    Sabine H van Rijt
    Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
    J Med Chem 52:7753-64. 2009
    ..In contrast, N,O-coordinated complexes 7 and 8 hydrolyzed slowly, did not bind to guanine or adenine, and were nontoxic...
  21. pmc Regioselective reactions for programmable resveratrol oligomer synthesis
    Scott A Snyder
    Department of Chemistry, Columbia University, Havemeyer Hall, 3000 Broadway, New York, New York 10027, USA
    Nature 474:461-6. 2011
    ....
  22. ncbi Bicycle-pedal isomerization in a rhodopsin chromophore model
    Igor Schapiro
    Department of Chemistry, University of Duisburg Essen, 45141 Essen, Germany
    J Am Chem Soc 131:16-7. 2009
    ..Furthermore restrained optimization of synchronous rotation mode shows that two-double-bond isomerization is barrierless for the conrotatory and disrotatory pathway...
  23. ncbi Theoretical study of geometrical and nonlinear optical properties of pyridinum N-phenolate betaine dyes
    Wawrzyniec Niewodniczański
    Institute of Physical and Theoretical Chemistry, Wroclaw University of Technology, Wybrzeze Wyspianskiego 27, Wrocław, Poland
    J Mol Model 13:793-800. 2007
    ..The analysis of the results of calculations for the investigated isomers indicates that there are important differences in their NLO activities. Additionally, it was shown that Z3PolX basis set works reasonable well for betaine dyes...
  24. ncbi Ergovaline movement across Caco-2 cells
    Nancy W Shappell
    USDA ARS Biosciences Research Laboratory, 1605 Albrecht Boulevard, Fargo, North Dakota 58105, USA
    In Vitro Cell Dev Biol Anim 41:245-51. 2005
    ..Either isomer, or a combination of both, could be involved in the pathogenesis of fescue toxicosis at sites distal to the intestine...
  25. ncbi Richness of isomerism in labile octahedral Werner-type cobalt(II) complexes demonstrated by 19F NMR spectroscopy: structure and stability
    Ghenadie Novitchi
    Laboratoire de Chimie Inorganique et Bioinorganique, Ecole Polytechnique Federale de Lausanne, CH 1015 Lausanne, Switzerland
    Magn Reson Chem 42:801-6. 2004
    ..8 K], but this stability difference almost vanishes with increasing temperature [DeltaGdegreesi,j (max) = 1.0 kJ mol(-1) at 265.0 K]. The values found for DeltaHdegreesi,j are relatively small and largely entropy compensated...
  26. ncbi Differentiation of three pairs of aconite alkaloid isomers from Aconitum nagarum var. lasiandrum by electrospray ionization tandem mass spectrometry
    Rui Li
    Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, PR China
    Rapid Commun Mass Spectrom 20:157-70. 2006
    ..Although there is no carbonyl group on some aconitine-type alkaloids, with hydroxyl and methoxyl on C15 and C16 respectively, CO was readily eliminated through tautomerization...
  27. ncbi Rapid differentiation of isobaric and positional isomers of structurally related glycosides from Phytolacca bogotensis
    Guillermo Montoya
    Grupo de Investigación en Sustancias Bioactivas, Sede de Investigación Universitaria, Universidad de Antioquia, AA 1226 Medellin, Colombia
    Rapid Commun Mass Spectrom 23:3361-71. 2009
    ..The differentiation of two pairs of positional isomers and four isobaric glycosides and the production of a library of 30 glycosides present in P. bogotensis were accomplished...
  28. ncbi Phosphorylation-specific prolyl isomerization: is there an underlying theme?
    Gerburg Wulf
    Cancer Biology Program, Division of Hematology Oncology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, 77 Avenue Louis Pasteur, NRB 1030, Boston, MA 02115, USA
    Nat Cell Biol 7:435-41. 2005
    ..Here, we provide an overview of the plethora of regulatory events that involve this unique enzyme, with a particular focus on oncogenic signalling and neurodegeneration...
  29. pmc Carbohydrate structural isomers analyzed by sequential mass spectrometry
    David J Ashline
    The Glycomics Center, Department of Biochemistry and Molecular Biology, University of New Hampshire, Durham, New Hampshire 03824, USA
    Anal Chem 79:3830-42. 2007
    ..Procedures were supported with bioinformatics tools for assimilating structure from the MSn data sets...
  30. ncbi A multi-method approach toward de novo glycan characterization: a Man-5 case study
    Justin M Prien
    Analytical Sciences, Amgen, Inc, 4000 Nelson Rd, Longmont, CO 80503, USA
    Glycobiology 20:629-47. 2010
    ..With this multi-method approach, we have the capabilities to comprehensively characterize a biotherapeutic's glycan array in a de novo manner, including structural isomers at >/=0.1% of the total chromatographic peak area...
  31. ncbi Mass spectrometric-based stable isotopic 2-aminobenzoic acid glycan mapping for rapid glycan screening of biotherapeutics
    Justin M Prien
    Analytical Sciences, Amgen, Inc, 4000 Nelson Rd, Longmont, Colorado 80503, USA
    Anal Chem 82:1498-508. 2010
    ..Here, we demonstrate a quantitative high-throughput MS-based mapping approach using stable isotope 2-aminobenzoic acid (2-AA) for rapid "high-level" glycan screening...
  32. ncbi Complementing ultrafast shape recognition with an optical isomerism descriptor
    Ting Zhou
    Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH 8057 Zurich, Switzerland
    J Mol Graph Model 29:443-9. 2010
    We introduce the mixed product of three vectors spanning four molecular locations as a descriptor of optical isomerism. This descriptor is very efficient as it does not require molecular superposition, and is very robust in ..
  33. ncbi Tautomerism in drug discovery
    Alan R Katritzky
    Center for Heterocyclic Compounds, Department of Chemistry, University of Florida, Gainesville, FL 32611 7200, USA
    J Comput Aided Mol Des 24:475-84. 2010
    ..The types of tautomerism encountered in the structure of drugs in current use are surveyed together with the effect of pH, solvent polarity, and temperature...
  34. ncbi Conjugated linoleic acid is a potent naturally occurring ligand and activator of PPARalpha
    S Y Moya-Camarena
    Department of Foods and Nutrition, Purdue University, West Lafayette, IN 47907, USA
    J Lipid Res 40:1426-33. 1999
    ..Also, (9Z,11E)-CLA is one of the most avid fatty acids yet described as a PPARalpha ligand...
  35. ncbi Mechanistic studies of the isomerization of peroxynitrite to nitrate catalyzed by distal histidine metmyoglobin mutants
    Susanna Herold
    Laboratorium für Anorganische Chemie, Eidgenossische Technische Hochschule, ETH Honggerberg, CH 8093 Zurich, Switzerland
    J Am Chem Soc 126:6945-55. 2004
    ..Again, the extent of nitration of the tyrosine residues of the metMb mutants correlates with the values of k(cat)...
  36. ncbi Structure of the I1 early intermediate of photoactive yellow protein by FTIR spectroscopy
    R Brudler
    Department of Molecular Biology and Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, USA
    Nat Struct Biol 8:265-70. 2001
    ..This excludes an I1 structural model proposed on the basis of time resolved Laue crystallography, but does agree with the cryotrapped structure of an I1 precursor...
  37. ncbi Computing positional isotopomer distributions from tandem mass spectrometric data
    Ari Rantanen
    Department of Computer Science, FIN 00014 University of Helsinki, Finland
    Metab Eng 4:285-94. 2002
    ..The computational techniques have been implemented in a MATLAB application called PIDC (Positional Isotopomer Distribution Calculator)...
  38. pmc Chicken retinas contain a retinoid isomerase activity that catalyzes the direct conversion of all-trans-retinol to 11-cis-retinol
    Nathan L Mata
    Sytera, Inc, La Jolla, California 92037, USA
    Biochemistry 44:11715-21. 2005
    ..Kinetic analysis of these two activities suggests that they act in concert to drive the formation of 11-cis-retinoids in chicken retinas. These activities may be part of a new visual cycle for the regeneration of chromophores in cones...
  39. pmc A structural basis for allosteric control of DNA recombination by lambda integrase
    Tapan Biswas
    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
    Nature 435:1059-66. 2005
    ..An intertwined layer of amino-terminal domains bound to accessory (arm) DNAs shapes the recombination complex in a way that suggests how arm binding shifts the reaction equilibrium in favour of recombinant products...
  40. ncbi A motif rich in charged residues determines product specificity in isomaltulose synthase
    Daohai Zhang
    Laboratory of Biosignals and Bioengineering, Institute of Molecular and Cell Biology, The National University of Singapore, Singapore 117609, Singapore
    FEBS Lett 534:151-5. 2003
    ..Mutation of these four residues increased trehalulose formation by 17-61% and decreased isomaltulose by 26-67%. We conclude that the 'RLDRD' motif controls the product specificity of PalI...
  41. ncbi Mechanistic pathways for the photoisomerization reaction of the anchored, tethered chromophore of the photoactive yellow protein and its mutants
    Yasushi Imamoto
    Graduate School of Materials Science, Nara Institute of Science and Technology, Ikoma, Nara, Japan
    Photochem Photobiol 76:584-9. 2002
    ..Absorption data of intermediates obtained from a microsecond time-resolved spectroscopic study of three PYP mutants (E46Q, T50V and R52Q) are consistent with the above analyses...
  42. ncbi Tautomeric equilibria in relation to pi-electron delocalization
    Ewa Daniela Raczyńska
    Department of Chemistry, Agricultural University, 02 776 Warsaw, Poland
    Chem Rev 105:3561-612. 2005
  43. ncbi Pharmacokinetics and pharmacodynamics of methadone enantiomers after a single oral dose of racemate
    D W Boulton
    Laboratory of Drug Disposition and Pharmacogenetics, Department of Psychiatry and Behavioral Sciences, Medical University of South Carolina, Charleston, USA
    Clin Pharmacol Ther 70:48-57. 2001
    ..Central nervous system effects were difficult to interpret on the basis of plasma R-methadone pharmacokinetics...
  44. pmc A brief history of phytochromes
    Nathan C Rockwell
    Department of Molecular and Cell Biology, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
    Chemphyschem 11:1172-80. 2010
    ..Despite this spectral diversity, all members of the extended family of phytochrome photosensors appear to share a common photochemical mechanism for light sensing: photoisomerization of the 15/16 double bond of the bilin chromophore...
  45. pmc The case of medium-dependent dual mechanisms for photoisomerization: one-bond-flip and hula-twist
    R S Liu
    Department of Chemistry, University of Hawaii, 2545 The Mall, Honolulu, HI 96822, USA
    Proc Natl Acad Sci U S A 97:11153-8. 2000
    ..While defining experiments are proposed, this dual mechanistic approach successfully accounts for all examples in the literature on photoisomerization reactions whether involving conformational changes or not...
  46. ncbi Single- and double-linkage isomerism in a six-coordinate iron porphyrin containing nitrosyl and nitro ligands
    Jonghyuk Lee
    Department of Chemistry and Biochemistry, University of Oklahoma, 620 Parrington Oval, Norman, Oklahoma 73019, USA
    J Am Chem Soc 126:7180-1. 2004
    ..57 eV, which is comparable to the 1.59 eV calculated previously for the nitrosyl-to-isonitrosyl linkage isomerism in the five-coordinate (porphine)Fe(NO) analogue.
  47. ncbi Initial steps of signal generation in photoactive yellow protein revealed with femtosecond mid-infrared spectroscopy
    Marie Louise Groot
    Faculty of Sciences, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands
    Biochemistry 42:10054-9. 2003
    ..Relaxation of the coumaryl tail of the chromophore occurs in 0.9-1 ns, which event we identify with the I(0) to I(1) transition observed in visible spectroscopy...
  48. ncbi Metmyoglobin and methemoglobin catalyze the isomerization of peroxynitrite to nitrate
    Susanna Herold
    Laboratorium für Anorganische Chemie, Eidgenossische Technische Hochschule, ETH Honggerberg, CH 8093 Zurich, Switzerland
    Biochemistry 42:14036-46. 2003
    ..Moreover, the globin offers very little protection, as the heme-free (apoMb) and heme-blocked (metMbCN) forms only partly prevent nitration of free tyrosine...
  49. pmc Stark spectroscopy on photoactive yellow protein, E46Q, and a nonisomerizing derivative, probes photo-induced charge motion
    L L Premvardhan
    Department of Biophysics and Physics of Complex Systems, Division of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit, De Boelelaan, 1081, 1081 HV Amsterdam, The Netherlands
    Biophys J 84:3226-39. 2003
    ..We hypothesize that this charge motion would consequently increase the flexibility of the thioester tail thereby decreasing the activation barrier for the rotation of this moiety in the excited state...
  50. ncbi Rate constants for the gas-phase reactions of a series of alkylnaphthalenes with the OH radical
    Patricia T Phousongphouang
    Environmental Toxicology Graduate Program, Air Pollution Research Center, University of California, Riverside 92521, USA
    Environ Sci Technol 36:1947-52. 2002
    ..9-3.8 h and naphthalene with a lifetime of 5.8 h. These differences in reactivity were confirmed by the nighttime/daytime concentration ratios of the alkylnaphthalenes measured in ambient Riverside, CA, samples...
  51. pmc LMSD: LIPID MAPS structure database
    Manish Sud
    LIPID MAPS Bioinformatics Core, San Diego Supercomputer Center San Diego, La Jolla, CA 92093, USA
    Nucleic Acids Res 35:D527-32. 2007
    ..Search results, in addition to structure and annotations, also include relevant links to external databases. The LMSD is publicly available at www.lipidmaps.org/data/structure/...
  52. ncbi Formulation considerations for proteins susceptible to asparagine deamidation and aspartate isomerization
    Aditya A Wakankar
    Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, Kansas 66047, USA
    J Pharm Sci 95:2321-36. 2006
    ....
  53. ncbi Conjugated linoleic acid isomers: differences in metabolism and biological effects
    Itziar Churruca
    Department of Food Science and Nutrition, Faculty of Pharmacy, University of the Basque Country, Paseo de la Universidad, 7 01006 Vitoria, Spain
    Biofactors 35:105-11. 2009
    ..Finally, with regard to the immune system it is not clear whether individual isomers of CLA could act similarly or differently...
  54. ncbi Metabolic and growth inhibitory effects of conjugated fatty acids in the cell line HT-29 with special regard to the conversion of t11,t13-CLA
    Christian Degen
    Friedrich Schiller University, Institute of Nutrition, Dept of Nutritional Physiology, Jena, Germany
    Biochim Biophys Acta 1811:1070-80. 2011
    ....
  55. ncbi Differentiation of isomeric N-glycan structures by normal-phase liquid chromatography-MALDI-TOF/TOF tandem mass spectrometry
    Sarah Maslen
    Chemistry Department, University of Cambridge, Lensfield Road, Cambridge, UK CB2 1EW
    Anal Chem 78:8491-8. 2006
    ..To our knowledge, this is the first MS/MS-based technique that allows confident identification of N-glycans containing 3-linked core fucose, which is a major allergenic determinant on insect and plant glycoproteins...
  56. pmc Proline isomerization preorganizes the Itk SH2 domain for binding to the Itk SH3 domain
    Andrew Severin
    Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA 50010, USA
    J Mol Biol 387:726-43. 2009
    ..Finally, we can compare this Itk complex with other examples of SH3 and SH2 domains engaging their ligands in a nonclassical manner. These small binding domains exhibit a surprising level of diversity in their binding repertoires...
  57. pmc Computational identification of slow conformational fluctuations in proteins
    Arvind Ramanathan
    Joint Carnegie Mellon University University of Pittsburgh Ph D Program in Computational Biology, Lane Center for Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
    J Phys Chem B 113:16669-80. 2009
    ..Overall, the identified slow conformational fluctuations in ubiquitin and CypA indicate that the intrinsic flexibility of these proteins is closely linked to their designated functions...
  58. pmc A functional proline switch in cytochrome P450cam
    Bo Ouyang
    Department of Chemistry, Brandeis University, 415 South Street, Waltham, MA 02454 9110, USA
    Structure 16:916-23. 2008
    ..A mutation in CYP101 that destabilizes the cis conformer of the Ile 88-Pro 89 amide bond results in weaker binding of Pdx. This work provides direct experimental evidence for involvement of X-proline isomerization in enzyme function...
  59. pmc Chromophore protonation state controls photoswitching of the fluoroprotein asFP595
    Lars V Schäfer
    Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Gottingen, Germany
    PLoS Comput Biol 4:e1000034. 2008
    ..These insights can guide the rational design and optimization of photoswitchable proteins...
  60. ncbi Unusual chromatographic behavior of oligonucleotide sequence isomers on two different anion exchange HPLC columns
    M Buncek
    Generi Biotech, Machkova 587, 500 11 Hradec Králové, Czech Republic
    Anal Biochem 348:300-6. 2006
    ..This is the first report of such a "same composition different sequence" effect, described for the short peptides, for synthetic oligonucleotides...
  61. ncbi Importance of entropy in the conformational equilibrium of phenylalanine: a matrix-isolation infrared spectroscopy and density functional theory study
    A Kaczor
    Department of Chemistry, University of Coimbra, P 3004 535 Coimbra, Portugal
    J Phys Chem A 110:2360-70. 2006
    ..Upon UV irradiation (lambda > 235 nm) of the matrix-isolated compound, unimolecular photodecomposition of phenylalanine is observed with production of CO(2) and phenethylamine...
  62. pmc Proline cis-trans isomerization controls autoinhibition of a signaling protein
    Paramita Sarkar
    Department of Chemistry, Rutgers University, Newark, NJ 07102, USA
    Mol Cell 25:413-26. 2007
    ..Proline isomerization appears to make an ideal switch that can regulate the kinetics of activation, thereby modulating the dynamics of signal response...
  63. ncbi QM/MM study of the monomeric red fluorescent protein DsRed.M1
    Elsa Sanchez-Garcia
    Max Planck Institut fur Kohlenforschung, Mulheim an der Ruhr
    J Phys Chem B 113:16622-31. 2009
    ..The published crystal structure of DsRed.M1 with an anionic acylimine chromophore indicates a quinoid structure, while the QM/MM calculations predict the phenolate form to be more stable...
  64. ncbi Elemental isomerism: a boron-nitrogen surrogate for a carbon-carbon double bond increases the chemical diversity of estrogen receptor ligands
    Hai Bing Zhou
    Department of Chemistry, University of Illinois, Urbana, IL 61801, USA
    Chem Biol 14:659-69. 2007
    ..determinants of stability and cellular bioactivity of a B-N for C=C substitution in nonsteroidal estrogens and provide a framework for further exploration of "elemental isomerism" for diversification of drug-like molecules.
  65. ncbi Prolyl cis-trans Isomerization as a molecular timer in Crk signaling
    Linda K Nicholson
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
    Mol Cell 25:483-5. 2007
    ....
  66. ncbi Preparation of (R)-(-)-mandelic acid and its derivatives from racemates by enantioselective degradation with a newly isolated bacterial strain Alcaligenes sp. ECU0401
    Yu Cai He
    Laboratory of Biocatalysis and Bioprocessing, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, People s Republic of China
    Bioprocess Biosyst Eng 31:445-51. 2008
    ..e. > 99.9%). (R)-(-)-Mandelic acid could also be obtained after 12 h of biotransformation with 41.5% isolated yield and >99.9% e.e...
  67. ncbi Role of protein dynamics in reaction rate enhancement by enzymes
    Pratul K Agarwal
    Computational Biology Institute, Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
    J Am Chem Soc 127:15248-56. 2005
    ..Therefore, coupled networks in enzymes have wide implications in understanding allostericity and cooperative effects, as well as protein engineering and drug design...
  68. ncbi Selective effect of conjugated linoleic acid isomers on atherosclerotic lesion development in apolipoprotein E knockout mice
    Jose M Arbones-Mainar
    Departamento de Bioquimica y Biologia Molecular y Celular, Universidad de Zaragoza, Facultad de Veterinaria, Miguel Servet, 177, E 50013 Zaragoza, Spain
    Atherosclerosis 189:318-27. 2006
    ..Plasma chitotriosidase is a better indicator of dietary fat interventions that alter plaque monocyte activity in this murine model...
  69. ncbi Cis-trans isomerization at a proline opens the pore of a neurotransmitter-gated ion channel
    Sarah C R Lummis
    Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK
    Nature 438:248-52. 2005
    ..Our results thus confirm the structure of the M2-M3 loop and the critical role of Pro 8* in the 5-HT3 receptor. In addition, they suggest that a molecular rearrangement at Pro 8* is the structural mechanism that opens the receptor pore...
  70. ncbi Cis/trans isomerization in HIV-1 capsid protein catalyzed by cyclophilin A: insights from computational and theoretical studies
    Pratul K Agarwal
    Computational Biology Institute and Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
    Proteins 56:449-63. 2004
    ..New protein-protein interactions distal to the active site (CypA Arg148-CA(N) Gln95 and CypA Arg148-CA(N) Asn121) are also identified...
  71. ncbi Stabilization of G-quadruplex DNA and down-regulation of oncogene c-myc by quindoline derivatives
    Tian Miao Ou
    School of Pharmaceutical Sciences, Sun Yat Sen University, Guangzhou 510080, People s Republic of China
    J Med Chem 50:1465-74. 2007
    ....
  72. ncbi Stabilization of very rare tautomers of 1-methylcytosine by an excess electron
    Maciej Haranczyk
    Chemical Sciences Division, Fundamental Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
    J Phys Chem A 109:11495-503. 2005
    ..Within the PCM hydration model, the anions become adiabatically bound with respect to the corresponding neutrals, and the two most stable tautomers have a carbon atom protonated...
  73. ncbi Trans-10, cis-12- and cis-9, trans-11-conjugated linoleic acid isomers selectively modify HDL-apolipoprotein composition in apolipoprotein E knockout mice
    Jose M Arbones-Mainar
    Departmento de Bioquímica y Biología Molecular y Celular, Trinity College, Dublin, Ireland
    J Nutr 136:353-9. 2006
    ..Cis-9, trans-11-CLA does not promote this detrimental effect...
  74. ncbi Isomerization through conical intersections
    Benjamin G Levine
    Department of Chemistry, Beckman Institute, Center for Biophysics and Computational Biology, and Frederick Seitz Materials Research Laboratory, University of Illinois, Urbana, IL 61801, USA
    Annu Rev Phys Chem 58:613-34. 2007
    ..In this chapter, we emphasize the role of conical intersections and charge transfer in the photoisomerization mechanism...
  75. ncbi Opposing effects of cis-9,trans-11 and trans-10,cis-12 conjugated linoleic acid on blood lipids in healthy humans
    Sabine Tricon
    Hugh Sinclair Unit of Human Nutrition, School of Food Biosciences, University of Reading, Whiteknights, Reading RG6 6AP, United Kingdom
    Am J Clin Nutr 80:614-20. 2004
    ..However, the effects of CLA on human health and, in particular, the effects of individual CLA isomers are unclear...
  76. ncbi Drug targeting of the c-MYC promoter to repress gene expression via a G-quadruplex silencer element
    Laurence H Hurley
    University of Arizona, College of Pharmacy, Tucson, AZ, USA
    Semin Oncol 33:498-512. 2006
    ..Furthermore, TMPyP4 has been shown to repress c-MYC expression, and this effect is mediated through the silencer element. Last, the in vivo activity of TMPyP4 in xenograph models is presented...
  77. ncbi Evidence for the isomerization and decarboxylation in the photoconversion of the red fluorescent protein DsRed
    Satoshi Habuchi
    Department of Chemistry, Katholieke Universiteit Leuven, Celestijnenlaan 200F, 3001 Heverlee, Belgium
    J Am Chem Soc 127:8977-84. 2005
    ..Our results demonstrate the importance of the chromophore conformation in the ground state on the brightness of the protein as well as the importance of the photon flux to control/avoid the photoconversion process...
  78. ncbi Relating kinetic rates and local energetic roughness by accelerated molecular-dynamics simulations
    Donald Hamelberg
    Howard Hughes Medical Institute, Center for Theoretical Biological Physics, Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, 92093 0365, USA
    J Chem Phys 122:241103. 2005
    ..We do not only recapture the slow kinetic rates, which is difficult in traditional MD, but also obtain the underlying roughness of the energy landscape of proteins at atomistic resolution...
  79. pmc Structure and mechanism of the reversible photoswitch of a fluorescent protein
    Martin Andresen
    Department of NanoBiophotonics, Theoretical and Computational Biophysics, and X Ray Crystallography, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Gottingen, Germany
    Proc Natl Acad Sci U S A 102:13070-4. 2005
    ..Reversible photoswitching of the protein chromophore system within intact crystals also constitutes a step toward the use of fluorescent proteins in three-dimensional data recording...
  80. ncbi Predisposition of the dark state of rhodopsin to functional changes in structure
    Basak Isin
    Department of Computational Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
    Proteins 65:970-83. 2006
    ..This model provides a detailed, mechanistic description of the activation process, extending experimental observations and yielding new insights for further tests...
  81. ncbi Conjugated linoleic acid: a functional nutrient in the different pathophysiological components of the metabolic syndrome?
    Sinead Toomey
    Nutrigenomics Research Group, Department of Clinical Medicine, Institute of Molecular Medicine, Trinity Health Sciences Centre, Trinity College Dublin, St James s Hospital, Dublin 8, Ireland
    Curr Opin Clin Nutr Metab Care 9:740-7. 2006
    ....
  82. pmc Catalysis of protein disulfide bond isomerization in a homogeneous substrate
    Elizabeth A Kersteen
    Department of Biochemistry, University of Wisconsin Madison, Madison, Wisconsin 53706 1544, USA
    Biochemistry 44:12168-78. 2005
    ..We conclude that catalysis of disulfide bond isomerization by PDI does not necessarily involve a cycle of substrate reduction/oxidation...
  83. ncbi In vitro metabolism of nitric oxide-donating aspirin: the effect of positional isomerism
    Jianjun Gao
    Division of Cancer Prevention, Department of Medicine, SUNY at Stony Brook, Stony Brook, NY 11794 8160, USA
    J Pharmacol Exp Ther 312:989-97. 2005
    NO-donating aspirin (NO-ASA) is a potentially important chemopreventive agent against cancer. Since positional isomerism affects strongly its potency in inhibiting colon cancer cell growth, we studied the metabolic transformations of its ..
  84. pmc 1.8 A bright-state structure of the reversibly switchable fluorescent protein Dronpa guides the generation of fast switching variants
    Andre C Stiel
    Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Gottingen, Germany
    Biochem J 402:35-42. 2007
    ..The findings reported in the present study support the view that a cis-trans isomerization is one of the key events common to the switching mechanism in RSFPs...
  85. ncbi Chemistry of the diazeniumdiolates: Z right harpoon over left harpoon E isomerism
    Yan ni Wang
    Advanced Biomedical Computing Center, SAIC Frederick, National Cancer Institute at Frederick, Frederick, Maryland 21702, USA
    J Am Chem Soc 127:5388-95. 2005
    ....
  86. ncbi Cis-trans isomerization and puckering of proline residue
    Young Kee Kang
    Department of Chemistry, Chungbuk National University, Cheongju, Chungbuk 361 763, South Korea
    Biophys Chem 111:135-42. 2004
    ....
  87. ncbi Geometrical isomerism of monounsaturated fatty acids: thiyl radical catalysis and influence of antioxidant vitamins
    Chryssostomos Chatgilialoglu
    ISOF, Consiglio Nazionale delle Ricerche, Bologna, Italy
    Free Radic Biol Med 33:1681-92. 2002
    ..This study contributes to the understanding of radical processes that can alter or protect the naturally occurring cis geometry of unsaturated lipids in cell membranes and demonstrates a new role of essential antioxidants...
  88. pmc Structural basis for reversible photoswitching in Dronpa
    Martin Andresen
    Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Gottingen, Germany
    Proc Natl Acad Sci U S A 104:13005-9. 2007
    ..We suggest a comprehensive model for the light-induced switching mechanism, connecting a cascade of structural rearrangements with different protonation states of the chromophore...
  89. ncbi Native state proline isomerization: an intrinsic molecular switch
    Amy H Andreotti
    Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames 50011, USA
    Biochemistry 42:9515-24. 2003
  90. pmc Amino acid racemization reveals differential protein turnover in osteoarthritic articular and meniscal cartilages
    Thomas V Stabler
    Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
    Arthritis Res Ther 11:R34. 2009
    ..We hypothesized that diseased tissue, as found in an osteoarthritic (OA) joint, would have increased turnover reflected by a decrease in the racemized amino acid content...
  91. pmc Solvation free energies of molecules. The most stable anionic tautomers of uracil
    Maciej Haranczyk
    Department of Chemistry, University of Southern California, 418 SGM Building, 3620 McClintock Avenue, Los Angeles, CA 90089 1062, USA
    Phys Chem Chem Phys 10:4442-8. 2008
    ..We found that in water solution three of the recently identified anionic tautomers are 6.5-3.6 kcal mol(-1) more stable than the anion of the canonical tautomer...
  92. pmc Off-label use of medicines in children: can available evidence avoid useless paediatric trials? The case of proton pump inhibitors for the treatment of gastroesophageal reflux disease
    Giovanni Tafuri
    Utrecht Institute for Pharmaceutical Sciences, Utrecht University, P O Box 80 082, 3508 TB, Utrecht, The Netherlands
    Eur J Clin Pharmacol 65:209-16. 2009
    ..In some cases of drug therapy, the available evidence might be sufficient to extend the indications to children without further clinical studies...
  93. ncbi Expanding the genetic alphabet: non-epimerizing nucleoside with the pyDDA hydrogen-bonding pattern
    Daniel Hutter
    Department of Chemistry and Department of Anatomy and Cell Biology, University of Florida, Gainesville, Florida 32611 7200
    J Org Chem 68:9839-42. 2003
    ..These results make nucleoside 4 a promising candidate for an expanded genetic alphabet...
  94. ncbi Conjugated linoleic acid isomers' roles in the regulation of PPAR-gamma and NF-kappaB DNA binding and subsequent expression of antioxidant enzymes in human umbilical vein endothelial cells
    Yukiko K Nakamura
    Department of Nutrition and Environmental Sciences, University of Nevada, Reno, USA
    Nutrition 25:800-11. 2009
    ....
  95. ncbi Unexpectedly fast cis/trans isomerization of Xaa-Pro peptide bonds in disulfide-constrained cyclic peptides
    Tiesheng Shi
    Department of Chemistry, University of California, Riverside, California 92521, USA
    J Am Chem Soc 126:790-6. 2004
    ....
  96. ncbi Optical switches for remote and noninvasive control of cell signaling
    Pau Gorostiza
    Institució Catalana de Recerca i Estudis Avançats and Institut de Bioenginyeria de Catalunya, Parc Cientific de Barcelona, Edifici Hèlix C Baldiri Reixac 15, Barcelona 08028, Spain
    Science 322:395-9. 2008
    ..Of particular interest is the development of chemically engineered proteins that are directly sensitive to light...
  97. ncbi Phosphorylation effects on cis/trans isomerization and the backbone conformation of serine-proline motifs: accelerated molecular dynamics analysis
    Donald Hamelberg
    Howard Hughes Medical Institute, Center for Theoretical Biological Physics, Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA 92093 0365, USA
    J Am Chem Soc 127:1969-74. 2005
    ....
  98. ncbi Advanced exact structure searching in large databases of chemical compounds
    Sergey V Trepalin
    Chemical Diversity Labs, Inc, 11575 Sorrento Valley Road, San Diego, California 92121, USA
    J Chem Inf Comput Sci 43:852-60. 2003
    ..The practical application of the proposed methodology is illustrated by several examples of successful recovery of tautomers and different forms of ionic compounds from real commercially available nonregistry databases...
  99. pmc Signaling states of rhodopsin. Formation of the storage form, metarhodopsin III, from active metarhodopsin II
    Martin Heck
    Institut fur Medizinische Physik und Biophysik, Universitatsklinikum Charite, Humboldt Universitat zu Berlin, Schumannstrasse 20 21, 10098 Berlin, Germany
    J Biol Chem 278:3162-9. 2003
    ..Therefore, Meta III could be a form of rhodopsin that is stored away, thus regulating photoreceptor regeneration...
  100. ncbi Impact of the C1' configuration of abasic sites on DNA duplex structure
    Carlos de Los Santos
    Department of Pharmacological Sciences, School of Medicine, State University of New York, Stony Brook, New York 11794 8651, USA
    Biochemistry 43:15349-57. 2004
    ..Our results challenge the suggestion that Ape1 is stereoselective and imply a plasticity at the active site of the enzyme for accommodating either anomer of the lesion...
  101. ncbi Dietary trans-10,cis-12 conjugated linoleic acid induces hyperinsulinemia and fatty liver in the mouse
    Lionel Clément
    Physiologie de la Nutrition, Ecole Nationale Supérieure de Biologie Appliquée à la Nutrition et à l Alimentation ENSBANA FRE2328 CNRS CESG Université de Bourgogne F 21000, Dijon, France
    J Lipid Res 43:1400-9. 2002
    ..Instead, t10,c12-CLA-induced hyperinsulinemia may trigger liver steatosis, by inducing both fatty acid uptake and lipogenesis...

Research Grants65

  1. Role of Pitx2 in Muscle Development and Regeneration
    Chrissa Kioussi; Fiscal Year: 2011
    ..Pitx2 gene deleted mice exhibit cardiac malformations, skeletal muscle defects, and right pulmonary and atrial isomerism that are indicative of the loss of left-sided identity...
  2. Nitrogen Oxides and Heme
    GEORGE RICHTER ADDO; Fiscal Year: 2007
    ..In Specific Aim 2, we will characterize the reaction pathways (NO linkage isomerism, reactions with H-donors, NO coupling reactions, etc) available to the FeNO group in heme and heme model ..
  3. OPTICAL PROPERTIES OF BIOLOGICAL MACROMOLECULES
    ROBERT WOODY; Fiscal Year: 2002
    ..Heme-heme interactions will be calculated for multi-heme proteins. Heme isomerism in cytochrome b5 will be studied experimentally and by MD-CD calculations...
  4. OPTICAL PROPERTIES OF BIOLOGICAL MACROMOLECULES
    ROBERT WOODY; Fiscal Year: 2003
    ..Heme-heme interactions will be calculated for multi-heme proteins. Heme isomerism in cytochrome b5 will be studied experimentally and by MD-CD calculations...
  5. EGF CFC GENES IN MAMMALIAN LEFT RIGHT AXIS DETERMINATION
    Michael Shen; Fiscal Year: 2004
    ..results in L-R laterality defects including randomization of abdominal situs, hyposplenia, and pulmonary right isomerism, as well as randomized embryo turning and cardiac looping...
  6. Synthesis of Macrolides, Steroids, Cyclopentanoids, etc.
    BARRY TROST; Fiscal Year: 2009
    ..These new synthetic methods apply to many structural types beyond those illustrated and constitutes a significant to gain access to complex molecular targets more easily. ..
  7. ASSEMBLIES OF SELF COMPLEMENTARY STRUCTURES
    Julius Rebek; Fiscal Year: 2005
    ..We also propose to synthesize new and larger capsules, especially those made up of many identical molecular subunits. ..
  8. STUDIES IN MOLECULAR RECOGNITION
    Julius Rebek; Fiscal Year: 2010
    ..These cavitands could allow the identification of genes whose expression is influenced by trimethylation of particular lysines of the histones. ..
  9. Chemical Mechanism of Guanine Deamination
    Rainer Glaser; Fiscal Year: 2003
    ..5. The computational studies will include studies of the bimolecular reaction mechanisms for dediazoniation of the nucleobase diazonium ions. ..
  10. Structural Studies of AIDS-Responsive Drugs
    Vivian Cody; Fiscal Year: 2010
    ..These results will help guide the design of species selective inhibitors. Mutagenesis studies will be carried out to test these possibilitiesin the structure-based correlations to help design novel pjDHFRinhibitors. ..
  11. EVOLUTION OF THE RIBONUCLEASE SUPERFAMILY
    Steven Benner; Fiscal Year: 2001
    ....
  12. Elementary Steps in DNA Polymerization
    Kenneth Johnson; Fiscal Year: 2008
    ..abstract_text> ..
  13. Fatty Acids and Cardiovascular Health
    Dariush Mozaffarian; Fiscal Year: 2007
    ..End of Abstract) [unreadable] [unreadable] [unreadable] [unreadable] [unreadable]..
  14. DNA Sequencing using Nanopores
    Steven Benner; Fiscal Year: 2007
    ..These will then be targeted against specific sequences extracted from mammalian genomes. [unreadable] [unreadable]..
  15. Polymerases for Sequencing by Synthesis
    Steven Benner; Fiscal Year: 2007
    ..unreadable] [unreadable]..
  16. NMR of basic-aromatic clusters
    Steven Smith; Fiscal Year: 2007
    ..The NMR measurements proposed will provide high resolution detail which is not available from crystallographic methods or more traditional solution NMR methods. [unreadable] [unreadable]..
  17. ENZYME CATALYSIS OF ELECTRON AND GROUP TRANSFER
    PERRY FREY; Fiscal Year: 2006
    ..The contributions of beta- amino acids produced by lysine 2,3-aminomutase and arginine 2,3-aminomutase to the functions of antibiotics are not known. The beta-aminoacids may become significant in drug development. ..
  18. Joint Action Analysis of Poly-drug Withdrawal
    Robert Raffa; Fiscal Year: 2006
    ..g., electrophysiologic or molecular biology techniques. An improved understanding of how withdrawal is influenced by poly-drug abuse could lead to development of enhanced clinical treatment. ..
  19. Retrospective validation of putative breast cancer predictive molecular markers
    Indira Poola; Fiscal Year: 2008
    ..Detection at the precancerous stage and treatment could lead to fewer incidences of breast cancer and deaths from it. [unreadable] [unreadable] [unreadable]..
  20. Response to Beta2-Agonists in Acute Severe Asthma
    Nicola Hanania; Fiscal Year: 2008
    ..abstract_text> ..
  21. Artificial Genetic Systems
    Steven A Benner; Fiscal Year: 2010
    ..Multiplexed PCR is the rate limiting step in many genomics analyses. Our long term, highly ambitious goal is to develop a "synthetic biology", a chemical system capable of Darwinian evolution, based on AEGIS components. ..
  22. Chemistry to Improve Human Genomic Array Analysis Architectures
    Steven A Benner; Fiscal Year: 2010
    ..This proposal seeks funds to benchmark the improvements in array performance generated by these new technologies, improve them by a cycle of test and redesign, and provide them to the genomics community. ..
  23. New proteome technologies: mapping adult D. melanogaster
    DAVID CLEMMER; Fiscal Year: 2008
    ..These models are chosen to display characteristics of diseased states (e.g., neurodegenerative conditions) for which genetic studies in humans are intractable. ..
  24. Pharmacology and Metabolism of Salvia divinorum
    David Yue Wei Lee; Fiscal Year: 2010
    ..divinorum and its metabolites may provide an opportunity for the discovery of novel ligands and the development of potential pharmacotherapies for treating drug addiction and other neurological disorders. ..
  25. Synthesis of the myrmicarin family of natural products
    Scott Snyder; Fiscal Year: 2005
    ....
  26. SYNTHESIS OF ANTICANCER AGENTS
    K C Nicolaou; Fiscal Year: 2010
    ..abstract_text> ..
  27. Dynamic and Catalysis by Alcohol Dehydrogenases
    BRYCE PLAPP; Fiscal Year: 2009
    ..Design of better inhibitors for treating the pathology of alcoholism depends on understanding the dynamics of catalysis by the rate-limiting enzyme in the pathway of alcohol metabolism. ..
  28. SAR OF NOVEL TOPO I INHIBITOR AGAINST PROSTATE CANCER
    YUE WEI LEE; Fiscal Year: 2001
    ..abstract_text> ..
  29. L-amino and acid taste in mice.
    Eugene Delay; Fiscal Year: 2005
    ..g., diabetics, cardiovascular disease, aged). ..
  30. COUNTER ION CONDENSATION AND THE ELECTROSTATIC POTENTIAL
    GERALD MANNING; Fiscal Year: 2001
    ....
  31. NOVEL NEUROSTEROIDS FOR ALCOHOL-RELATED CONDITIONS
    YUE WEI LEE; Fiscal Year: 2002
    ..abstract_text> ..
  32. Quantifying the impact of diet on carcinogen exposure
    JAMES FELTON; Fiscal Year: 2003
    ..Once the impact of dietary factors is understood, then it will be possible to emphasize prevention strategies that will eliminate or modify the risk. ..
  33. HETEROCYCLIC RING COMPOUNDS FOR ALKALOID SYNTHESIS
    Albert Padwa; Fiscal Year: 2007
    ..The generation of biologically active compounds by new synthetic methods remains an important part of both health related and chemical research. ..
  34. TOTAL SYNTHESIS OF NATURAL PRODUCTS
    K Nicolaou; Fiscal Year: 2002
    ..3] sigmatropic rearrangement and a radical based ring closure to form the bicyclic skeleton. ..
  35. INFLAMMATION AND INHIBITORS IN THE ALKALI-INJURED EYE
    Roswell Pfister; Fiscal Year: 2004
    ..There is considerable expectation that this basic pathophysiologic approach will lead to the use of novel treatments, which are based on the molecular pathology found in the alkali-injured eye. ..
  36. TRAINING IN SMOOTH AND CARDIAC MUSCLE BIOLOGY
    Richard Paul; Fiscal Year: 2003
    ..This arrangement promotes scientific interactions and enhance the breadth of educational and research experiences in our cardiovascular training program. ..
  37. KINETIC ANALYSIS OF MICROTUBULE-DEPENDENT ATPASES
    Kenneth Johnson; Fiscal Year: 2003
    ..The combination of approaches outlined here will provide rigorous and direct information to define the structural and mechanistic basis for force production by kinesin. ..
  38. SYNTHESIS OF FUSED HETEROCYCLIC COMPOUNDS
    Albert Padwa; Fiscal Year: 2002
    ..The generation of biologically active compounds by new synthetic methods remains an important part of both health related and chemical research. ..
  39. NA-PUMP ISOFORM-SPECIFIC REGULATION OF VASCULAR FUNCTION
    Richard Paul; Fiscal Year: 2004
    ..The applicant will test the hypotheses that these isoforms are independently regulated and that the observed glucose-sensitivity of activation of vascular smooth muscle is a consequence of NKA alpha-isoform distribution. ..
  40. MECHANISMS OF PYRIDOXAL-5'-PHOSPHATE DEPENDENT ENZYMES
    Robert Phillips; Fiscal Year: 2004
    ..Thus the results of this research are likely to make a significant contribution to the goal of improving health care for Americans in the future. ..
  41. Function and Regulation of Pin2/TRF1 and PinX1
    Kun Ping Lu; Fiscal Year: 2005
    ..These studies should yield new insights into telomere maintenance, cell growth control and oncogenesis, and may lead to the development of new anticancer therapy. ..
  42. REGULATION OF EXPRESSION OF NO SYNTHASE
    Louis Ignarro; Fiscal Year: 2002
    ..The proposed research represents a continuing long-term effort to elucidate the biological factors influencing the vascular and related actions of NO in health and disease. ..
  43. NON-STANDARD BASE PAIRS AS BIOMEDICAL RESEARCH TOOLS
    Steven Benner; Fiscal Year: 2004
    ....
  44. Function and Regulation of the Phosphorylation-Specific Prolyl lsomerase Pin 1
    Kun Ping Lu; Fiscal Year: 2010
    ..In lay language, we have identified a new enzyme called Pin1 critical for cancer development and will continue to investigate the function and regulation of Pin1 during cancer development and hope to identify new drug targets. ..
  45. Prolyl Isomerase Pin 1 and Neurodegeneration
    Kun Ping Lu; Fiscal Year: 2009
    ..These studies should help elucidate the molecular mechanisms of AD and related disorders, and may also have novel implications for their therapies. ..
  46. Ribonucleotide monophosphates and umami taste
    Eugene Delay; Fiscal Year: 2003
    ..If IMP and GMP have identical taste qualities, and these qualities are the same as MSG and the other "umami" substance. ..
  47. PHAGOCYTE RESOLVING METABOLISM
    Charles Serhan; Fiscal Year: 2009
    ..abstract_text> ..
  48. PHOTODYNAMICS OF ULTRAVIOLET EPIDERMAL CHROMOPHORES
    John Simon; Fiscal Year: 2002
    ....
  49. MOLECULAR RECOGNITION IN NUCLEAR PROTEIN TRANSPORT
    ROBERT STANDAERT; Fiscal Year: 2002
    ..It is anticipated that signal-protein conjugates, introduced into living cells, would have light-dependent localization that could be used to control cellular processes such as gene transcription. ..
  50. MECHANISMS OF ENZYMATIC REACTIONS
    PERRY FREY; Fiscal Year: 2006
    ..unreadable] [unreadable]..
  51. TNF Modulation of Mammary Proliferation
    MARGOT IP; Fiscal Year: 2007
    ..Thus, as part of this aim, the efficacy of anti-TNF therapy vs local TNF therapy against mammary tumors will be compared. ..
  52. Inhibitors of pox virus Holliday juction resolvase
    Anca Segall; Fiscal Year: 2005
    ....
  53. ATOMIC FORCE MICROSCOPE
    Steven Smith; Fiscal Year: 2005
    ..The research that will be supported by the instrument falls into three general areas: protein-DNA interactions, amyloid formation and inhibition, and membrane protein complexes and arrays. ..
  54. Phosphine-Catalyzed Annulations and Their Applications
    Ohyun Kwon; Fiscal Year: 2010
    ..For example, hirsutine, one of the target natural products, shows to be 11 to 20 times more effective against the influenza A virus (subtype H3N2) than the clinically used ribavirin. ..
  55. Addressable Digital Array Maps: Mapping Human Plasma with 2D Ion Mobility, Mass S
    STEPHEN VALENTINE; Fiscal Year: 2007
    ..These studies will allow the development of disease biomarker databases that can be used in assessments of disease predisposition for our personalized medicine business model. [unreadable] [unreadable] [unreadable]..
  56. A screen for small molecule inhibitors of soluble Abeta oligomer assembly
    Harry LeVine; Fiscal Year: 2007
    ..Anti-oligomer compounds could potentially block the cognitive impairment symptoms that oligomers elicit in animal models and interfere with the progression of Alzheimer's disease. [unreadable] [unreadable] [unreadable]..
  57. CYTOSTATIC ROLE OF THE ARGININE-NITRIC OXIDE PATHWAY
    Louis Ignarro; Fiscal Year: 2001
    ..The proposed research should advance our understanding of the biological role of NO synthase in regulating cell proliferation. ..
  58. Novel antibiotics that trap Holliday junctions
    Anca Segall; Fiscal Year: 2008
    ..6) Investigate the effect of the peptides on Salmonella and Staph infections in mice in two well-studied infectious disease model systems. ..
  59. VIRAL REPLICATION INHIBITORS TARGETED AT HIV INTEGRASE
    Vasu Nair; Fiscal Year: 2004
    ..This is a significant focus of the current proposal. ..
  60. SPECIFICITY AND FUNCTION OF ALCOHOL DEHYDROGENASES
    BRYCE PLAPP; Fiscal Year: 2004
    ....
  61. LCAT AND PATHOPHYSIOLOGY OF PHOSPHOLIPID SPECIES
    Papasani Subbaiah; Fiscal Year: 2002
    ..These studies should provide novel insights into the physiological importance of LCAT beyond its role in cholesterol esterification. ..