Jie Zheng

Summary

Affiliation: University of Akron
Country: USA

Publications

  1. ncbi Molecular modeling of two distinct triangular oligomers in amyloid beta-protein
    Jie Zheng
    Department of Chemical and Biomolecular Engineering, University of Akron, Akron, Ohio 44325, USA
    J Phys Chem B 114:463-70. 2010
  2. ncbi Molecular dynamics simulations of Alzheimer Abeta40 elongation and lateral association
    Jie Zheng
    Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, Ohio 44325, USA
    Front Biosci 13:3919-30. 2008
  3. ncbi Beta2-microglobulin amyloid fragment organization and morphology and its comparison to Abeta suggests that amyloid aggregation pathways are sequence specific
    Jie Zheng
    Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, Ohio 44325, USA
    Biochemistry 47:2497-509. 2008
  4. ncbi Atomic-scale simulations confirm that soluble beta-sheet-rich peptide self-assemblies provide amyloid mimics presenting similar conformational properties
    Xiang Yu
    Department of Chemical and Biomolecular Engineering, University of Akron, Akron, Ohio, USA
    Biophys J 98:27-36. 2010
  5. ncbi Probing ion channel activity of human islet amyloid polypeptide (amylin)
    Jun Zhao
    Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, OH 44325, USA
    Biochim Biophys Acta 1818:3121-30. 2012
  6. ncbi Molecular dynamics simulations of low-ordered alzheimer β-amyloid oligomers from dimer to hexamer on self-assembled monolayers
    Jun Zhao
    Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, Ohio 44325, USA
    Langmuir 27:14876-87. 2011
  7. ncbi Structural, morphological, and kinetic studies of β-amyloid peptide aggregation on self-assembled monolayers
    Qiuming Wang
    Department of Chemical and Biomolecular Engineering, University of Akron, Akron, Ohio 44325, USA
    Phys Chem Chem Phys 13:15200-10. 2011
  8. ncbi Effect of film thickness on the antifouling performance of poly(hydroxy-functional methacrylates) grafted surfaces
    Chao Zhao
    Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, Ohio 44325, USA
    Langmuir 27:4906-13. 2011
  9. ncbi Comparative molecular dynamics study of Abeta adsorption on the self-assembled monolayers
    Qiuming Wang
    Department of Chemical and Biomolecular Engineering University of Akron, Akron, Ohio 44325, USA
    Langmuir 26:3308-16. 2010
  10. ncbi Mutational analysis and allosteric effects in the HIV-1 capsid protein carboxyl-terminal dimerization domain
    Xiang Yu
    Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, Ohio 44325, USA
    Biomacromolecules 10:390-9. 2009

Collaborators

Detail Information

Publications68

  1. ncbi Molecular modeling of two distinct triangular oligomers in amyloid beta-protein
    Jie Zheng
    Department of Chemical and Biomolecular Engineering, University of Akron, Akron, Ohio 44325, USA
    J Phys Chem B 114:463-70. 2010
    ..Both models display many common features similar to other amyloid oligomers and therefore are likely to be biologically relevant...
  2. ncbi Molecular dynamics simulations of Alzheimer Abeta40 elongation and lateral association
    Jie Zheng
    Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, Ohio 44325, USA
    Front Biosci 13:3919-30. 2008
    ....
  3. ncbi Beta2-microglobulin amyloid fragment organization and morphology and its comparison to Abeta suggests that amyloid aggregation pathways are sequence specific
    Jie Zheng
    Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, Ohio 44325, USA
    Biochemistry 47:2497-509. 2008
    ....
  4. ncbi Atomic-scale simulations confirm that soluble beta-sheet-rich peptide self-assemblies provide amyloid mimics presenting similar conformational properties
    Xiang Yu
    Department of Chemical and Biomolecular Engineering, University of Akron, Akron, Ohio, USA
    Biophys J 98:27-36. 2010
    ..These results provide further insight into the usefulness of such mimics for nanostructure design...
  5. ncbi Probing ion channel activity of human islet amyloid polypeptide (amylin)
    Jun Zhao
    Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, OH 44325, USA
    Biochim Biophys Acta 1818:3121-30. 2012
    ....
  6. ncbi Molecular dynamics simulations of low-ordered alzheimer β-amyloid oligomers from dimer to hexamer on self-assembled monolayers
    Jun Zhao
    Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, Ohio 44325, USA
    Langmuir 27:14876-87. 2011
    ..This work provides atomic-level understanding of Aβ peptides at interface...
  7. ncbi Structural, morphological, and kinetic studies of β-amyloid peptide aggregation on self-assembled monolayers
    Qiuming Wang
    Department of Chemical and Biomolecular Engineering, University of Akron, Akron, Ohio 44325, USA
    Phys Chem Chem Phys 13:15200-10. 2011
    ..A postulated mechanism is proposed to describe the structure and kinetics of Aβ aggregation from aqueous solution to the SAMs, providing valuable insights into Aβ aggregation on biological cell membranes...
  8. ncbi Effect of film thickness on the antifouling performance of poly(hydroxy-functional methacrylates) grafted surfaces
    Chao Zhao
    Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, Ohio 44325, USA
    Langmuir 27:4906-13. 2011
    ..The excellent antifouling ability and long-term stability of polyHEMA and polyHPMA brushes make them, especially for polyHEMA, effective and stable antifouling materials for usage in blood-contacting devices...
  9. ncbi Comparative molecular dynamics study of Abeta adsorption on the self-assembled monolayers
    Qiuming Wang
    Department of Chemical and Biomolecular Engineering University of Akron, Akron, Ohio 44325, USA
    Langmuir 26:3308-16. 2010
    ..This work may provide parallel insights into the interactions of Abeta with lipid bilayers...
  10. ncbi Mutational analysis and allosteric effects in the HIV-1 capsid protein carboxyl-terminal dimerization domain
    Xiang Yu
    Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, Ohio 44325, USA
    Biomacromolecules 10:390-9. 2009
    ....
  11. ncbi Alzheimer Abeta(1-42) monomer adsorbed on the self-assembled monolayers
    Qiuming Wang
    Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, Ohio 44325, USA
    Langmuir 26:12722-32. 2010
    ..This work provides parallel insights into the understanding of Abeta structure and aggregation on cell membrane...
  12. ncbi Cholesterol promotes the interaction of Alzheimer β-amyloid monomer with lipid bilayer
    Xiang Yu
    Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, OH 44325, USA
    J Mol Biol 421:561-71. 2012
    ..This work supports that cholesterol acts as a promoter for Aβ--membrane interactions, which would facilitate Aβ aggregation and membrane insertion...
  13. ncbi Synthesis and characterization of poly(N-hydroxyethylacrylamide) for long-term antifouling ability
    Chao Zhao
    Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, Ohio 44325, United States
    Biomacromolecules 12:4071-9. 2011
    ..All these data indicate that polyHEAA can serve as promising biomaterials with long-term biocompatibility and durability suitable for applications in complex biological media...
  14. ncbi Annular structures as intermediates in fibril formation of Alzheimer Abeta17-42
    Jie Zheng
    Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, Ohio 44325, USA
    J Phys Chem B 112:6856-65. 2008
    ....
  15. ncbi Structural determination of Abeta25-35 micelles by molecular dynamics simulations
    Xiang Yu
    Department of Chemical and Biomolecular Engineering, University of Akron, Akron, Ohio, USA
    Biophys J 99:666-74. 2010
    ..The strong binding affinity of our micelles to antibodies implies that micelles may be a biologically relevant species...
  16. ncbi Heterogeneous triangular structures of human islet amyloid polypeptide (amylin) with internal hydrophobic cavity and external wrapping morphology reveal the polymorphic nature of amyloid fibrils
    Jun Zhao
    Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, Ohio 44325, United States
    Biomacromolecules 12:1781-94. 2011
    ....
  17. ncbi Structural polymorphism of human islet amyloid polypeptide (hIAPP) oligomers highlights the importance of interfacial residue interactions
    Jun Zhao
    Department of Chemical and Biomolecular Engineering, University of Akron, Akron, Ohio 44325, United States
    Biomacromolecules 12:210-20. 2011
    ..The proposed models are compatible with recent experimental data in overall size, cross-section area, and molecular weight. A general hIAPP aggregation mechanism is proposed on the basis of our simulated models and experimental data...
  18. ncbi Comparative molecular dynamics study of human islet amyloid polypeptide (IAPP) and rat IAPP oligomers
    Guizhao Liang
    Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, OH 44325, USA
    Biochemistry 52:1089-100. 2013
    ....
  19. ncbi Cross-seeding and conformational selection between three- and four-repeat human Tau proteins
    Xiang Yu
    Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, Ohio 44325, USA
    J Biol Chem 287:14950-9. 2012
    ..If the seeding conformations lead to too much divergence in the energy landscape, it could impede fibril formation. Such an effect could also contribute to the asymmetric barrier between K18 and K19...
  20. ncbi Achieving highly effective nonfouling performance for surface-grafted poly(HPMA) via atom-transfer radical polymerization
    Chao Zhao
    Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, Ohio 44325, United States
    Langmuir 26:17375-82. 2010
    ..This work provides an alternative surface polymerization approach to preparing effective antifouling poly(HPMA) materials for potential applications in blood-contacting medical devices...
  21. ncbi Dual functionality of antimicrobial and antifouling of poly(N-hydroxyethylacrylamide)/salicylate hydrogels
    Chao Zhao
    Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, Ohio 44325, United States
    Langmuir 29:1517-24. 2013
    ..This work demonstrates that the hybrid polyHEAA/SA hydrogels can be engineered to possess both antifouling and antimicrobial properties, which can be used for different in vitro and in vivo applications against bacterial infection...
  22. ncbi Polymorphic structures of Alzheimer's β-amyloid globulomers
    Xiang Yu
    Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, Ohio, United States of America
    PLoS ONE 6:e20575. 2011
    ..But, the lack of atomic-level structural information for these Aβ species leads to the difficulty in the understanding of their biological roles in amyloid toxicity and amyloid formation...
  23. ncbi Models of beta-amyloid ion channels in the membrane suggest that channel formation in the bilayer is a dynamic process
    Hyunbum Jang
    Center for Cancer Research Nanobiology Program, SAIC Frederick, National Cancer Institute Frederick, Frederick, MD 21702, USA
    Biophys J 93:1938-49. 2007
    ..The observed loosely connected subunit organization suggests that amyloid channel formation in the bilayer is a dynamic, fluid process involving subunit association, dissociation, and channel rearrangements...
  24. ncbi Modeling the Alzheimer Abeta17-42 fibril architecture: tight intermolecular sheet-sheet association and intramolecular hydrated cavities
    Jie Zheng
    Basic Research Program, SAIC Frederick Center for Cancer Research, Nanobiology Program, NCI Frederick, Frederick, Maryland 21702, USA
    Biophys J 93:3046-57. 2007
    ..Thus, we propose that Abeta fiber architecture consists of alternating layers of tight packing and hydrated cavities running along the fibrillar axis, which might be possibly detected by high-resolution imaging...
  25. ncbi Stability of tubular structures based on beta-helical proteins: self-assembled versus polymerized nanoconstructs and wild-type versus mutated sequences
    David Zanuy
    Departament d Enginyeria Quimica, ETS d Enginyeria Industrial de Barcelona, Universitat Politecnica de Catalunya, Diagonal 647, Barcelona, Spain
    Biomacromolecules 8:3135-46. 2007
    ....
  26. ncbi Crystal structures of the Dab homology domains of mouse disabled 1 and 2
    Mikyung Yun
    Department of Structural Biology, St Jude Children s Research Hospital, Memphis, Tennessee 38105 2794, USA
    J Biol Chem 278:36572-81. 2003
    ..These findings suggest that simultaneous interaction of the rigid DH domain with the NPXY sequence and PtdIns-4,5-P2 plays a role in the attachment of Dab proteins to the APP/lipoprotein receptors and phosphoinositide-rich membranes...
  27. ncbi Structural stability and dynamics of an amyloid-forming peptide GNNQQNY from the yeast prion sup-35
    Jie Zheng
    Basic Research Program, SAIC-Frederick, Center for Cancer Research Nanobiology Program, NCI-Frederick, Frederick, Maryland 21702, USA
    Biophys J 91:824-33. 2006
    ..Mutant simulations show that substitution of Asn-2, Gln-4, or Asn-6 by Ala would disrupt this steric zipper, leading to unstable oligomers...
  28. ncbi Strong repulsive forces between protein and oligo (ethylene glycol) self-assembled monolayers: a molecular simulation study
    Jie Zheng
    Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, USA
    Biophys J 89:158-66. 2005
    ..Results show that a tightly bound water layer adjacent to the OEG-SAMs is mainly responsible for the large repulsive hydration force...
  29. ncbi A substrate specific functional polymorphism of human gamma-glutamyl hydrolase alters catalytic activity and methotrexate polyglutamate accumulation in acute lymphoblastic leukaemia cells
    Qing Cheng
    Department of Pharmaceutical Sciences, Hematological Malignancies Program, St Jude Children's Research Hospital, Memphis, Tennessee, USA
    Pharmacogenetics 14:557-67. 2004
    ..These studies demonstrate a substrate specific functional SNP (452C>T) in the human GGH gene that is associated with lower catalytic activity and higher accumulation of long-chain MTX-PG in leukaemia cells of patients treated with HDMTX...
  30. ncbi Efficient selection of unique and popular oligos for large EST databases
    Jie Zheng
    Department of Computer Science and Engineering, University of California, Riverside, CA 92521, USA
    Bioinformatics 20:2101-12. 2004
    ..We present simulation results on the synthetic data and a preliminary analysis of the barley unigene database. AVAILABILITY: Available on request from the authors...
  31. ncbi Targeted contrast agent helps to monitor advanced plaque during progression: a magnetic resonance imaging study in rabbits
    Jie Zheng
    Mallinckrodt Institute of Radiology, Washington University, St Louis, Missouri 63110, USA
    Invest Radiol 43:49-55. 2008
    ..The aim of this study was to examine the use of Gadofluorine M to monitor the progression of advanced plaques in a rabbit model...
  32. ncbi New structures help the modeling of toxic amyloidbeta ion channels
    Hyunbum Jang
    Center for Cancer Research Nanobiology Program, SAIC Frederick Inc NCI Frederick, Frederick, MD 21702, USA
    Trends Biochem Sci 33:91-100. 2008
    ..Molecular dynamics modeling can provide blueprints of 3D structural conformations for many other amyloids whose membrane association is key to their toxicity...
  33. ncbi Concurrent multimodality image segmentation by active contours for radiotherapy treatment planning
    Issam El Naqa
    Department of Radiation Oncology, School of Medicine, Washington University, St Louis, Missouri 63110, USA
    Med Phys 34:4738-49. 2007
    ....
  34. ncbi Characterization of the Kremen-binding site on Dkk1 and elucidation of the role of Kremen in Dkk-mediated Wnt antagonism
    Ke Wang
    State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China
    J Biol Chem 283:23371-5. 2008
    ..These results suggest that Kremen may not be essential for Dkk1-mediated Wnt antagonism and that Kremen may only play a role when cells express a high level of LRP5/6...
  35. ncbi Fast mapping of myocardial blood flow with MR first-pass perfusion imaging
    Thomas A Goldstein
    Mallinckrodt Institute of Radiology, Washington University School of Medicine, St Louis, Missouri 63110, USA
    Magn Reson Med 59:1394-400. 2008
    ..In addition to its accuracy, this method can also be optimized to run relatively fast, providing potential for fast and accurate myocardial perfusion mapping in a clinical setting...
  36. ncbi Separation and determination of warfarin enantiomers in human plasma using a novel polymeric surfactant for micellar electrokinetic chromatography-mass spectrometry
    Jingguo Hou
    Department of Chemistry, Center of Biotechnology and Drug Design, Georgia State University, Atlanta, GA 30303, USA
    J Chromatogr A 1159:208-16. 2007
    ..1 microg/mL in human plasma. The method was successfully applied to determine WAR enantiomeric ratio in patients' plasma undergoing warfarin therapy...
  37. ncbi Simultaneous chiral separation of ephedrine alkaloids by MEKC-ESI-MS using polymeric surfactant II: application in dietary supplements
    Jingguo Hou
    Department of Chemistry, Center of Biotechnology and Drug Design, Georgia State University, Atlanta, GA 30303, USA
    Electrophoresis 28:1426-34. 2007
    ..019 mg/g, for (-)-norephedrine from 0.36 to 0.0031 mg/g, for (+)-norpseudoephedrine from 0.68 to 0.0052 mg/g, for (-)-methylephedrine from 1.18 to 0.0092 mg/g and for (+)-methylpseudoephedrine from 0.086 to 0.00037 mg/g in the SRMs...
  38. ncbi Simultaneous chiral separation and determination of ephedrine alkaloids by MEKC-ESI-MS using polymeric surfactant I: method development
    Jingguo Hou
    Department of Chemistry, Center of Biotechnology and Drug Design, Georgia State University, Atlanta, GA 30303, USA
    Electrophoresis 28:1352-63. 2007
    ..5 delivered at 5 microL/min. Finally, compared to MEKC-UV, the use of poly-L-SUCL in MEKC-MS provided significantly higher sensitivity for stereoisomers of ephedrine and related compounds...
  39. ncbi Accurate myocardial T1 measurements: toward quantification of myocardial blood flow with arterial spin labeling
    Haosen Zhang
    Mallinckrodt Institute of Radiology, Washington University, St Louis, MO 63110, USA
    Magn Reson Med 53:1135-42. 2005
    ..In summary, the modified ASL technique and T(1) regression algorithm proposed here provide an accurate measurement of myocardial T(1) and demonstrate potential for reliably assessing MBF at steady state...
  40. ncbi Structural features of the focal adhesion kinase-paxillin complex give insight into the dynamics of focal adhesion assembly
    Craig M Bertolucci
    Department of Structural Biology, MS 311, St. Jude Children's Research Hospital, 332 N. Lauderdale, Memphis, TN 38105, USA
    Protein Sci 14:644-52. 2005
    ....
  41. ncbi Interaction between the internal motif KTXXXI of Idax and mDvl PDZ domain
    Timothy B C London
    Department of Structural Biology, St Jude Children s Research Hospital, Memphis, TN 38105, USA
    Biochem Biophys Res Commun 322:326-32. 2004
    ..Such internal motif identified in this study suggests a new type of sequence motif recognition for Dvl PDZ domain...
  42. ncbi 3D MRI-based multicomponent FSI models for atherosclerotic plaques
    Dalin Tang
    Mathematical Sciences Department, Worcester Polytechnic Institute, Worcester, MA 01609, USA
    Ann Biomed Eng 32:947-60. 2004
    ..Large-scale patient studies are needed to validate the computational findings for possible plaque vulnerability assessment and rupture predictions...
  43. ncbi Relationship of apparent myocardial T2 and oxygenation: towards quantification of myocardial oxygen extraction fraction
    Jie Zheng
    Mallinckrodt Institute of Radiology, Washington University School of Medicine, 510 S Kingshighway Boulevard, Box 8225, St Louis, MO 63110, USA
    J Magn Reson Imaging 20:233-41. 2004
    ..To explore the relationship of myocardial T(2) and oxygenation for the quantification of myocardial oxygen extraction fraction (OEF)...
  44. ncbi The LRP5 high-bone-mass G171V mutation disrupts LRP5 interaction with Mesd
    Yazhou Zhang
    Department of Genetics and Developmental Biology, University of Connecticut Health Center, 263 Farmington Ave, Farmington, CT 06410, USA
    Mol Cell Biol 24:4677-84. 2004
    ....
  45. ncbi DNA-templated Ag nanocluster formation
    Jeffrey T Petty
    School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332 0400 USA
    J Am Chem Soc 126:5207-12. 2004
    ..Fluorescence, absorption, mass, and NMR spectra all indicate that multiple species are present, but that their creation is both nucleotide- and time-dependent...
  46. ncbi Effect of stenosis asymmetry on blood flow and artery compression: a three-dimensional fluid-structure interaction model
    Dalin Tang
    Mathematical Sciences Department, Worcester Polytechnic Institute, Worcester, MA 01609, USA
    Ann Biomed Eng 31:1182-93. 2003
    ..Stenosis asymmetry leads to higher artery compression, higher shear stress and a larger flow separation region. Computational results are verified by available experimental data...
  47. ncbi Direct binding of the PDZ domain of Dishevelled to a conserved internal sequence in the C-terminal region of Frizzled
    Hing C Wong
    Department of Structural Biology, St Jude Children s Research Hospital, Memphis, TN 38105, USA
    Mol Cell 12:1251-60. 2003
    ..Together, our results identify a missing molecular connection within the Wnt pathway. Differences in the binding affinity of the Dvl PDZ domain and its binding partners may be important in regulating signal transduction by Dvl...
  48. ncbi Key residues responsible for acyl carrier protein and beta-ketoacyl-acyl carrier protein reductase (FabG) interaction
    Yong-Mei Zhang
    Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
    J Biol Chem 278:52935-43. 2003
    ..The specific FabG-ACP interactions involve the most conserved ACP residues, which accounts for the ability of ACPs and the type II proteins from different species to function interchangeably...
  49. ncbi Altered left ventricular geometry changes the border zone temporal distribution of stress in an experimental model of left ventricular aneurysm: a finite element model study
    Pavlos Moustakidis
    Department of Surgery, Division of Cardiothoracic Surgery, Washington University, St. Louis, MO, USA
    Circulation 106:I168-75. 2002
    ..Correlation of this finding with the corresponding regional blood flow, oxygen consumption, and mechanical systolic performance may help elucidate the mechanism underlying the observed global LV dysfunction...
  50. ncbi 1H, 15N and 13C assignments of the targeting (FAT) domain of focal adhesion kinase
    Gaohua Liu
    J Biomol NMR 23:75-6. 2002
  51. ncbi Structural insight into the mechanisms of targeting and signaling of focal adhesion kinase
    Gaohua Liu
    Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
    Mol Cell Biol 22:2751-60. 2002
    ..Such conformational change is proposed to precede departure of FAK from focal adhesions, which starts focal adhesion turnover...
  52. ncbi Quantitative assessment of coronary artery plaque vulnerability by high-resolution magnetic resonance imaging and computational biomechanics: a pilot study ex vivo
    Jie Zheng
    Mallinckrodt Institute of Radiology, Washington University School of Medicine, St Louis, Missouri 63110, USA
    Magn Reson Med 54:1360-8. 2005
    ..Noninvasive quantification of the MR contrast and mechanical properties of plaque may provide a comprehensive biomarker for the assessment of vulnerability of atherosclerotic plaques...
  53. ncbi Identification of a specific inhibitor of the dishevelled PDZ domain
    Jufang Shan
    Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
    Biochemistry 44:15495-503. 2005
    ..This compound provides a basis for rational design of high-affinity inhibitors of the PDZ domain, which can block Wnt signaling by interrupting the Fz-Dvl interaction...
  54. ncbi Quantifying effects of plaque structure and material properties on stress distributions in human atherosclerotic plaques using 3D FSI models
    Dalin Tang
    Mathematical Sciences Department, Worcester Polytechnic Institute, Worcester, MA 01609, USA
    J Biomech Eng 127:1185-94. 2005
    ..Atherosclerotic plaques may rupture without warning and cause acute cardiovascular syndromes such as heart attack and stroke. Methods to assess plaque vulnerability noninvasively and predict possible plaque rupture are urgently needed...
  55. ncbi Sequence analysis of p53 response-elements suggests multiple binding modes of the p53 tetramer to DNA targets
    Buyong Ma
    Basic Research Program, SAIC Frederick Inc, Center for Cancer Research Nanobiology Program, NCI Frederick, Frederick, MD 21702, USA
    Nucleic Acids Res 35:2986-3001. 2007
    ..We propose that the palindromic sequence couplings may encode such potential preferred multiple binding modes of the p53 tetramer to DNA...
  56. ncbi Changing the charge distribution of beta-helical-based nanostructures can provide the conditions for charge transfer
    Nurit Haspel
    School of Computer Science Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel
    Biophys J 93:245-53. 2007
    ....
  57. ncbi Principles of nanostructure design with protein building blocks
    Chung Jung Tsai
    Basic Research Program, SAIC Frederick, Inc, Center for Cancer Research Nanobiology Program, NCI Frederick, Frederick, Maryland 21702, USA
    Proteins 68:1-12. 2007
    ..Here we focus on the principles of nanostructure design with protein building blocks...
  58. ncbi Polymeric sulfated amino acid surfactants: a class of versatile chiral selectors for micellar electrokinetic chromatography (MEKC) and MEKC-MS
    Syed Asad Ali Rizvi
    Department of Chemistry, Center of Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia 30303, USA
    Anal Chem 79:879-98. 2007
    ....
  59. ncbi Nanostructure design using protein building blocks enhanced by conformationally constrained synthetic residues
    Jie Zheng
    Basic Research Program, SAIC Frederick, Inc, Center for Cancer Research Nanobiology Program, NCI FCRDC, Frederick, Maryland 21702, USA
    Biochemistry 46:1205-18. 2007
    ..For the selected synthetic residue, similar size, hydrophobicity, and backbone conformational tendencies are desirable as in the Ac3c...
  60. ncbi Large movement in the C terminus of CLC-0 chloride channel during slow gating
    Ekaterina A Bykova
    Department of Physiology and Membrane Biology, University of California, Davis, California 95616, USA
    Nat Struct Mol Biol 13:1115-9. 2006
    ..When combined with recent structural information on the CLC C terminus, our findings provide a structural model for understanding the conformational changes linked to slow gating in CLC transport proteins...
  61. ncbi Molecular simulation studies of the structure of phosphorylcholine self-assembled monolayers
    Jie Zheng
    Department of Chemical Engineering, University of Washington, Seattle, WA 98195, USA
    J Chem Phys 125:174714. 2006
    ..The P-->N vector of the head groups forms an angle of 82 degrees with respect to the surface normal. The tilt direction of molecular chains was observed to be towards their next nearest neighbor...
  62. ncbi Assignment of orthologous genes via genome rearrangement
    Xin Chen
    Department of Computer Science and Engineering, University of California, Riverside, CA 92521, USA
    IEEE/ACM Trans Comput Biol Bioinform 2:302-15. 2005
    ..The simulation results demonstrate that SOAR, in general, performs better than the iterated exemplar algorithm in terms of computing the reversal distance and assigning correct orthologs...
  63. ncbi Consensus features in amyloid fibrils: sheet-sheet recognition via a (polar or nonpolar) zipper structure
    Jie Zheng
    Basic Research Program, SAIC-Frederick, Inc, Center for Cancer Research Nanobiology Program, NCI-Frederick, Frederick, MD 21702, USA
    Phys Biol 3:P1-4. 2006
    ....
  64. ncbi The third 20 amino acid repeat is the tightest binding site of APC for beta-catenin
    Jing Liu
    Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
    J Mol Biol 360:133-44. 2006
    ..In addition, our CD and NMR studies demonstrate that the central region of APC is unstructured in the absence of beta-catenin and Axin, and suggest that beta-catenin may interact with each of the APC 15aa and 20aa repeats independently...
  65. ncbi The influence of phosphorylation on the activity and structure of the neuronal IQ motif protein, PEP-19
    J Bradley Dickerson
    Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
    Brain Res 1092:16-27. 2006
    ..We submit that PEP-19 is a PKC substrate, and that the phosphorylation state of PEP-19 may play a role in the modulation of calmodulin-dependent signaling...
  66. ncbi Designing a nanotube using naturally occurring protein building blocks
    Chung-Jung Tsai
    Basic Research Program, SAIC-Frederick, Inc, Center for Cancer Research, Nanobiology Program, National Cancer Institute-Frederick, Frederick, Maryland, United States of America
    PLoS Comput Biol 2:e42. 2006
    ..The nanotube models can be used to verify a nanostructure observed by low-resolution experiments, and to study the mechanism of tube formation...
  67. ncbi Concepts and schemes for the re-engineering of physical protein modules: generating nanodevices via targeted replacements with constrained amino acids
    Carlos Aleman
    Departament d Enginyeria Quimica, ETS d Enginyeria Industrial de Barcelona, Universitat Politecnica de Catalunya, Diagonal 647, Barcelona E 08028, Spain
    Phys Biol 3:S54-62. 2006
    ..The major challenge facing nanobiology is to be able to exercise fine control over the performance of these target-specific molecular machines...
  68. ncbi The solution structure of acyl carrier protein from Mycobacterium tuberculosis
    Hing C Wong
    Department of Structural Biology, St Jude Children s Research Hospital, Memphis, Tennessee 38105, USA
    J Biol Chem 277:15874-80. 2002
    ....