B Urbanc

Summary

Affiliation: Boston University
Country: USA

Publications

  1. pmc Neurotoxic effects of thioflavin S-positive amyloid deposits in transgenic mice and Alzheimer's disease
    B Urbanc
    Center for Polymer Studies and Department of Physics, Boston University, Boston, MA 02215, USA
    Proc Natl Acad Sci U S A 99:13990-5. 2002
  2. pmc Molecular dynamics simulation of amyloid beta dimer formation
    B Urbanc
    Center for Polymer Studies, Department of Physics, Boston University, Boston, Massachusetts 02215, USA
    Biophys J 87:2310-21. 2004
  3. pmc In silico study of amyloid beta-protein folding and oligomerization
    B Urbanc
    Center for Polymer Studies, Department of Physics, Boston University, 590 Commonwealth Avenue, Boston, MA 02215, USA
    Proc Natl Acad Sci U S A 101:17345-50. 2004
  4. ncbi request reprint Computer simulations of Alzheimer's amyloid beta-protein folding and assembly
    Brigita Urbanc
    Center for Polymer Studies, Department of Physics, Boston University, Boston, MA 02215, USA
    Curr Alzheimer Res 3:493-504. 2006
  5. ncbi request reprint Discrete molecular dynamics simulations of peptide aggregation
    S Peng
    Center for Polymer Studies and Department of Physics, Boston University, Boston, Massachusetts 02215, USA
    Phys Rev E Stat Nonlin Soft Matter Phys 69:041908. 2004
  6. doi request reprint Effects of the Arctic (E22-->G) mutation on amyloid beta-protein folding: discrete molecular dynamics study
    A R Lam
    Center for Polymer Studies, Physics Department, Boston University, Boston, Massachusetts 02215, USA
    J Am Chem Soc 130:17413-22. 2008
  7. pmc Role of electrostatic interactions in amyloid beta-protein (A beta) oligomer formation: a discrete molecular dynamics study
    Sijung Yun
    Center for Polymer Studies, Department of Physics, Boston University, Boston, Massachusetts, USA
    Biophys J 92:4064-77. 2007
  8. pmc Age-related reduction in microcolumnar structure correlates with cognitive decline in ventral but not dorsal area 46 of the rhesus monkey
    L Cruz
    Department of Physics, Drexel University, Philadelphia, PA 19104, USA
    Neuroscience 158:1509-20. 2009
  9. ncbi request reprint Ab initio discrete molecular dynamics approach to protein folding and aggregation
    Brigita Urbanc
    Department of Physics, Center for Polymer Studies, Boston University, Massachusetts 02215, USA
    Methods Enzymol 412:314-38. 2006
  10. pmc Solvent and mutation effects on the nucleation of amyloid beta-protein folding
    Luis Cruz
    Center for Polymer Studies and Department of Physics, Boston University, Boston, MA 02215, USA
    Proc Natl Acad Sci U S A 102:18258-63. 2005

Collaborators

Detail Information

Publications20

  1. pmc Neurotoxic effects of thioflavin S-positive amyloid deposits in transgenic mice and Alzheimer's disease
    B Urbanc
    Center for Polymer Studies and Department of Physics, Boston University, Boston, MA 02215, USA
    Proc Natl Acad Sci U S A 99:13990-5. 2002
    ..These results, along with computer simulations, suggest that Abeta develops neurotoxic properties in vivo when it adopts a fibrillar beta-pleated sheet conformation...
  2. pmc Molecular dynamics simulation of amyloid beta dimer formation
    B Urbanc
    Center for Polymer Studies, Department of Physics, Boston University, Boston, Massachusetts 02215, USA
    Biophys J 87:2310-21. 2004
    ..Our results suggest that Abeta oligomerization is not accompanied by the formation of thermodynamically stable planar beta-strand dimers...
  3. pmc In silico study of amyloid beta-protein folding and oligomerization
    B Urbanc
    Center for Polymer Studies, Department of Physics, Boston University, 590 Commonwealth Avenue, Boston, MA 02215, USA
    Proc Natl Acad Sci U S A 101:17345-50. 2004
    ..These structural differences imply a different degree of hydrophobic core exposure between pentamers of the two alloforms, with the hydrophobic core of the Abeta42 pentamer being more exposed and thus more prone to form larger oligomers...
  4. ncbi request reprint Computer simulations of Alzheimer's amyloid beta-protein folding and assembly
    Brigita Urbanc
    Center for Polymer Studies, Department of Physics, Boston University, Boston, MA 02215, USA
    Curr Alzheimer Res 3:493-504. 2006
    ....
  5. ncbi request reprint Discrete molecular dynamics simulations of peptide aggregation
    S Peng
    Center for Polymer Studies and Department of Physics, Boston University, Boston, Massachusetts 02215, USA
    Phys Rev E Stat Nonlin Soft Matter Phys 69:041908. 2004
    ..An important feature of our results is that the aggregates contain free edges, which may allow for further aggregation of model peptides to form elongated fibrils...
  6. doi request reprint Effects of the Arctic (E22-->G) mutation on amyloid beta-protein folding: discrete molecular dynamics study
    A R Lam
    Center for Polymer Studies, Physics Department, Boston University, Boston, Massachusetts 02215, USA
    J Am Chem Soc 130:17413-22. 2008
    ..Consequently, the N-terminal folded structure of the Arctic mutants closely resembles the N-terminal structure of Abeta42, suggesting that both Arctic Abeta peptides might assemble into structures similar to toxic Abeta42 oligomers...
  7. pmc Role of electrostatic interactions in amyloid beta-protein (A beta) oligomer formation: a discrete molecular dynamics study
    Sijung Yun
    Center for Polymer Studies, Department of Physics, Boston University, Boston, Massachusetts, USA
    Biophys J 92:4064-77. 2007
    ..These results suggest that inhibitors targeting the C-terminal region of A beta 42 oligomers may be able to prevent oligomer formation or structurally modify the assemblies to reduce their toxicity...
  8. pmc Age-related reduction in microcolumnar structure correlates with cognitive decline in ventral but not dorsal area 46 of the rhesus monkey
    L Cruz
    Department of Physics, Drexel University, Philadelphia, PA 19104, USA
    Neuroscience 158:1509-20. 2009
    ....
  9. ncbi request reprint Ab initio discrete molecular dynamics approach to protein folding and aggregation
    Brigita Urbanc
    Department of Physics, Center for Polymer Studies, Boston University, Massachusetts 02215, USA
    Methods Enzymol 412:314-38. 2006
    ..The in silico findings also provide further insights into the structure and dynamics of Abeta folding and oligomer formation that are amenable to in vitro testing...
  10. pmc Solvent and mutation effects on the nucleation of amyloid beta-protein folding
    Luis Cruz
    Center for Polymer Studies and Department of Physics, Boston University, Boston, MA 02215, USA
    Proc Natl Acad Sci U S A 102:18258-63. 2005
    ....
  11. pmc Folding events in the 21-30 region of amyloid beta-protein (Abeta) studied in silico
    Jose M Borreguero
    Center for Polymer Studies and Department of Physics, Boston University, Boston, MA 02215, USA
    Proc Natl Acad Sci U S A 102:6015-20. 2005
    ..Substitutions may alter the frequency of Glu-22 or Asp-23 involvement in contact formation and affect the stability of the folding nucleus formed in the Abeta(21-30) region...
  12. ncbi request reprint A statistically based density map method for identification and quantification of regional differences in microcolumnarity in the monkey brain
    Luis Cruz
    Department of Physics, Center for Polymer Studies, Boston University, 590 Commonwealth Ave, Boston, MA 02215, USA
    J Neurosci Methods 141:321-32. 2005
    ....
  13. pmc Generating a model of the three-dimensional spatial distribution of neurons using density maps
    Luis Cruz
    Center for Polymer Studies and Department of Physics, Boston University, Boston, MA 02215, USA
    Neuroimage 40:1105-15. 2008
    ....
  14. pmc Age-related reduction in microcolumnar structure in area 46 of the rhesus monkey correlates with behavioral decline
    Luis Cruz
    Center for Polymer Studies and Department of Physics, Boston University, 590 Commonwealth Avenue, Boston, MA 02215, USA
    Proc Natl Acad Sci U S A 101:15846-51. 2004
    ..Therefore, quantitative measurement of microcolumnar structure may provide a sensitive morphological method to assay microcolumnar function in aging and other conditions...
  15. pmc Structural basis for Aβ1–42 toxicity inhibition by Aβ C-terminal fragments: discrete molecular dynamics study
    B Urbanc
    Department of Physics, Drexel University, Philadelphia, PA 19104, USA
    J Mol Biol 410:316-28. 2011
    ..These findings suggest that region D1-R5, which was more exposed to the solvent in Aβ(1-42) than in Aβ(1-40) oligomers, is involved in mediating Aβ(1-42) oligomer neurotoxicity...
  16. doi request reprint Elucidation of amyloid beta-protein oligomerization mechanisms: discrete molecular dynamics study
    B Urbanc
    Department of Physics, Drexel University, Philadelphia, Pennsylvania 19104, USA
    J Am Chem Soc 132:4266-80. 2010
    ..The oligomer structure of both Arctic peptides resembled Abeta(1-42) more than Abeta(1-40), consistent with their potentially more toxic nature...
  17. pmc Neuron recognition by parallel Potts segmentation
    S Peng
    Center for Polymer Studies and Department of Physics, Boston University, Boston, MA 02215, USA
    Proc Natl Acad Sci U S A 100:3847-52. 2003
    ..We apply our parallel segmentation method to control individuals and to AD patients and achieve recognition of 98% (for a control) and 93% (for an AD patient), with at most 3% false clusters...
  18. pmc Automated identification of neurons and their locations
    A Inglis
    Center for Polymer Studies, Department of Physics, Boston University, Boston, MA 02215, USA
    J Microsc 230:339-52. 2008
    ....
  19. pmc C-terminal peptides coassemble into Abeta42 oligomers and protect neurons against Abeta42-induced neurotoxicity
    Erica A Fradinger
    Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
    Proc Natl Acad Sci U S A 105:14175-80. 2008
    ..Thus, Abeta(31-42) and Abeta(39-42) are leads for obtaining mechanism-based drugs for treatment of AD using a systematic structure-activity approach...
  20. ncbi request reprint Elucidating amyloid beta-protein folding and assembly: A multidisciplinary approach
    David B Teplow
    Department of Neurology, David Geffen School of Medicine, Brain Research Institute, and Molecular Biology Institute, University of California, Los Angeles, California 90095, USA
    Acc Chem Res 39:635-45. 2006
    ..An integrated multidisciplinary program is required. We discuss here the synergistic application of in hydro, in vacuo, and in silico methods to the study of the amyloid beta-protein, the key pathogenetic agent in Alzheimer's disease...