Browsing by Author "Wang, Qinghua"

Now showing 1 - 5 of 5
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    Deformable complex network for refining low-resolution X-ray structures
    (International Union of Crystallography, 2015) Zhang, Chong; Wang, Qinghua; Ma, Jianpeng; Applied Physics Program
    In macromolecular X-ray crystallography, building more accurate atomic models based on lower resolution experimental diffraction data remains a great challenge. Previous studies have used a deformable elastic network (DEN) model to aid in low-resolution structural refinement. In this study, the development of a new refinement algorithm called the deformable complex network (DCN) is reported that combines a novel angular network-based restraint with the DEN model in the target function. Testing of DCN on a wide range of low-resolution structures demonstrated that it constantly leads to significantly improved structural models as judged by multiple refinement criteria, thus representing a new effective refinement tool for low-resolution structural determination.
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    Identification of a novel PRC2 recruiter in mammalian cells
    (2013-04-18) Gou, Yufeng; Ma, Jianpeng; Diehl, Michael R.; Tao, Yizhi Jane; Wang, Qinghua
    Polycomb repressive complex (PRC) 2 functions to repress thousands of target genes, and they are responsible for stem cell differentiation and carcinogenesis. However, how PRC2 are recruited to specific regions of their target genes remains elusive. In Drosophila, nine sequence-specific transcription factors including Zeste have been shown to act as PRC2 recruiters, but little is known about their homologues in mammalian cells, as a straightforward homology search failed to work in most cases. Aided by three-dimensional structure prediction and the use of the genomes of intermediate bridging species, we have identified a new protein, Zeste Homologue in humans (ZH), as the human homologue of Drosophila Zeste. Gel shift assays indicated that ZH binds to Zeste recognition sequence via its N-terminal DNA binding domain. ZH physically interacted with the components of PRC2 in GST-pull down assays. Chip-seq and Chip-qPCR experiments show the co-localization of ZH and PRC2 complex. Together, these findings revealed the critical function of ZH in recruiting PRC2 complexes to their target genes.
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    Lowered pH Leads to Fusion Peptide Release and a Highly Dynamic Intermediate of Influenza Hemagglutinin
    (American Chemical Society, 2016) Lin, Xingcheng; Noel, Jeffrey K.; Wang, Qinghua; Ma, Jianpeng; Onuchic, José Nelson; Center for Theoretical Biological Physics
    Hemagglutinin (HA), the membrane-bound fusion protein of the influenza virus, enables the entry of virus into host cells via a structural rearrangement. There is strong evidence that the primary trigger for this rearrangement is the low pH environment of a late endosome. To understand the structural basis and the dynamic consequences of the pH trigger, we employed explicit-solvent molecular dynamics simulations to investigate the initial stages of the HA transition. Our results indicate that lowered pH destabilizes HA and speeds up the dissociation of the fusion peptides (FPs). A buried salt bridge between the N-terminus and Asp1122 of HA stem domain locks the FPs and may act as one of the pH sensors. In line with recent observations from simplified protein models, we find that, after the dissociation of FPs, a structural order–disorder transition in a loop connecting the central coiled-coil to the C-terminal domains produces a highly mobile HA. This motion suggests the existence of a long-lived asymmetric or “symmetry-broken” intermediate during the HA conformational change. This intermediate conformation is consistent with models of hemifusion, and its early formation during the conformational change has implications for the aggregation seen in HA activity.
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    Structural and Functional Studies on the Infectious Salmon Anemia Virus Nucleoprotein
    (2013-10-25) Zheng, Wenjie; Tao, Yizhi Jane; Beckingham, Kathleen M.; Nikonowicz, Edward P.; Suh, Junghae; Wang, Qinghua
    Genome packaging for viruses with segmented genomes is often a complex problem. This is particularly true for influenza viruses and other orthomyxoviruses which are able to cause infectious disease, and even worldwide pandemics. The genome of Orthomyxovirus consists of 6-8 negative-sense RNAs encapsidated as ribonucleoprotein (RNP) complexes which perform multiple essential functions throughout the virus life cycle. To better understand the structural features of orthomyxovirus RNPs that allow them to be specifically packaged, we performed structural/functional studies of the nucleoprotein (NP), the major protein component of the RNPs, from the infectious salmon anemia virus (ISAV). The crystal structure of the ISAV-NP was determined to 2.7Å resolution. The ISAV-NP possesses a 112-aa N-terminal domain and a bi-lobular core structure that strongly resembles the structure of the influenza virus NP. Because the ISAV-NP forms homogenous dimers that are stable in solution, I was able to study the NP:RNA binding affinity as well as stoichiometry with fluorescence polarization, using recombinant proteins and synthetic oligos. Surprisingly, the RNA binding analysis revealed that each NP binds ~12 nts of RNA, shorter than the 24-28 nts originally estimated for the influenza A virus NP. The 12-nt stoichiometry was further confirmed by results from electron microscopy and dynamic light scattering. These results suggest that free RNA exists in the orthomyxovirus RNPs, and selective RNP packaging is likely accomplished through direct RNA-RNA interactions.
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    Structural Basis of Actin Filament Nucleation by Tandem W Domains
    (Cell Press, 2013) Chen, Xiaorui; Ni, Fengyun; Tian, Xia; Kondrashkina, Elena; Wang, Qinghua; Ma, Jianpeng
    Spontaneous nucleation of actin is very inefficient in cells. To overcome this barrier, cells have evolved a set of actin filament nucleators to promote rapid nucleation and polymerization in response to specific stimuli. However, the molecular mechanism of actin nucleation remains poorly understood. This is hindered largely by the fact that actin nucleus, once formed, rapidly polymerizes into filament, thus making it impossible to capture stable multisubunit actin nucleus. Here, we report an effective doublemutant strategy to stabilize actin nucleus by preventing further polymerization. Employing this strategy, we solved the crystal structure of AMPPNP-actin in complex with the first two tandem W domains of Cordon-bleu (Cobl), a potent actin filament nucleator. Further sequence comparison and functional studies suggest that the nucleation mechanism of Cobl is probably shared by the p53 cofactor JMY, but not Spire. Moreover, the double-mutant strategy opens the way for atomic mechanistic study of actin nucleation and polymerization.