This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Red clover necrotic mosaic virus is a small, icosahedral plant virus (Tombusviridae family) with a single-stranded RNA genome. RCNMV virions were analyzed by cryo-electron microscopy (cryoEM) and three-dimensional reconstruction at 8 resolution. The virion capsids have prominent protrusions; inside the capsid there is an inner cage formed by complexes of genomic RNA and amino terminal portion of the coat protein. Separate reconstructions were obtained at 12 and 16 resolution, respectively, for virion samples that had Ca2+ alone or both Mg2+ and Ca2+ divalent cations selectively extracted. Virions treated in this way exhibited dramatic conformational changes, as obtained from NMFF, in both capsid and inner cage, though the particle diameters remained unchanged. Removal of Ca2+ ions alone appears to trigger movement and rotation of the S and P domains at the quasi 3-fold axis of symmetry. Additional removal of Mg2+ led to the formation of 11-13 diameter channels that extend through the virion shell at the quasi 3-fold axis of symmetry and noticeably alter the inner cage conformation. Despite their relatively small size, these channels are sufficiently large to allow RNA to pass through the protein capsid shell. Structural and infectivity studies suggest the divalent cation induced dynamics may be involved in viral reorganization, which renders the viral RNA accessible for translation early in infection.

National Institute of Health (NIH)
National Center for Research Resources (NCRR)
Biotechnology Resource Grants (P41)
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Special Emphasis Panel (ZRG1-BCMB-E (40))
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Scripps Research Institute
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Salmon, Loïc; Ahlstrom, Logan S; Horowitz, Scott et al. (2016) Capturing a Dynamic Chaperone-Substrate Interaction Using NMR-Informed Molecular Modeling. J Am Chem Soc 138:9826-39
Bruno, Paul A; Morriss-Andrews, Alex; Henderson, Andrew R et al. (2016) A Synthetic Loop Replacement Peptide That Blocks Canonical NF-?B Signaling. Angew Chem Int Ed Engl 55:14997-15001
Montiel-García, Daniel J; Mannige, Ranjan V; Reddy, Vijay S et al. (2016) Structure based sequence analysis of viral and cellular protein assemblies. J Struct Biol 196:299-308
Rosen, Laura E; Kathuria, Sagar V; Matthews, C Robert et al. (2015) Non-native structure appears in microseconds during the folding of E. coli RNase H. J Mol Biol 427:443-53
Cheng, Shanshan; Brooks 3rd, Charles L (2015) Protein-Protein Interfaces in Viral Capsids Are Structurally Unique. J Mol Biol 427:3613-3624
Carrillo-Tripp, Mauricio; Montiel-García, Daniel Jorge; Brooks 3rd, Charles L et al. (2015) CapsidMaps: protein-protein interaction pattern discovery platform for the structural analysis of virus capsids using Google Maps. J Struct Biol 190:47-55
Ahlstrom, Logan S; Law, Sean M; Dickson, Alex et al. (2015) Multiscale modeling of a conditionally disordered pH-sensing chaperone. J Mol Biol 427:1670-80
Mustoe, Anthony M; Brooks, Charles L; Al-Hashimi, Hashim M (2014) Hierarchy of RNA functional dynamics. Annu Rev Biochem 83:441-66
Nobrega, R Paul; Arora, Karunesh; Kathuria, Sagar V et al. (2014) Modulation of frustration in folding by sequence permutation. Proc Natl Acad Sci U S A 111:10562-7
Arthur, Evan J; King, John T; Kubarych, Kevin J et al. (2014) Heterogeneous preferential solvation of water and trifluoroethanol in homologous lysozymes. J Phys Chem B 118:8118-27

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