Yongli Zhang

Summary

Affiliation: Lawrence Berkeley National Laboratory
Country: USA

Publications

  1. pmc Analysis of in-vivo LacR-mediated gene repression based on the mechanics of DNA looping
    Yongli Zhang
    Departments of Chemistry and Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
    PLoS ONE 1:e136. 2006
  2. pmc Statistical-mechanical theory of DNA looping
    Yongli Zhang
    Department of Molecular Biophysics, Yale University, New Haven, Connecticut, USA
    Biophys J 90:1903-12. 2006
  3. pmc Anomalous DNA binding by E2 regulatory protein driven by spacer sequence TATA
    Zhiqun Xi
    Department of Chemistry, Yale University, New Haven, CT 06511, USA
    Nucleic Acids Res 38:3827-33. 2010
  4. doi request reprint DNA translocation of ATP-dependent chromatin remodeling factors revealed by high-resolution optical tweezers
    Yongli Zhang
    Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut, USA
    Methods Enzymol 513:3-28. 2012
  5. pmc Predicting indirect readout effects in protein-DNA interactions
    Yongli Zhang
    Departments of Chemistry and Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
    Proc Natl Acad Sci U S A 101:8337-41. 2004
  6. ncbi request reprint Single-Molecule Protein Folding Experiments Using High-Precision Optical Tweezers
    Junyi Jiao
    Department of Cell Biology, School of Medicine and Integrated Graduate Program in Physical and Engineering Biology, Yale University, 333 Cedar Street, New Haven, CT, 06520, USA
    Methods Mol Biol 1486:357-390. 2017
  7. pmc Hidden Markov Modeling with Detailed Balance and Its Application to Single Protein Folding
    Yongli Zhang
    Department of Cell Biology, School of Medicine, Yale University, New Haven, Connecticut Electronic address
    Biophys J 111:2110-2124. 2016
  8. pmc Structure-Based Derivation of Protein Folding Intermediates and Energies from Optical Tweezers
    Aleksander A Rebane
    Department of Cell Biology, School of Medicine, Yale University, New Haven, Connecticut Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut Department of Physics, Yale University, New Haven, Connecticut
    Biophys J 110:441-54. 2016
  9. pmc Kinetically coupled folding of a single HIV-1 glycoprotein 41 complex in viral membrane fusion and inhibition
    Junyi Jiao
    Department of Cell Biology, Yale University, School of Medicine, New Haven, CT 06511 Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, CT 06511
    Proc Natl Acad Sci U S A 112:E2855-64. 2015
  10. pmc High-throughput approach for detection of DNA bending and flexibility based on cyclization
    Yongli Zhang
    Departments of Molecular Biophysics and Biochemistry and Chemistry, Yale University, New Haven, CT 06511, USA
    Proc Natl Acad Sci U S A 100:3161-6. 2003

Collaborators

  • Zippora Shakked
  • Aleksander A Rebane
  • Junyi Jiao
  • Lu Ma
  • Xinming Zhang
  • Zhiqun Xi
  • Ying Gao
  • Donald M Crothers
  • Rashmi S Hegde

Detail Information

Publications12

  1. pmc Analysis of in-vivo LacR-mediated gene repression based on the mechanics of DNA looping
    Yongli Zhang
    Departments of Chemistry and Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
    PLoS ONE 1:e136. 2006
    ....
  2. pmc Statistical-mechanical theory of DNA looping
    Yongli Zhang
    Department of Molecular Biophysics, Yale University, New Haven, Connecticut, USA
    Biophys J 90:1903-12. 2006
    ..We derive a rigorous theory of loop formation that connects global mechanical and geometric properties of both DNA and protein and demonstrates the importance of protein flexibility in loop-mediated protein-DNA interactions...
  3. pmc Anomalous DNA binding by E2 regulatory protein driven by spacer sequence TATA
    Zhiqun Xi
    Department of Chemistry, Yale University, New Haven, CT 06511, USA
    Nucleic Acids Res 38:3827-33. 2010
    ..In the case of Mg(2+), additional ions are bound to TATA that require displacement for protein binding. We suggest that the TATA sequence may bias the DNA structure towards a conformation that binds the protein relatively weakly...
  4. doi request reprint DNA translocation of ATP-dependent chromatin remodeling factors revealed by high-resolution optical tweezers
    Yongli Zhang
    Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut, USA
    Methods Enzymol 513:3-28. 2012
    ..We show that optical tweezer force microscopy is a powerful and friendly tool for studies of chromatin structures and remodeling...
  5. pmc Predicting indirect readout effects in protein-DNA interactions
    Yongli Zhang
    Departments of Chemistry and Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
    Proc Natl Acad Sci U S A 101:8337-41. 2004
    ..The sole exception was traced to differential magnesium ion binding...
  6. ncbi request reprint Single-Molecule Protein Folding Experiments Using High-Precision Optical Tweezers
    Junyi Jiao
    Department of Cell Biology, School of Medicine and Integrated Graduate Program in Physical and Engineering Biology, Yale University, 333 Cedar Street, New Haven, CT, 06520, USA
    Methods Mol Biol 1486:357-390. 2017
    ....
  7. pmc Hidden Markov Modeling with Detailed Balance and Its Application to Single Protein Folding
    Yongli Zhang
    Department of Cell Biology, School of Medicine, Yale University, New Haven, Connecticut Electronic address
    Biophys J 111:2110-2124. 2016
    ..Together, we demonstrated an efficient, versatile, and reliable method of HMM for kinetics studies of macromolecules under thermodynamic equilibrium...
  8. pmc Structure-Based Derivation of Protein Folding Intermediates and Energies from Optical Tweezers
    Aleksander A Rebane
    Department of Cell Biology, School of Medicine, Yale University, New Haven, Connecticut Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut Department of Physics, Yale University, New Haven, Connecticut
    Biophys J 110:441-54. 2016
    ....
  9. pmc Kinetically coupled folding of a single HIV-1 glycoprotein 41 complex in viral membrane fusion and inhibition
    Junyi Jiao
    Department of Cell Biology, Yale University, School of Medicine, New Haven, CT 06511 Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, CT 06511
    Proc Natl Acad Sci U S A 112:E2855-64. 2015
    ..The inhibition was abolished by a T20-resistant gp41 mutation. The energetics and kinetics of gp41 folding established by us provides a basis to understand viral membrane fusion, infection, and therapeutic intervention. ..
  10. pmc High-throughput approach for detection of DNA bending and flexibility based on cyclization
    Yongli Zhang
    Departments of Molecular Biophysics and Biochemistry and Chemistry, Yale University, New Haven, CT 06511, USA
    Proc Natl Acad Sci U S A 100:3161-6. 2003
    ..We found that, although the nicks hardly alter the bending flexibility, they significantly increase the torsional flexibility, and that the AT repeat has 28% (+/-12%) lower bending rigidity than a generic DNA sequence...
  11. pmc Statistical mechanics of sequence-dependent circular DNA and its application for DNA cyclization
    Yongli Zhang
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511, USA
    Biophys J 84:136-53. 2003
    ..J factors calculated by our new approach are well consistent with Monte Carlo simulations, whereas the new theory has much greater efficiency in computations. Simulation of experimental results has been demonstrated...
  12. pmc High-resolution optical tweezers for single-molecule manipulation
    Xinming Zhang
    Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut
    Yale J Biol Med 86:367-83. 2013
    ..These past and future applications demonstrate the unique advantages of high-resolution optical tweezers in quantitatively characterizing complex multi-scale dynamics of biomacromolecules. ..