Publications of Wenjun Zheng


For a complete list of publications and citations, see Google Scholar

    2017

  • Zheng W. Probing the Energetics of Dynactin Filament Assembly and the Binding of Cargo Adaptor Proteins Using Molecular Dynamics Simulation and Electrostatics-Based Structural Modeling. Biochemistry 56, 313-23 (2017). (pubmed) (pdf)

  • Zheng W and Wen H. A survey of coarse-grained methods for modeling protein conformational transitions. Current Opinion in Structural Biology 42, 24-30 (2017). (pubmed) (pdf)

  • Zheng W. Probing the structural dynamics of the CRISPR-Cas9 RNA-guided DNA-cleavage system by coarse-grained modeling. Proteins 85, 342-53 (2017). (pubmed) (pdf)


    • 2016

  • Wen H, Qin F, and Zheng W. Toward elucidating the heat activation mechanism of the TRPV1 channel gating by molecular dynamics simulation. Proteins 84, 1938-49 (2016). (pubmed) (pdf)

  • Zheng W. Probing the structural dynamics of the SNARE recycling machine based on coarse-grained modeling. Proteins 84, 1055-66 (2016). (pubmed) (pdf)

  • Zheng W, Hitchcock-DeGregori SE, and Barua B. Investigating the effects of tropomyosin mutations on its flexibility and interactions with filamentous actin using molecular dynamics simulation. Journal of Muscle Research and Cell Motility , epub (2016). (pubmed) (pdf)


    • 2015

  • Zheng W. Toward decrypting the allosteric mechanism of the ryanodine receptor based on coarse-grained structural and dynamic modeling. Proteins 83, 2307-18 (2015). (pubmed) (pdf)

  • Zheng W & Qin F. A combined coarse-grained and all-atom simulation of TRPV1 channel gating and heat activation . J. Gen. Physiology 145, 443-456 (2015). (pubmed) (pdf)

  • Zheng W & Glenn P. Probing the folded state and mechanical unfolding pathways of T4 lysozyme using all-atom and coarse-grained molecular simulation. J. Chem. Phys. 142, 035101 (2015). (pubmed) (pdf)

  • Chakraborty S & Zheng W. Decrypting the structural, dynamic, and energetic basis of a monomeric Kinesin interacting with a tubulin dimer in three ATPase States by all-atom molecular dynamics simulation. Biochemistry 54, 859-69 (2015). (pubmed) (pdf)


    • 2014

  • Zheng W. All-atom and coarse-grained simulations of the forced unfolding pathways of the SNARE complex. Proteins 82, 1376-86 (2014). (pubmed) (pdf)

  • Zheng W & Tekpinar M . Analysis of protein conformational transitions using elastic network model. Methods Mol Biol. 1084, 159-72 (2014). (pubmed) (pdf)


    • 2013

  • Li M & Zheng W. All-Atom Molecular Dynamics Simulations of Actin-Myosin Interactions: A Comparative Study of Cardiac alpha Myosin, beta Myosin, and Fast Skeletal Muscle Myosin. Biochemistry 52, 8393-405 (2013). (pubmed) (pdf)

  • Zheng W, Barua B, and Hitchcock-DeGregori SE. Probing the flexibility of tropomyosin and its binding to filamentous actin using molecular dynamics simulations. Biophys. J. 105, 1882-92 (2013). (pubmed) (pdf)

  • Tekpinar M & Zheng W. Coarse-grained and all-atom modeling of structural states and transitions in hemoglobin. Proteins 81, 240-52 (2013). (pubmed) (pdf)


    • 2012

  • Zheng W & Tekpinar M. Structure-Based Simulations of the Translocation Mechanism of the Hepatitis C Virus NS3 Helicase along Single-Stranded Nucleic Acid. Biophys. J. 103, 1343-53 (2012). (pubmed) (pdf)

  • Li M & Zheng W. All-Atom Structural Investigation of Kinesin-Microtubule Complex Constrained by High-Quality Cryo-Electron-Microscopy Maps. Biochemistry 51, 5022-32(2012). (pubmed) (pdf)

  • Zheng W. Coarse-grained modeling of the structural states and transition underlying the powerstroke of dynein motor domain. J. Chem. Phys. 136, 155103 (2012). (pubmed) (pdf)


    • 2011

  • Zheng W & Tekpinar M. Accurate flexible fitting of high-resolution protein structures to small-angle x-ray scattering data using a coarse-grained model with implicit hydration shell. Biophys. J. 101, 2981-91 (2011). (pdf)

  • Li M & Zheng W. Probing the Structural and Energetic Basis of Kinesin-Microtubule Binding Using Computational Alanine-Scanning Mutagenesis. Biochemistry 50, 8645-55 (2011). (pdf)

  • Hafner J & Zheng W. All-atom modeling of anisotropic atomic fluctuations in protein crystal structures. J. Chem. Phys. 135, 144114 (2011). (pdf)

  • Zheng W. Coarse-grained modeling of conformational transitions underlying the processive stepping of myosin V dimer along filamentous actin. Proteins 79 2291-305 (2011). (pdf)

  • Zheng W. Accurate Flexible Fitting of High-Resolution Protein Structures into Cryo-Electron Microscopy Maps Using Coarse-Grained Pseudo-Energy Minimization. Biophys. J. 100, 478-88 (2011). (pdf)

  • Zheng W & Auerbach A. Decrypting the Sequence of Structural Events during the Gating Transition of Pentameric Ligand-Gated Ion Channels Based on an Interpolated Elastic Network Model. PLoS Computational Biology 7, e1001046 (2011). (pdf)


    • 2010

  • Tekpinar M & Zheng W. Predicting order of conformational changes during protein conformational transitions using an interpolated elastic network model. Proteins 78, 2469-81 (2010). (pdf)

  • Zheng W. Anharmonic normal mode analysis of elastic network model improves the modeling of atomic fluctuations in protein crystal structures. Biophys. J. 98, 3025-34 (2010). (pdf)

  • Hafner J & Zheng W. Optimal modeling of atomic fluctuations in protein crystal structures for weak crystal contact interactions. J. Chem. Phys. 132, 014111 (2010). (pdf)

  • Zheng W. Multiscale modeling of structural dynamics underlying force generation and product release in actomyosin complex. Proteins 78, 638-60 (2010). (pubmed) (pdf)


    • 2009

  • Zheng W & Tekpinar M. Large-scale evaluation of dynamically important residues in proteins predicted by the perturbation analysis of a coarse-grained elastic model. BMC Struct. Biol. 9, 45 (2009). (pubmed) (pdf)

  • Hafner J & Zheng W. Approximate normal mode analysis based on vibrational subsystem analysis with high accuracy and efficiency. J. Chem. Phys. 130, 194111 (2009). (pubmed) (pdf)

  • Zheng W, Brooks BR & Thirumalai D. Allosteric Transitions in Biological Nanomachines are Described by Robust Normal Modes of Elastic Networks. Curr. Protein Pept. Sci. 10, 128-32 (2009). (pubmed) (pdf)

  • Zheng W. Normal mode based modeling of allosteric couplings that underlie cyclic conformational transition in F1 ATPase. Proteins 76, 747-62 (2009). (pubmed) (pdf)

  • Zheng W & Thirumalai D. Coupling between normal modes drives protein conformational dynamics: illustrations using allosteric transitions in myosin II. Biophys. J. 96, 2128-37 (2009). (pubmed) (pdf)

  • Zheng W. A structure-based sequential mechano-chemical model of hexameric helicases. Int. J. Int. Bio. 5, 34-48 (2009). (pdf)


    2008

  • Zheng W. A unification of the elastic network model and the Gaussian network model for optimal description of protein conformational motions and fluctuations. Biophys. J. 94, 3853-57 (2008). (pubmed) (pdf)

  • Miller BT, Zheng W, Venable RM, Pastor RW & Brooks BR. Langevin network model of myosin. J. Phys. Chem. B. 112, 6274-81 (2008). (pubmed) (pdf)

  • Woodcock HL, Zheng W, Ghysels A, Shao Y, Kong J & Brooks BR. Vibrational subsystem analysis: A method for probing free energies and correlations in the harmonic limit. J. Chem. Phys. 129, 214109 (2008). (pubmed) (pdf)


    • 2007

  • Zheng W, Brooks BR & Thirumalai D. Allosteric transitions in the chaperonin GroEL are captured by a dominant normal mode that is most robust to sequence variations. Biophys. J. 93, 2289-99 (2007). (pubmed) (pdf)

  • Zheng W, Brooks BR & Hummer G. Protein conformational transitions explored by mixed elastic network models. Proteins. 69, 43-57 (2007). (pubmed) (pdf)

  • Zheng W, Liao JC, Brooks BR & Doniach S. Toward the mechanism of dynamical couplings and translocation in hepatitis C virus NS3 helicase using elastic network model. Proteins. 67, 886-96 (2007). (pubmed) (pdf)


    • 2006

  • Zheng W, Brooks BR & Thirumalai D. Low-frequency normal modes that describe allosteric transitions in biological nanomachines are robust to sequence variations. Proc. Natl. Acad. Sci. 103, 7664-9 (2006). (pubmed) (pdf)

  • Zheng W & Brooks BR. Modeling protein conformational changes by iterative fitting of distance constraints using reoriented normal modes. Biophys. J. 90, 4327-36 (2006). (pubmed) (pdf)


    • 2005

  • Zheng W & Brooks BR. Identification of dynamical correlations within the myosin motor domain by the normal mode analysis of an elastic network model. J. Mol. Biol. 346, 745-59 (2005). (pubmed) (pdf)

  • Zheng W, Brooks BR, Doniach S & Thirumalai D. Network of dynamically important residues in the open/closed transition in polymerases is strongly conserved. Structure 13, 565-77 (2005). (pubmed) (pdf)

  • Zheng W & Brooks BR. Probing the local dynamics of nucleotide-binding pocket coupled to the global dynamics: myosin versus kinesin. Biophys. J. 89, 167-78 (2005). (pubmed) (pdf)

  • Zheng W & Brooks BR. Normal modes based prediction of protein conformational changes guided by distance constraints. Biophys. J. 88, 3109-17 (2005). (pubmed) (pdf)

  • Zheng W & Doniach S. Fold recognition aided by constraints from small angle X-ray scattering data. Protein Eng Des Sel.18, 209-19 (2005). (pubmed) (pdf)


    • Early papers

  • Zheng W & Doniach S. A comparative study of motor-protein motions by using a simple elastic network model. Proc. Natl. Acad. Sci. 100, 13253-8 (2003). (pubmed) (pdf)

  • Zheng W & Doniach S. Protein structure prediction constrained by solution X-ray scattering data and structural homology identification. J. Mol. Biol. 316, 173-87 (2002). (pubmed) (pdf)





    • Last update 10/01/2012