Junjie Zhang

Publications (13) View all

• Article: Cryo-EM model validation using independent map reconstructions.

  Frank Dimaio, Junjie Zhang, Wah Chiu, David Baker
  [show abstract] [hide abstract]
  ABSTRACT: An increasing number of cryo-electron microscopy (cryo-EM) density maps are being generated with suitable resolution to trace the protein backbone and guide sidechain placement. Generating and evaluating atomic models based on such maps would be greatly facilitated by independent validation metrics for assessing the fit of the models to the data. We describe such a metric based on the fit of atomic models with independent test maps from single particle reconstructions not used in model refinement. The metric provides a means to determine the proper balance between the fit to the density and model energy and stereochemistry during refinement, and is likely to be useful in determining values of model building and refinement metaparameters quite generally.
  Protein Science 04/2013; · 2.80 Impact Factor
• Article: Cryo-EM Structure of a Molluscan Hemocyanin Suggests Its Allosteric Mechanism.

  Qinfen Zhang, Xinghong Dai, Yao Cong, Junjie Zhang, Dong-Hua Chen, Matthew T Dougherty, Jiangyong Wang, Steven J Ludtke, Michael F Schmid, Wah Chiu
  [show abstract] [hide abstract]
  ABSTRACT: Hemocyanins are responsible for transporting O2 in the arthropod and molluscan hemolymph. Haliotis diversicolor molluscan hemocyanin isoform 1 (HdH1) is an 8 MDa oligomer. Each subunit is made up of eight functional units (FUs). Each FU contains two Cu ions, which can reversibly bind an oxygen molecule. Here, we report a 4.5 Å cryo-EM structure of HdH1. The structure clearly shows ten asymmetric units arranged with D5 symmetry. Each asymmetric unit contains two structurally distinct but chemically identical subunits. The map is sufficiently resolved to trace the entire subunit Cα backbone and to visualize densities corresponding to some large side chains, Cu ion pairs, and interaction networks of adjacent subunits. A FU topology path intertwining between the two subunits of the asymmetric unit is unambiguously determined. Our observations suggest a structural mechanism for the stability of the entire hemocyanin didecamer and 20 "communication clusters" across asymmetric units responsible for its allosteric property upon oxygen binding.
  Structure 03/2013; · 6.35 Impact Factor
• Source

  Available from: pnas.org

  Article: Multiscale natural moves refine macromolecules using single-particle electron microscopy projection images.

  Junjie Zhang, Peter Minary, Michael Levitt
  [show abstract] [hide abstract]
  ABSTRACT: The method presented here refines molecular conformations directly against projections of single particles measured by electron microscopy. By optimizing the orientation of the projection at the same time as the conformation, the method is well-suited to two-dimensional class averages from cryoelectron microscopy. Such direct use of two-dimensional images circumvents the need for a three-dimensional density map, which may be difficult to reconstruct from projections due to structural heterogeneity or preferred orientations of the sample on the grid. Our refinement protocol exploits Natural Move Monte Carlo to model a macromolecule as a small number of segments connected by flexible loops, on multiple scales. After tests on artificial data from lysozyme, we applied the method to the Methonococcus maripaludis chaperonin. We successfully refined its conformation from a closed-state initial model to an open-state final model using just one class-averaged projection. We also used Natural Moves to iteratively refine against heterogeneous projection images of Methonococcus maripaludis chaperonin in a mix of open and closed states. Our results suggest a general method for electron microscopy refinement specially suited to macromolecules with significant conformational flexibility. The algorithm is available in the program Methodologies for Optimization and Sampling In Computational Studies.
  Proceedings of the National Academy of Sciences 06/2012; 109(25):9845-50. · 9.68 Impact Factor
• Article: Cryo-EM structure of a group II chaperonin in the prehydrolysis ATP-bound state leading to lid closure.

  Junjie Zhang, Boxue Ma, Frank DiMaio, Nicholai R Douglas, Lukasz A Joachimiak, David Baker, Judith Frydman, Michael Levitt, Wah Chiu
  [show abstract] [hide abstract]
  ABSTRACT: Chaperonins are large ATP-driven molecular machines that mediate cellular protein folding. Group II chaperonins use their "built-in lid" to close their central folding chamber. Here we report the structure of an archaeal group II chaperonin in its prehydrolysis ATP-bound state at subnanometer resolution using single particle cryo-electron microscopy (cryo-EM). Structural comparison of Mm-cpn in ATP-free, ATP-bound, and ATP-hydrolysis states reveals that ATP binding alone causes the chaperonin to close slightly with a ∼45° counterclockwise rotation of the apical domain. The subsequent ATP hydrolysis drives each subunit to rock toward the folding chamber and to close the lid completely. These motions are attributable to the local interactions of specific active site residues with the nucleotide, the tight couplings between the apical and intermediate domains within the subunit, and the aligned interactions between two subunits across the rings. This mechanism of structural changes in response to ATP is entirely different from those found in group I chaperonins.
  Structure 05/2011; 19(5):633-9. · 6.35 Impact Factor
• Article: Dual action of ATP hydrolysis couples lid closure to substrate release into the group II chaperonin chamber.

  Nicholai R Douglas, Stefanie Reissmann, Junjie Zhang, Bo Chen, Joanita Jakana, Ramya Kumar, Wah Chiu, Judith Frydman
  [show abstract] [hide abstract]
  ABSTRACT: Group II chaperonins are ATP-dependent ring-shaped complexes that bind nonnative polypeptides and facilitate protein folding in archaea and eukaryotes. A built-in lid encapsulates substrate proteins within the central chaperonin chamber. Here, we describe the fate of the substrate during the nucleotide cycle of group II chaperonins. The chaperonin substrate-binding sites are exposed, and the lid is open in both the ATP-free and ATP-bound prehydrolysis states. ATP hydrolysis has a dual function in the folding cycle, triggering both lid closure and substrate release into the central chamber. Notably, substrate release can occur in the absence of a lid, and lid closure can occur without substrate release. However, productive folding requires both events, so that the polypeptide is released into the confined space of the closed chamber where it folds. Our results show that ATP hydrolysis coordinates the structural and functional determinants that trigger productive folding.
  Cell 01/2011; 144(2):240-52. · 32.40 Impact Factor